6RXT

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


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
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
PF04147Nop14-like family (Nop14)Nop14-like family- 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
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
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)Domain of unknown function (DUF1726)- 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
PF00177Ribosomal protein S7p/S5e (Ribosomal_S7)Ribosomal protein S7p/S5eThis family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.Domain
PF01251Ribosomal protein S7e (Ribosomal_S7e)Ribosomal protein S7e- 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
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
PF00380Ribosomal protein S9/S16 (Ribosomal_S9)Ribosomal protein S9/S16- Family
PF00410Ribosomal protein S8 (Ribosomal_S8)Ribosomal protein S8- Domain
PF00164Ribosomal protein S12/S23 (Ribosom_S12_S23)Ribosomal protein S12/S23- Family
PF01200Ribosomal protein S28e (Ribosomal_S28e)Ribosomal protein S28e- Family
PF15375Domain of unknown function (DUF4602) (DUF4602)Domain of unknown function (DUF4602)- Family
PF04003Dip2/Utp12 Family (Utp12)Dip2/Utp12 Family- Family
PF03914CBF/Mak21 family (CBF)CBF/Mak21 family- Family
PF08640U3 small nucleolar RNA-associated protein 6 (U3_assoc_6)U3 small nucleolar RNA-associated protein 6- Family
PF00416Ribosomal protein S13/S18 (Ribosomal_S13)Ribosomal protein S13/S18- Family
PF05291Bystin (Bystin)Bystin- Family
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
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

Gene Product Annotation Gene Product Annotation

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Periodic tryptophan protein 2-like protein
        Utp13"
            Utp14
                Utp15
                    Utp17
                          Utp18
                                Putative U3 snoRNP protein
                                    Utp24nonenonenone
                                    Utp30
                                          Nop1
                                            Putative nucleolar protein
                                              Utp2
                                                Nop58
                                                  snu13
                                                  Rrp9
                                                    RNA 3'-terminal phosphate cyclase-like protein
                                                    Bms1
                                                      Imp3
                                                          Putative U3 small nucleolar ribonucleoprotein
                                                                Putative U3 small nucleolar ribonucleoprotein protein
                                                                    Sof1
                                                                        Emg1
                                                                          Utp3
                                                                                KRR1 small subunit processome component
                                                                                  Pre-rRNA-processing protein PNO1
                                                                                  Kre33
                                                                                  Fcf2
                                                                                      40S ribosomal protein S1
                                                                                        40S ribosomal protein s5-like protein
                                                                                          40S ribosomal protein S7
                                                                                            40S ribosomal protein s9-like protein
                                                                                              40S ribosomal protein S13-like protein
                                                                                                40S ribosomal protein S14-like protein
                                                                                                  Utp4
                                                                                                        40S ribosomal protein S16-like protein
                                                                                                          40S ribosomal protein S22-like protein
                                                                                                            40S ribosomal protein s23-like protein
                                                                                                              40S ribosomal protein S28-like protein
                                                                                                                Faf1
                                                                                                                      35S ribosomal RNAnonenonenone
                                                                                                                      U3 snoRNAnonenonenone
                                                                                                                      Utp8
                                                                                                                          Utp5"
                                                                                                                                Noc4
                                                                                                                                  Utp6
                                                                                                                                      Putative ribosomal protein
                                                                                                                                        Enp1
                                                                                                                                              Utp16
                                                                                                                                                  Utp7
                                                                                                                                                      UTP10
                                                                                                                                                          U3 small nucleolar RNA-associated protein 11
                                                                                                                                                              Utp12