9XAD | pdb_00009xad

Cryo-EM structure of the pre-40S ribosome (Enp1-Rrp12 WT) from Chaetomium thermophilum, state Rrp12-A2


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
A [auth E]SCOP2B SuperfamilyRibosomal S3Ae-like 8094667 3002166 SCOP2B (2022-06-29)
C [auth I]SCOP2B SuperfamilyRibosomal protein S7 8095683 3000799 SCOP2B (2022-06-29)
I [auth P]SCOP2B SuperfamilyL30e-like 8106204 3001739 SCOP2B (2022-06-29)
K [auth R]SCOP2B SuperfamilyTranslational machinery components 8095757 3000571 SCOP2B (2022-06-29)
M [auth T]SCOP2B SuperfamilyRibosomal protein S5 domain 2-like 8097794 3000100 SCOP2B (2022-06-29)
N [auth V]SCOP2B SuperfamilyS13-like H2TH domain 8106180 3000053 SCOP2B (2022-06-29)
O [auth W]SCOP2B SuperfamilyWinged helix DNA-binding domain 8095685 3000034 SCOP2B (2022-06-29)
P [auth Z]SCOP2B SuperfamilyRibosomal protein S8 8095563 3000709 SCOP2B (2022-06-29)
R [auth b]SCOP2B SuperfamilyRibosomal proteins S24e, L23 and L15e 8098446 3000210 SCOP2B (2022-06-29)
S [auth c]SCOP2B SuperfamilyWinged helix DNA-binding domain 8106172 3000034 SCOP2B (2022-06-29)
U [auth f]SCOP2B SuperfamilyNucleic acid-binding proteins 8095187 3000135 SCOP2B (2022-06-29)
FA [auth SA]SCOP2B SuperfamilySIS domain/Ribosomal protein S2-like 8106164 3001397 SCOP2B (2022-06-29)
IA [auth SV]SCOP2B SuperfamilyGlucocorticoid receptor-like (DNA-binding domain) 8106206 3000068 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth E]PF01667Ribosomal protein S27 (Ribosomal_S27e)Ribosomal protein S27- Family
B [auth H]PF00900Ribosomal family S4e (Ribosomal_S4e)Ribosomal family S4e- Family
B [auth H]PF1612140S ribosomal protein S4 C-terminus (40S_S4_C)40S ribosomal protein S4 C-terminus- Family
B [auth H]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
B [auth H]PF00467KOW motif (KOW)KOW motif- Family
C [auth I]PF00177Ribosomal protein S7p/S5e (Ribosomal_S7)Ribosomal protein S7p/S5eThis family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes. Domain
C [auth I]PF01599Ribosomal protein S27a (Ribosomal_S27)Ribosomal protein S27aThis family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesised as a C-terminal extension of ubiquitin (CEP). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins ...This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesised as a C-terminal extension of ubiquitin (CEP). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis [3]. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [2].
