6RXV

Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state B2


Protein Family Annotation Pfam Database Homepage

ChainsAccessionIdentifierDescriptionCommentsSource
PF04003Dip2/Utp12 Family (Utp12)Dip2/Utp12 Family- Family
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
PF04147Nop14-like family (Nop14)Nop14-like family- Family
PF09368Sas10 C-terminal domain (Sas10)Sas10 C-terminal domainSas10 is an Essential subunit of U3-containing Small Subunit (SSU) processome complex involved in the production of the 18S rRNA and assembly of the small ribosomal subunit.Domain
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
PF08640U3 small nucleolar RNA-associated protein 6 (U3_assoc_6)U3 small nucleolar RNA-associated protein 6- Family
PF08146BP28CT (NUC211) domain (BP28CT)BP28CT (NUC211) domainThis C terminal domain is found in BAP28-like nucleolar proteins [1].Domain
PF12397U3 small nucleolar RNA-associated protein 10 (U3snoRNP10)U3 small nucleolar RNA-associated protein 10- Family
PF03998Utp11 protein (Utp11)Utp11 protein- Family
PF04003Dip2/Utp12 Family (Utp12)Dip2/Utp12 Family- Family
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
PF08625Utp13 specific WD40 associated domain (Utp13)Utp13 specific WD40 associated domainUtp13 is a component of the five protein Pwp2 complex that forms part of a stable particle subunit independent of the U3 small nucleolar ribonucleoprotein that is essential for the initial assembly steps of the 90S pre-ribosome [1]. Pwp2 is capable o ...Utp13 is a component of the five protein Pwp2 complex that forms part of a stable particle subunit independent of the U3 small nucleolar ribonucleoprotein that is essential for the initial assembly steps of the 90S pre-ribosome [1]. Pwp2 is capable of interacting directly with the 35 S pre-rRNA 5' end [1].
Domain
PF04615Utp14 protein (Utp14)Utp14 protein- Family
PF09384UTP15 C terminal (UTP15_C)UTP15 C terminal- Family
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
PF04192Utp21 specific WD40 associated putative domain (Utp21)Utp21 specific WD40 associated putative domainUtp21 is a subunit of U3 snoRNP, which is essential for synthesis of 18S rRNA.Domain
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
PF00687Ribosomal protein L1p/L10e family (Ribosomal_L1)Ribosomal protein L1p/L10e familyThis family includes prokaryotic L1 and eukaryotic L10.Domain
PF01269Fibrillarin (Fibrillarin)Fibrillarin- Domain
PF08156NOP5NT (NUC127) domain (NOP5NT)NOP5NT (NUC127) domainThis N terminal domain is found in RNA-binding proteins of the NOP5 family [1].Domain
PF01798snoRNA binding domain, fibrillarin (Nop)snoRNA binding domain, fibrillarin- Family
PF08156NOP5NT (NUC127) domain (NOP5NT)NOP5NT (NUC127) domainThis N terminal domain is found in RNA-binding proteins of the NOP5 family [1].Domain
PF01798snoRNA binding domain, fibrillarin (Nop)snoRNA binding domain, fibrillarin- Family
PF01248Ribosomal protein L7Ae/L30e/S12e/Gadd45 family (Ribosomal_L7Ae)Ribosomal protein L7Ae/L30e/S12e/Gadd45 familyThis family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD11 ...This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118 [1].
Domain
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
PF05189RNA 3'-terminal phosphate cyclase (RTC), insert domain (RTC_insert)RNA 3'-terminal phosphate cyclase (RTC), insert domainRNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organisms. They catalyse the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation o ...RNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organisms. They catalyse the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation of the covalent AMP-cyclase intermediate [1]. The structure of RTC demonstrates that RTCs are comprised two domain. The larger domain contains an insert domain of approximately 100 amino acids [1].
Domain
PF01137RNA 3'-terminal phosphate cyclase (RTC)RNA 3'-terminal phosphate cyclaseRNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organisms. They catalyse the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation o ...RNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organisms. They catalyse the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation of the covalent AMP-cyclase intermediate [1]. The structure of RTC demonstrates that RTCs are comprised two domain. The larger domain contains an insert domain of approximately 100 amino acids [1].
Domain
PF08142AARP2CN (NUC121) domain (AARP2CN)AARP2CN (NUC121) domainThis domain is the central domain of AARP2. It is weakly similar to the GTP-binding domain of elongation factor TU [1].Domain
PF0495040S ribosome biogenesis protein Tsr1 and BMS1 C-terminal (RIBIOP_C)40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal- Family
PF00163Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4)Ribosomal protein S4/S9 N-terminal domain- Family
PF01479S4 domain (S4)S4 domainThe S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast pro ...The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation [1]. The S4 domain probably mediates binding to RNA.
Domain
PF04427Brix domain (Brix)Brix domain- Domain
PF04006Mpp10 protein (Mpp10)Mpp10 protein- Family
PF04158Sof1-like domain (Sof1)Sof1-like domain- Family
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
PF03587EMG1/NEP1 methyltransferase (EMG1)EMG1/NEP1 methyltransferase- Family
PF17903Krr1 KH1 domain (KH_8)Krr1 KH1 domainThis entry represents the first KH domain in the KRR1 protein [1]. Krr1 is a ribosomal assembly factor. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif and is involved in binding another assembly factor, Kri1 [1].Domain
PF13725Possible tRNA binding domain (tRNA_bind_2)Possible tRNA binding domain- Family
PF08351Domain of unknown function (DUF1726) (DUF1726)tRNA(Met) cytidine acetyltransferase TmcA, N-terminal- Family
PF13718GNAT acetyltransferase 2 (GNAT_acetyltr_2)GNAT acetyltransferase 2- Family
