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
PF08149BING4CT (NUC141) domain (BING4CT)BING4CT (NUC141) domainThis C terminal domain is found in the BING4 family of nucleolar WD40 repeat proteins [1].Domain
PF04003Dip2/Utp12 Family (Utp12)Dip2/Utp12 Family- Family
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
PF09384UTP15 C terminal (UTP15_C)UTP15 C terminal- Family
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
PF04427Brix domain (Brix)Brix domain- Domain
PF04158Sof1-like domain (Sof1)Sof1-like domain- Family
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
PF01015Ribosomal S3Ae family (Ribosomal_S3Ae)Ribosomal S3Ae family- 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
PF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
PF00410Ribosomal protein S8 (Ribosomal_S8)Ribosomal protein S8- Domain
PF05291Bystin (Bystin)Bystin- Family
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
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
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
PF04006Mpp10 protein (Mpp10)Mpp10 protein- Family
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
PF04000Sas10/Utp3/C1D family (Sas10_Utp3)Sas10/Utp3/C1D family- 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)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
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
PF08069Ribosomal S13/S15 N-terminal domain (Ribosomal_S13_N)Ribosomal S13/S15 N-terminal domainThis domain is found at the N-terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [1].Domain
PF00312Ribosomal protein S15 (Ribosomal_S15)Ribosomal protein S15- Domain
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
PF00380Ribosomal protein S9/S16 (Ribosomal_S9)Ribosomal protein S9/S16- Family
PF00164Ribosomal protein S12/S23 (Ribosom_S12_S23)Ribosomal protein S12/S23- Family
PF01200Ribosomal protein S28e (Ribosomal_S28e)Ribosomal protein S28e- 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
PF08297U3 snoRNA associated (U3_snoRNA_assoc)U3 snoRNA associated- 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

Gene Product Annotation Gene Product Annotation

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Periodic tryptophan protein 2-like protein
        Utp7
            Utp12
                Utp15
                    Utp24nonenonenone
                    RNA 3'-terminal phosphate cyclase-like protein
                    Putative U3 small nucleolar ribonucleoprotein
                          Sof1
                              Pre-rRNA-processing protein PNO1
                              40S ribosomal protein S1
                                40S ribosomal protein s9-like protein
                                  40S ribosomal protein S14-like protein
                                    40S ribosomal protein S22-like protein
                                      Faf1nonenonenone
                                      Utp8
                                          Enp1
                                                Utp13"
                                                    Utp14
                                                        Utp17
                                                              Utp18
                                                                    Putative U3 snoRNP protein
                                                                        Utp30
                                                                              Nop1
                                                                                Putative nucleolar protein
                                                                                  Utp2
                                                                                    Nop58
                                                                                      snu13
                                                                                      Rrp9
                                                                                        Bms1
                                                                                          Imp3
                                                                                              Putative U3 small nucleolar ribonucleoprotein protein
                                                                                                  Emg1
                                                                                                    Utp3
                                                                                                          KRR1 small subunit processome component
                                                                                                            Kre33
                                                                                                            Fcf2
                                                                                                                40S ribosomal protein s5-like protein
                                                                                                                  40S ribosomal protein S7
                                                                                                                    40S ribosomal protein S13-like protein
                                                                                                                      Utp4
                                                                                                                            40S ribosomal protein S16-like protein
                                                                                                                              40S ribosomal protein s23-like protein
                                                                                                                                40S ribosomal protein S28-like protein
                                                                                                                                  WA [auth C1]
                                                                                                                                  35S ribosomal RNAnonenonenone
                                                                                                                                  XA [auth C2]
                                                                                                                                  U3 snoRNAnonenonenone
                                                                                                                                  Utp5"
                                                                                                                                        Noc4
                                                                                                                                          Utp6
                                                                                                                                              Putative ribosomal protein
                                                                                                                                                Utp16
                                                                                                                                                    UTP10
                                                                                                                                                        U3 small nucleolar RNA-associated protein 11