Domain
D [auth J]PF01092Ribosomal protein S6e (Ribosomal_S6e)Ribosomal protein S6e- Family
E [auth K]PF01251Ribosomal protein S7e (Ribosomal_S7e)Ribosomal protein S7e- Family
F [auth L]PF01201Ribosomal protein S8e (Ribosomal_S8e)Ribosomal protein S8e- Family
G [auth M]PF00163Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4)Ribosomal protein S4/S9 N-terminal domain- Family
G [auth M]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
H [auth O]PF00366Ribosomal protein S17 (Ribosomal_S17)Ribosomal protein S17Domain
H [auth O]PF16205Ribosomal_S17 N-terminal (Ribosomal_S17_N)Ribosomal_S17 N-terminal- Family
I [auth P]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
J [auth Q]PF00312Ribosomal protein S15 (Ribosomal_S15)Ribosomal protein S15Domain
K [auth R]PF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
L [auth S]PF00203Ribosomal protein S19 (Ribosomal_S19)Ribosomal protein S19Domain
M [auth T]PF00380Ribosomal protein S9/S16 (Ribosomal_S9)Ribosomal protein S9/S16- Family
N [auth V]PF00416Ribosomal protein S13/S18 (Ribosomal_S13)Ribosomal protein S13/S18- Family
O [auth W]PF01090Ribosomal protein S19e (Ribosomal_S19e)Ribosomal protein S19e- Family
P [auth Z]PF00410Ribosomal protein S8 (Ribosomal_S8)Ribosomal protein S8Domain
X [auth A]PF00164Ribosomal protein S12/S23 (Ribosom_S12_S23)Ribosomal protein S12/S23This protein is known as S12 in bacteria and archaea and S23 in eukaryotes. Domain
Z [auth 1]PF12589Methyltransferase involved in Williams-Beuren syndrome (WBS_methylT)Methyltransferase involved in Williams-Beuren syndrome- Family
Z [auth 1]PF08241Methyltransferase domain (Methyltransf_11)Methyltransferase domainMembers of this family are SAM dependent methyltransferases. Domain
AA [auth 2]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
AA [auth 2]PF22298Tsr1, G-like domain (Tsr1_G-like)Tsr1, G-like domainThis entry represents the G-like (guanine nucleotide-binding domain) domain, found in Tsr1, a protein required for normal export of the pre-40S particles from the nucleus to the cytoplasm during 40S ribosomal subunit synthesis [1-5]. This domain adop ...This entry represents the G-like (guanine nucleotide-binding domain) domain, found in Tsr1, a protein required for normal export of the pre-40S particles from the nucleus to the cytoplasm during 40S ribosomal subunit synthesis [1-5]. This domain adopts a GTPase-like fold, but lacks a P-loop and is not predicted to bind GTP.
Domain
AA [auth 2]PF0495040S ribosome biogenesis protein Tsr1 and BMS1 C-terminal (RIBIOP_C)40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal- Family
BA [auth 3]PF22891Eukaryotic type KH-domain (KH-domain type I) (KH_PNO1_2nd)Eukaryotic type KH-domain (KH-domain type I)This entry represents the second KH domain found in the PNO1 protein. PNO1 is part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit. Domain
EA [auth 7]PF25772RRP12-like, N-terminal HEAT repeats (HEAT_RRP12_N)RRP12-like, N-terminal HEAT repeats- Repeat
EA [auth 7]PF08161Ribosomal RNA-processing protein 12, HEAT repeats (RRP12_HEAT)Ribosomal RNA-processing protein 12, HEAT repeats- Repeat
FA [auth SA]PF00318Ribosomal protein S2 (Ribosomal_S2)Ribosomal protein S2- Family
GA [auth SC]PF03719Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C)Ribosomal protein S5, C-terminal domainDomain
GA [auth SC]PF00333Ribosomal protein S5, N-terminal domain (Ribosomal_S5)Ribosomal protein S5, N-terminal domainDomain
IA [auth SV]PF01249Ribosomal protein S21e (Ribosomal_S21e)Ribosomal protein S21e- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth E]Small ribosomal subunit protein eS1