PF05127Helicase (Helicase_RecD)HelicaseThis domain contains a P-loop (Walker A) motif, suggesting that it has ATPase activity, and a Walker B motif. In tRNA(Met) cytidine acetyltransferase (TmcA) it may function as an RNA helicase motor (driven by ATP hydrolysis) which delivers the wobble ...This domain contains a P-loop (Walker A) motif, suggesting that it has ATPase activity, and a Walker B motif. In tRNA(Met) cytidine acetyltransferase (TmcA) it may function as an RNA helicase motor (driven by ATP hydrolysis) which delivers the wobble base to the active centre of the GCN5-related N-acetyltransferase (GNAT) domain [1]. It is found in the bacterial exodeoxyribonuclease V alpha chain (RecD), which has 5'-3' helicase activity. It is structurally similar to the motor domain 1A in other SF1 helicases [2].
Domain
PF08698Fcf2 pre-rRNA processing (Fcf2)Fcf2 pre-rRNA processing- Family
PF01015Ribosomal S3Ae family (Ribosomal_S3Ae)Ribosomal S3Ae family- Family
PF00900Ribosomal family S4e (Ribosomal_S4e)Ribosomal family S4e- Family
PF1612140S ribosomal protein S4 C-terminus (40S_S4_C)40S ribosomal protein S4 C-terminus- Family
PF08071RS4NT (NUC023) domain (RS4NT)RS4NT (NUC023) domainThis is the N-terminal domain of Ribosomal S4 / S4e proteins. This domain is associated with S4 and KOW domains [1].Domain
PF01479S4 domain (S4)S4 domainThe S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast pro ...The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation [1]. The S4 domain probably mediates binding to RNA.
Domain
PF00177Ribosomal protein S7p/S5e (Ribosomal_S7)Ribosomal protein S7p/S5eThis family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.Domain
PF01092Ribosomal protein S6e (Ribosomal_S6e)Ribosomal protein S6e- Family
PF01251Ribosomal protein S7e (Ribosomal_S7e)Ribosomal protein S7e- Family
PF01201Ribosomal protein S8e (Ribosomal_S8e)Ribosomal protein S8e- Family
PF00163Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4)Ribosomal protein S4/S9 N-terminal domain- Family
PF01479S4 domain (S4)S4 domainThe S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast pro ...The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation [1]. The S4 domain probably mediates binding to RNA.
Domain
PF00312Ribosomal protein S15 (Ribosomal_S15)Ribosomal protein S15- Domain
PF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
PF00380Ribosomal protein S9/S16 (Ribosomal_S9)Ribosomal protein S9/S16- Family
PF16205Ribosomal_S17 N-terminal (Ribosomal_S17_N)Ribosomal_S17 N-terminal- Family
PF00366Ribosomal protein S17 (Ribosomal_S17)Ribosomal protein S17- Domain
PF00410Ribosomal protein S8 (Ribosomal_S8)Ribosomal protein S8- Domain
PF00164Ribosomal protein S12/S23 (Ribosom_S12_S23)Ribosomal protein S12/S23- Family
PF01282Ribosomal protein S24e (Ribosomal_S24e)Ribosomal protein S24e- Family
PF01200Ribosomal protein S28e (Ribosomal_S28e)Ribosomal protein S28e- Family
PF15375Domain of unknown function (DUF4602) (DUF4602)Domain of unknown function (DUF4602)- Family
PF03813Nrap protein domain 1 (Nrap)Nrap protein domain 1Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ...Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [1]. This domain has a nucleotidyltransferase structure.
Domain
PF17403Nrap protein PAP/OAS-like domain (Nrap_D2)Nrap protein PAP/OAS-like domainMembers of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ...Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [1].
Domain
PF17406Nrap protein PAP/OAS1-like domain 5 (Nrap_D5)Nrap protein PAP/OAS1-like domain 5Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ...Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [1].
Domain
PF17407Nrap protein domain 6 (Nrap_D6)Nrap protein domain 6Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ...Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [1].
Domain
PF17404Nrap protein domain 3 (Nrap_D3)Nrap protein domain 3Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ...Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [1].
Domain
PF17405Nrap protein nucleotidyltransferase domain 4 (Nrap_D4)Nrap protein nucleotidyltransferase domain 4Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ...Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [1].
Domain
PF17799Rrp7 RRM-like N-terminal domain (RRM_Rrp7)Rrp7 RRM-like N-terminal domainThis domain corresponds to the N-terminal RNA-binding domain found in the Rrp7 protein. It has an RRM-like fold with a circular permutation [1].Domain
PF12923Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain (RRP7)Ribosomal RNA-processing protein 7 (RRP7) C-terminal domainRRP7 is an essential protein in yeast that is involved in pre-rRNA processing and ribosome assembly [1]. It is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle [1-2].Domain
PF07539Down-regulated in metastasis (DRIM)Down-regulated in metastasis- Family
PF04003Dip2/Utp12 Family (Utp12)Dip2/Utp12 Family- Family
PF03914CBF/Mak21 family (CBF)CBF/Mak21 family- Family
PF00416Ribosomal protein S13/S18 (Ribosomal_S13)Ribosomal protein S13/S18- Family
PF05291Bystin (Bystin)Bystin- Family
PF08164Apoptosis-antagonizing transcription factor, C-terminal (TRAUB)Apoptosis-antagonizing transcription factor, C-terminalThis C terminal domain is found in traube proteins [1]. This is the domain of the AATF proteins that interacts with BLOS2 or Ceap, that functions as an adaptor in processes such as protein and vesicle processing and transport, and perhaps transcripti ...This C terminal domain is found in traube proteins [1]. This is the domain of the AATF proteins that interacts with BLOS2 or Ceap, that functions as an adaptor in processes such as protein and vesicle processing and transport, and perhaps transcription.
Domain
PF08297U3 snoRNA associated (U3_snoRNA_assoc)U3 snoRNA associated- Family
PF08149BING4CT (NUC141) domain (BING4CT)BING4CT (NUC141) domainThis C terminal domain is found in the BING4 family of nucleolar WD40 repeat proteins [1].Domain

