6RXV

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


Protein Family Annotation Pfam Database Homepage

ChainsAccessionIdentifierDescriptionCommentsSource
APF04003Dip2/Utp12 Family (Utp12)Dip2/Utp12 Family- Family
APF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
BPF04147Nop14-like family (Nop14)Nop14-like family- Family
CPF09368Sas10 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
CPF04000Sas10/Utp3/C1D family (Sas10_Utp3)Sas10/Utp3/C1D family- Family
DPF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
EPF08640U3 small nucleolar RNA-associated protein 6 (U3_assoc_6)U3 small nucleolar RNA-associated protein 6- Family
FPF08149BING4CT (NUC141) domain (BING4CT)BING4CT (NUC141) domainThis C terminal domain is found in the BING4 family of nucleolar WD40 repeat proteins [1].Domain
GPF08146BP28CT (NUC211) domain (BP28CT)BP28CT (NUC211) domainThis C terminal domain is found in BAP28-like nucleolar proteins [1].Domain
GPF12397U3 small nucleolar RNA-associated protein 10 (U3snoRNP10)U3 small nucleolar RNA-associated protein 10- Family
HPF03998Utp11 protein (Utp11)Utp11 protein- Family
IPF04003Dip2/Utp12 Family (Utp12)Dip2/Utp12 Family- Family
IPF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
JPF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
JPF08625Utp13 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
LPF09384UTP15 C terminal (UTP15_C)UTP15 C terminal- Family
LPF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
MPF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
OPF04192Utp21 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
OPF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
QPF00687Ribosomal protein L1p/L10e family (Ribosomal_L1)Ribosomal protein L1p/L10e familyThis family includes prokaryotic L1 and eukaryotic L10.Domain
R, SPF01269Fibrillarin (Fibrillarin)Fibrillarin- Domain
TPF08156NOP5NT (NUC127) domain (NOP5NT)NOP5NT (NUC127) domainThis N terminal domain is found in RNA-binding proteins of the NOP5 family [1].Domain
TPF01798snoRNA binding domain, fibrillarin (Nop)snoRNA binding domain, fibrillarin- Family
UPF08156NOP5NT (NUC127) domain (NOP5NT)NOP5NT (NUC127) domainThis N terminal domain is found in RNA-binding proteins of the NOP5 family [1].Domain
UPF01798snoRNA binding domain, fibrillarin (Nop)snoRNA binding domain, fibrillarin- Family
V, WPF01248Ribosomal 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
XPF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
YPF05189RNA 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
YPF01137RNA 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
ZPF08142AARP2CN (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
ZPF0495040S ribosome biogenesis protein Tsr1 and BMS1 C-terminal (RIBIOP_C)40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal- Family
AAPF00163Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4)Ribosomal protein S4/S9 N-terminal domain- Family
AAPF01479S4 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
BAPF04427Brix domain (Brix)Brix domain- Domain
CAPF04006Mpp10 protein (Mpp10)Mpp10 protein- Family
DAPF04158Sof1-like domain (Sof1)Sof1-like domain- Family
DAPF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
EA, FAPF03587EMG1/NEP1 methyltransferase (EMG1)EMG1/NEP1 methyltransferase- Family
GAPF17903Krr1 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
IA, JAPF13725Possible tRNA binding domain (tRNA_bind_2)Possible tRNA binding domain- Family
IA, JAPF08351Domain of unknown function (DUF1726) (DUF1726)Domain of unknown function (DUF1726)- Family
IA, JAPF13718GNAT acetyltransferase 2 (GNAT_acetyltr_2)GNAT acetyltransferase 2- Family
IA, JAPF05127Helicase (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
KAPF08698Fcf2 pre-rRNA processing (Fcf2)Fcf2 pre-rRNA processing- Family
LAPF01015Ribosomal S3Ae family (Ribosomal_S3Ae)Ribosomal S3Ae family- Family
MAPF00900Ribosomal family S4e (Ribosomal_S4e)Ribosomal family S4e- Family
MAPF1612140S ribosomal protein S4 C-terminus (40S_S4_C)40S ribosomal protein S4 C-terminus- Family
MAPF08071RS4NT (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
MAPF01479S4 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
NAPF00177Ribosomal protein S7p/S5e (Ribosomal_S7)Ribosomal protein S7p/S5eThis family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.Domain
OAPF01092Ribosomal protein S6e (Ribosomal_S6e)Ribosomal protein S6e- Family
PAPF01251Ribosomal protein S7e (Ribosomal_S7e)Ribosomal protein S7e- Family
QAPF01201Ribosomal protein S8e (Ribosomal_S8e)Ribosomal protein S8e- Family
RAPF00163Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4)Ribosomal protein S4/S9 N-terminal domain- Family
RAPF01479S4 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
SAPF08069Ribosomal 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
SAPF00312Ribosomal protein S15 (Ribosomal_S15)Ribosomal protein S15- Domain
TAPF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
UAPF00380Ribosomal protein S9/S16 (Ribosomal_S9)Ribosomal protein S9/S16- Family
VAPF00366Ribosomal protein S17 (Ribosomal_S17)Ribosomal protein S17- Domain
VAPF16205Ribosomal_S17 N-terminal (Ribosomal_S17_N)Ribosomal_S17 N-terminal- Family
WAPF00410Ribosomal protein S8 (Ribosomal_S8)Ribosomal protein S8- Domain
XAPF00164Ribosomal protein S12/S23 (Ribosom_S12_S23)Ribosomal protein S12/S23- Family
YAPF01282Ribosomal protein S24e (Ribosomal_S24e)Ribosomal protein S24e- Family
ZAPF01200Ribosomal protein S28e (Ribosomal_S28e)Ribosomal protein S28e- Family
ABPF15375Domain of unknown function (DUF4602) (DUF4602)Domain of unknown function (DUF4602)- Family
DBPF03813Nrap 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
DBPF17403Nrap 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
DBPF17406Nrap 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
DBPF17407Nrap 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
DBPF17404Nrap 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
DBPF17405Nrap 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
EBPF17799Rrp7 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
EBPF12923Ribosomal 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
FBPF08159NUC153 domain (NUC153)NUC153 domainThis small domain is found in a a novel nucleolar family [1].Domain
GBPF07539Down-regulated in metastasis (DRIM)Down-regulated in metastasis- Family
IB, OBPF04003Dip2/Utp12 Family (Utp12)Dip2/Utp12 Family- Family
JBPF03914CBF/Mak21 family (CBF)CBF/Mak21 family- Family
KBPF00416Ribosomal protein S13/S18 (Ribosomal_S13)Ribosomal protein S13/S18- Family
LBPF05291Bystin (Bystin)Bystin- Family
MBPF04000Sas10/Utp3/C1D family (Sas10_Utp3)Sas10/Utp3/C1D family- Family
NBPF13339Apoptosis antagonizing transcription factor (AATF-Che1)Apoptosis antagonizing transcription factor- Family
NBPF08164Apoptosis-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
PBPF08297U3 snoRNA associated (U3_snoRNA_assoc)U3 snoRNA associated- Family