B [auth H]40S ribosomal protein S4
C [auth I]40S ribosomal protein s5-like protein
D [auth J]40S ribosomal protein S6
E [auth K]40S ribosomal protein S7
F [auth L]40S ribosomal protein S8
G [auth M]40S ribosomal protein s9-like protein
H [auth O]40S ribosomal protein S11-like protein
I [auth P]40S ribosomal protein S12
J [auth Q]40S ribosomal protein S13-like protein
K [auth R]40S ribosomal protein S14-like protein
L [auth S]40S ribosomal protein s15-like protein
M [auth T]40S ribosomal protein S16-like protein
N [auth V]Putative ribosomal protein
O [auth W]40S ribosomal protein S19-like protein
P [auth Z]40S ribosomal protein S22-like protein
Q [auth a]40S ribosomal protein s23-like protein
R [auth b]Small ribosomal subunit protein eS24
S [auth c]40S ribosomal protein S25- -
T [auth e]Ribosomal protein s27-like protein
U [auth f]40S ribosomal protein S28-like protein
V [auth h]40S ribosomal protein S30---
W [auth i]40S ribosomal protein S27a-like protein
X [auth A]18S rRNA---
Y [auth 0]Trm112---
Z [auth 1]Methyltransferase-like protein
AA [auth 2]Bms1-type G domain-containing protein
BA [auth 3]Pre-rRNA-processing protein PNO1
CA [auth 4]Bystin-like protein
DA [auth 5]Putative low-temperature viability protein-
EA [auth 7]Ribosomal RNA-processing protein 12-like conserved domain-containing protein- -
FA [auth SA]Small ribosomal subunit protein uS2
GA [auth SC]Small ribosomal subunit protein uS5
HA [auth SR]40S ribosomal protein S17-like protein
IA [auth SV]40S ribosomal protein S21-like protein

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A [auth E]IPR001593Small ribosomal subunit protein eS1Family
A [auth E]IPR018281Small ribosomal subunit protein eS1, conserved siteConserved Site
A [auth E]IPR027500Small ribosomal subunit protein eS1, eukaryotaFamily
B [auth H]IPR018199Small ribosomal subunit protein eS4, N-terminal, conserved siteConserved Site
B [auth H]IPR013843Small ribosomal subunit protein eS4, N-terminalDomain
B [auth H]IPR032277Small ribosomal subunit protein eS4, C-terminal domainDomain
B [auth H]IPR002942RNA-binding S4 domainDomain
B [auth H]IPR013845Small ribosomal subunit protein eS4, central regionDomain
B [auth H]IPR000876Small ribosomal subunit protein eS4Family
B [auth H]IPR014722Large ribosomal subunit protein uL2, domain 2Homologous Superfamily
B [auth H]IPR038237Small ribosomal subunit protein eS4, central domain superfamilyHomologous Superfamily
B [auth H]IPR041982Small ribosomal subunit protein eS4, KOW domainDomain
B [auth H]IPR036986RNA-binding S4 domain superfamilyHomologous Superfamily
B [auth H]IPR005824KOWDomain
C [auth I]IPR020606Small ribosomal subunit protein uS7, conserved siteConserved Site
C [auth I]IPR000235Small ribosomal subunit protein uS7Family
C [auth I]IPR036823Small ribosomal subunit protein uS7 domain superfamilyHomologous Superfamily
C [auth I]IPR023798Small ribosomal subunit protein uS7 domainDomain
C [auth I]IPR005716Ribosomal protein uS7, eukaryotic/archaealFamily
D [auth J]IPR014401Small ribosomal subunit protein eS6-likeFamily
D [auth J]IPR001377Small ribosomal subunit protein eS6Family
D [auth J]IPR018282Small ribosomal subunit protein eS6, conserved siteConserved Site
E [auth K]IPR000554Small ribosomal subunit protein eS7Family
E [auth K]IPR047861Small ribosomal subunit protein eS7, conserved siteConserved Site
F [auth L]IPR001047Small ribosomal subunit protein eS8Family
F [auth L]IPR042563Small ribosomal subunit protein eS8 subdomain, eukaryotaHomologous Superfamily
F [auth L]IPR022309Ribosomal protein eS8/ribosomal biogenesis NSA2Family
G [auth M]IPR018079Small ribosomal subunit protein uS4, conserved siteConserved Site