Gene Product Annotation Gene Product Annotation

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Periodic tryptophan protein 2-like protein
        Utp2
          Utp3
                Utp4
                      Utp6
                          UTP10
                              U3 small nucleolar RNA-associated protein 11
                                  Utp12
                                      Utp13
                                          Utp14
                                              Utp15
                                                  Utp17
                                                        Utp18
                                                              Utp21
                                                                  Utp24nonenonenone
                                                                  Utp30
                                                                        Nop1
                                                                          Nop56
                                                                            Nop58
                                                                              Snu13
                                                                              Rrp9
                                                                                RNA 3'-terminal phosphate cyclase-like protein
                                                                                Bms1
                                                                                  Imp3
                                                                                      Imp4
                                                                                            Mpp10
                                                                                                Sof1
                                                                                                    Emg1
                                                                                                      KRR1 small subunit processome component
                                                                                                        Pre-rRNA-processing protein PNO1
                                                                                                        Kre33
                                                                                                        Fcf2
                                                                                                            40S ribosomal protein S1
                                                                                                              40S ribosomal protein S4
                                                                                                                40S ribosomal protein s5-like protein
                                                                                                                  40S ribosomal protein S6
                                                                                                                    40S ribosomal protein S7
                                                                                                                      40S ribosomal protein S8
                                                                                                                        40S ribosomal protein s9-like protein
                                                                                                                          40S ribosomal protein S13-like protein
                                                                                                                            40S ribosomal protein S14-like protein
                                                                                                                              40S ribosomal protein S16-like protein
                                                                                                                                40S ribosomal protein S11-like protein
                                                                                                                                  40S ribosomal protein S22-like protein
                                                                                                                                    40S ribosomal protein s23-like protein
                                                                                                                                      40S ribosomal protein S24
                                                                                                                                      40S ribosomal protein S28-like protein
                                                                                                                                        Faf1
                                                                                                                                              35S ribosomal RNAnonenonenone
                                                                                                                                              U3 snoRNAnonenonenone
                                                                                                                                              U3 small nucleolar RNA-associated protein 22
                                                                                                                                                Rrp7
                                                                                                                                                      Ribosome biogenesis protein ENP2
                                                                                                                                                          Utp20
                                                                                                                                                                Utp8
                                                                                                                                                                    Utp5
                                                                                                                                                                          Noc4
                                                                                                                                                                            Rps18
                                                                                                                                                                              Enp1
                                                                                                                                                                                    U3 small nucleolar ribonucleoprotein protein lcp5-like protein
                                                                                                                                                                                          Bfr2
                                                                                                                                                                                              Utp16
                                                                                                                                                                                                  Utp7