8I9R
Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State 5S RNP
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
K [auth CN] | SCOP2B Superfamily | Pentein | 8084662 | 3000640 | SCOP2B (2022-06-29) |
P [auth LB] | SCOP2B Superfamily | Translational proteins | 8106162 | 3000811 | SCOP2B (2022-06-29) |
Q [auth LC] | SCOP2B Superfamily | Ribosomal protein L4 | 8077111 | 3001146 | SCOP2B (2022-06-29) |
W [auth LN] | SCOP2B Superfamily | Ribosomal proteins S24e, L23 and L15e | 8106168 | 3000210 | SCOP2B (2022-06-29) |
CA [auth LV] | SCOP2B Superfamily | 50S Ribosomal protein L14-like | 8106208 | 3000433 | SCOP2B (2022-06-29) |
DA [auth LY] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8106166 | 3000334 | SCOP2B (2022-06-29) |
EA [auth Le] | SCOP2B Superfamily | Ribosomal protein L32e | 8106182 | 3000982 | SCOP2B (2022-06-29) |
FA [auth Lf] | SCOP2B Superfamily | Translational proteins | 8106190 | 3000811 | SCOP2B (2022-06-29) |
TA [auth LJ] | SCOP2B Superfamily | RL5-like | 8077505 | 3001709 | SCOP2B (2022-06-29) |
UA [auth LD] | SCOP2B Superfamily | Translational machinery components | 8106194 | 3000571 | SCOP2B (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
J [auth CM] | F_UNCLASSIFIED | e8i9rCM1 | A: a+b two layers | X: Ribosomal protein L30p/L7e (From Topology) | H: Ribosomal protein L30p/L7e (From Topology) | T: Ribosomal protein L30p/L7e | F: F_UNCLASSIFIED | ECOD (1.6) |
S [auth LF] | F_UNCLASSIFIED | e8i9rLF1 | A: a+b two layers | X: Ribosomal protein L30p/L7e (From Topology) | H: Ribosomal protein L30p/L7e (From Topology) | T: Ribosomal protein L30p/L7e | F: F_UNCLASSIFIED | ECOD (1.6) |
K [auth CN] | F_UNCLASSIFIED | e8i9rCN1 | A: a+b duplicates or obligate multimers | X: Pentein (From Topology) | H: Pentein (From Topology) | T: Pentein | F: F_UNCLASSIFIED | ECOD (1.6) |
P [auth LB] | F_UNCLASSIFIED | e8i9rLB1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: Alanine racemase-C | F: F_UNCLASSIFIED | ECOD (1.6) |
Q [auth LC] | F_UNCLASSIFIED | e8i9rLC2 | A: a/b three-layered sandwiches | X: Ribosomal protein L4 (From Topology) | H: Ribosomal protein L4 (From Topology) | T: Ribosomal protein L4 | F: F_UNCLASSIFIED | ECOD (1.6) |
Q [auth LC] | F_UNCLASSIFIED | e8i9rLC1 | A: extended segments | X: C-terminal helical region in 60S ribosomal protein L4 (L4p) (From Topology) | H: C-terminal helical region in 60S ribosomal protein L4 (L4p) (From Topology) | T: C-terminal helical region in 60S ribosomal protein L4 (L4p) | F: F_UNCLASSIFIED | ECOD (1.6) |
R [auth LE] | F_UNCLASSIFIED | e8i9rLE1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: F_UNCLASSIFIED | ECOD (1.6) |
T [auth LG] | F_UNCLASSIFIED | e8i9rLG1 | A: a+b three layers | X: Bacillus chorismate mutase-like | H: L30e-like (From Topology) | T: L30e-like | F: F_UNCLASSIFIED | ECOD (1.6) |
U [auth LL] | F_UNCLASSIFIED | e8i9rLL1 | A: extended segments | X: RPL13 (From Topology) | H: RPL13 (From Topology) | T: RPL13 | F: F_UNCLASSIFIED | ECOD (1.6) |
V [auth LM] | F_UNCLASSIFIED | e8i9rLM1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: F_UNCLASSIFIED | ECOD (1.6) |
W [auth LN] | F_UNCLASSIFIED | e8i9rLN1 | A: a+b two layers | X: Alpha-beta plaits | H: Ribosomal proteins S24e, L23 and L15e (From Topology) | T: Ribosomal proteins S24e, L23 and L15e | F: F_UNCLASSIFIED | ECOD (1.6) |
X [auth LO] | F_UNCLASSIFIED | e8i9rLO1 | A: a/b three-layered sandwiches | X: Ribosomal protein L13/L15p/L18e/L32e | H: Ribosomal protein L13 and L16-A (From Topology) | T: Ribosomal protein L13 and L16-A | F: F_UNCLASSIFIED | ECOD (1.6) |
Y [auth LP] | F_UNCLASSIFIED | e8i9rLP1 | A: a+b two layers | X: Enolase-N/ribosomal protein | H: Ribosomal protein L22 (From Topology) | T: Ribosomal protein L22 | F: F_UNCLASSIFIED | ECOD (1.6) |