G [auth M]IPR002942RNA-binding S4 domainDomain
G [auth M]IPR001912Small ribosomal subunit protein uS4, N-terminalDomain
G [auth M]IPR036986RNA-binding S4 domain superfamilyHomologous Superfamily
G [auth M]IPR022801Small ribosomal subunit protein uS4Family
G [auth M]IPR005710Small ribosomal subunit protein uS4, eukaryota/archaeaFamily
H [auth O]IPR019979Small ribosomal subunit protein uS17, conserved siteConserved Site
H [auth O]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
H [auth O]IPR000266Small ribosomal subunit protein uS17Family
H [auth O]IPR032440Small ribosomal subunit protein uS17, N-terminalDomain
H [auth O]IPR028333Small ribosomal subunit protein uS17, archaeal/eukaryoticFamily
I [auth P]IPR000530Small ribosomal subunit protein eS12Family
I [auth P]IPR004038Ribosomal protein eL8/eL30/eS12/Gadd45Domain
I [auth P]IPR029064Ribosomal protein eL30-like superfamilyHomologous Superfamily
I [auth P]IPR047860Small ribosomal subunit protein eS12, conserved siteConserved Site
J [auth Q]IPR012606Small ribosomal subunit protein uS15, N-terminalDomain
J [auth Q]IPR009068uS15/NS1, RNA-binding domain superfamilyHomologous Superfamily
J [auth Q]IPR023029Small ribosomal subunit protein uS15, archaea/eukaryotaFamily
J [auth Q]IPR000589Small ribosomal subunit protein uS15Family
K [auth R]IPR001971Small ribosomal subunit protein uS11Family
K [auth R]IPR036967Small ribosomal subunit protein uS11 superfamilyHomologous Superfamily
K [auth R]IPR018102Small ribosomal subunit protein uS11, conserved siteConserved Site
L [auth S]IPR002222Small ribosomal subunit protein uS19Family
L [auth S]IPR023575Small ribosomal subunit protein uS19, superfamilyHomologous Superfamily
L [auth S]IPR020934Small ribosomal subunit protein uS19, conserved siteConserved Site
L [auth S]IPR005713Small ribosomal subunit protein uS19, eukaryota/archaeaFamily
M [auth T]IPR020574Small ribosomal subunit protein uS9, conserved siteConserved Site
M [auth T]IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
M [auth T]IPR000754Small ribosomal subunit protein uS9Family
M [auth T]IPR014721Small ribosomal subunit protein uS5 domain 2-type fold, subgroupHomologous Superfamily
N [auth V]IPR027437Small ribosomal subunit protein uS13, C-terminalHomologous Superfamily
N [auth V]IPR001892Small ribosomal subunit protein uS13Family
N [auth V]IPR018269Small ribosomal subunit protein uS13, conserved siteConserved Site
N [auth V]IPR010979Small ribosomal subunit protein uS13-like, H2THHomologous Superfamily
O [auth W]IPR001266Small ribosomal subunit protein eS19Family
O [auth W]IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
O [auth W]IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
P [auth Z]IPR000630Small ribosomal subunit protein uS8Family
P [auth Z]IPR047863Small ribosomal subunit protein uS8, conserved siteConserved Site
P [auth Z]IPR035987Small ribosomal subunit protein uS8 superfamilyHomologous Superfamily
Q [auth a]IPR006032Small ribosomal subunit protein uS12Family
Q [auth a]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
Q [auth a]IPR005680Small ribosomal subunit protein uS12, eukaryota/archaeaFamily
R [auth b]IPR053709Eukaryotic Ribosomal Protein eS24Homologous Superfamily
R [auth b]IPR001976Small ribosomal subunit protein eS24Family
R [auth b]IPR012678Ribosomal protein uL23/eL15/eS24 core domain superfamilyHomologous Superfamily
R [auth b]IPR018098Small ribosomal subunit protein eS24 conserved siteConserved Site
S [auth c]IPR004977Small ribosomal subunit protein eS25Family
S [auth c]IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