Gene Product Annotation Gene Product Annotation

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
UAPeriodic tryptophan protein 2-like protein
UBUtp2
UCUtp3
UDUtp4
UFUtp6
UGUtp7
UJUTP10
UKU3 small nucleolar RNA-associated protein 11
ULUtp12
UMUtp13
UNUtp14
UOUtp15
UQUtp17
URUtp18
UUUtp21
UXUtp24none none none
UZUtp30
CA, CBNop1
CCNop56
CDNop58
CE, CFSnu13
CGRrp9
CHRNA 3'-terminal phosphate cyclase-like protein
CIBms1
CJImp3
CKImp4
CLMpp10
CMSof1
CN, COEmg1
CPKRR1 small subunit processome component
CQPre-rRNA-processing protein PNO1
CR, CSKre33
CTFcf2
Ca40S ribosomal protein S1
Cb40S ribosomal protein S4
Cc40S ribosomal protein s5-like protein
Cd40S ribosomal protein S6
Ce40S ribosomal protein S7
Cf40S ribosomal protein S8
Cg40S ribosomal protein s9-like protein
Ch40S ribosomal protein S13-like protein
Ci40S ribosomal protein S14-like protein
Cj40S ribosomal protein S16-like protein
Ck40S ribosomal protein S11-like protein
Cm40S ribosomal protein S22-like protein
Cn40S ribosomal protein s23-like protein
Co40S ribosomal protein S24
Cp40S ribosomal protein S28-like protein
CUFaf1
C135S ribosomal RNAnone none none
C2U3 snoRNAnone none none
UVU3 small nucleolar RNA-associated protein 22
CVRrp7
CWRibosome biogenesis protein ENP2
UTUtp20
UHUtp8
UE, UIUtp5
USNoc4
ClRps18
CXEnp1
CYU3 small nucleolar ribonucleoprotein protein lcp5-like protein
CZBfr2
UPUtp16