T [auth e]IPR023407Small ribosomal subunit protein eS27, zinc-binding domain superfamilyHomologous Superfamily
T [auth e]IPR000592Small ribosomal subunit protein eS27Family
T [auth e]IPR011332Zinc-binding ribosomal proteinHomologous Superfamily
U [auth f]IPR028626Ribosomal protein eS28 conserved siteConserved Site
U [auth f]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
U [auth f]IPR000289Small ribosomal subunit protein eS28Family
W [auth i]IPR019954Ubiquitin conserved siteConserved Site
W [auth i]IPR000626Ubiquitin-like domainDomain
W [auth i]IPR038582Small ribosomal subunit protein eS31 eukaryotic superfamilyHomologous Superfamily
W [auth i]IPR002906Small ribosomal subunit protein eS31Domain
W [auth i]IPR019956Ubiquitin domainDomain
W [auth i]IPR050158Ubiquitin and ubiquitin-likeFamily
W [auth i]IPR029071Ubiquitin-like domain superfamilyHomologous Superfamily
W [auth i]IPR011332Zinc-binding ribosomal proteinHomologous Superfamily
Z [auth 1]IPR02223818S rRNA (guanine(1575)-N(7))-methyltransferase Bud23, C-terminalDomain
Z [auth 1]IPR03976918S rRNA (guanine(1575)-N(7))-methyltransferase Bud23-likeFamily
Z [auth 1]IPR029063S-adenosyl-L-methionine-dependent methyltransferase superfamilyHomologous Superfamily
Z [auth 1]IPR013216Methyltransferase type 11Domain
AA [auth 2]IPR007034Ribosome biogenesis protein BMS1/TSR1, C-terminalDomain
AA [auth 2]IPR030387Bms1/Tsr1-type G domainDomain
AA [auth 2]IPR039761Ribosome biogenesis protein Bms1/Tsr1Family
AA [auth 2]IPR012948AARP2CNDomain
BA [auth 3]IPR004087K Homology domainDomain
BA [auth 3]IPR055211PNO1, second type I KH domainDomain
BA [auth 3]IPR036612K Homology domain, type 1 superfamilyHomologous Superfamily
BA [auth 3]IPR055212PNO1, first type I KH domainDomain
CA [auth 4]IPR007955BystinFamily
DA [auth 5]IPR007307Low temperature viability protein Ltv1Family
EA [auth 7]IPR012978RRP12, HEAT domainDomain
EA [auth 7]IPR057860RRP12, N-terminal HEAT domainDomain
EA [auth 7]IPR011989Armadillo-like helicalHomologous Superfamily
EA [auth 7]IPR016024Armadillo-type foldHomologous Superfamily
EA [auth 7]IPR052087Ribosomal RNA-processing protein RRP12Family
FA [auth SA]IPR023591Small ribosomal subunit protein uS2, flavodoxin-like domain superfamilyHomologous Superfamily
FA [auth SA]IPR018130Small ribosomal subunit protein uS2, conserved siteConserved Site
FA [auth SA]IPR001865Small ribosomal subunit protein uS2Family
FA [auth SA]IPR005707Small ribosomal subunit protein uS2, eukaryota/archaeaFamily
FA [auth SA]IPR027498Small ribosomal subunit protein uS2, eukaryotaFamily
GA [auth SC]IPR005711Small ribosomal subunit protein uS5, eukaryota_archaeaFamily
GA [auth SC]IPR000851Small ribosomal subunit protein uS5Family
GA [auth SC]IPR005324Small ribosomal subunit protein uS5, C-terminalDomain
GA [auth SC]IPR013810Small ribosomal subunit protein uS5, N-terminalDomain
GA [auth SC]IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
GA [auth SC]IPR018192Small ribosomal subunit protein uS5, N-terminal, conserved siteConserved Site
GA [auth SC]IPR014721Small ribosomal subunit protein uS5 domain 2-type fold, subgroupHomologous Superfamily
HA [auth SR]IPR036401Small ribosomal subunit protein eS17 superfamilyHomologous Superfamily
HA [auth SR]IPR001210Small ribosomal subunit protein eS17Family
HA [auth SR]IPR018273Small ribosomal subunit protein eS17, conserved siteConserved Site
IA [auth SV]IPR038579Small ribosomal subunit protein eS21 superfamilyHomologous Superfamily
IA [auth SV]IPR018279Small ribosomal subunit protein eS21, conserved siteConserved Site
IA [auth SV]IPR001931Small ribosomal subunit protein eS21Family