Z [auth LQ] | F_UNCLASSIFIED | e8i9rLQ1 | A: a/b three-layered sandwiches | X: Ribosomal protein L13/L15p/L18e/L32e | H: Ribosomal proteins L15p and L18e (From Topology) | T: Ribosomal proteins L15p and L18e | F: F_UNCLASSIFIED | ECOD (1.6) |
AA [auth LS] | F_UNCLASSIFIED | e8i9rLS2 | A: a+b two layers | X: GP2-like | H: RplX-like (From Topology) | T: RplX-like | F: F_UNCLASSIFIED | ECOD (1.6) |
BA [auth LT] | F_UNCLASSIFIED | e8i9rLT1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: F_UNCLASSIFIED | ECOD (1.6) |
CA [auth LV] | F_UNCLASSIFIED | e8i9rLV1 | A: beta barrels | X: Ribosomal protein L14-like | H: Ribosomal protein L14-related (From Topology) | T: Ribosomal protein L14-related | F: F_UNCLASSIFIED | ECOD (1.6) |
DA [auth LY] | F_UNCLASSIFIED | e8i9rLY1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: F_UNCLASSIFIED | ECOD (1.6) |
EA [auth Le] | F_UNCLASSIFIED | e8i9rLe1 | A: a/b three-layered sandwiches | X: Ribosomal protein L13/L15p/L18e/L32e | H: Ribosomal protein L32e (From Topology) | T: Ribosomal protein L32e | F: F_UNCLASSIFIED | ECOD (1.6) |
FA [auth Lf] | F_UNCLASSIFIED | e8i9rLf1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: Alanine racemase-C | F: F_UNCLASSIFIED | ECOD (1.6) |
GA [auth Lh] | F_UNCLASSIFIED | e8i9rLh1 | A: alpha bundles | X: Long alpha-hairpin | H: Ribosomal protein L29 (L29p) (From Topology) | T: Ribosomal protein L29 (L29p) | F: F_UNCLASSIFIED | ECOD (1.6) |
HA [auth Li] | F_UNCLASSIFIED | e8i9rLi1 | A: alpha arrays | X: 60S ribosomal protein rpL36 (L36e) (From Topology) | H: 60S ribosomal protein rpL36 (L36e) (From Topology) | T: 60S ribosomal protein rpL36 (L36e) | F: F_UNCLASSIFIED | ECOD (1.6) |
IA [auth Lj] | F_UNCLASSIFIED | e8i9rLj1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: F_UNCLASSIFIED | ECOD (1.6) |
JA [auth Cc] | F_UNCLASSIFIED | e8i9rCc1 | A: alpha superhelices | X: Repetitive alpha hairpins | H: ARM repeat (From Topology) | T: ARM repeat | F: F_UNCLASSIFIED | ECOD (1.6) |
NA [auth Cy] | F_UNCLASSIFIED | e8i9rCy1 | A: a/b three-layered sandwiches | X: Anticodon-binding domain of Class II aaRS (From Topology) | H: Anticodon-binding domain of Class II aaRS (From Topology) | T: Anticodon-binding domain of Class II aaRS | F: F_UNCLASSIFIED | ECOD (1.6) |
OA [auth Cg] | F_UNCLASSIFIED | e8i9rCg1 | A: a/b three-layered sandwiches | X: Anticodon-binding domain of Class II aaRS (From Topology) | H: Anticodon-binding domain of Class II aaRS (From Topology) | T: Anticodon-binding domain of Class II aaRS | F: F_UNCLASSIFIED | ECOD (1.6) |
PA [auth CP] | F_UNCLASSIFIED | e8i9rCP2 | A: a+b two layers | X: Alpha-beta plaits | H: NOL1/NOP2/sun N-terminal ferredoxin-like domain (From Topology) | T: NOL1/NOP2/sun N-terminal ferredoxin-like domain | F: F_UNCLASSIFIED | ECOD (1.6) |
PA [auth CP] | F_UNCLASSIFIED | e8i9rCP1 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: S-adenosyl-L-methionine-dependent methyltransferases | F: F_UNCLASSIFIED | ECOD (1.6) |
QA [auth CG] | F_UNCLASSIFIED | e8i9rCG1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: PUA domain | F: F_UNCLASSIFIED | ECOD (1.6) |
QA [auth CG] | F_UNCLASSIFIED | e8i9rCG2 | A: a+b two layers | X: Cystatin-like | H: Pre-PUA domain (From Topology) | T: Pre-PUA domain | F: F_UNCLASSIFIED | ECOD (1.6) |
RA [auth Lq] | F_UNCLASSIFIED | e8i9rLq2 | A: a+b two layers | X: a+b domain in Ribosomal protein L1 (From Topology) | H: a+b domain in Ribosomal protein L1 (From Topology) | T: a+b domain in Ribosomal protein L1 | F: F_UNCLASSIFIED | ECOD (1.6) |
RA [auth Lq] | F_UNCLASSIFIED | e8i9rLq1 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Rossmann-like domain in Ribosomal protein L1 (From Topology) | T: Rossmann-like domain in Ribosomal protein L1 | F: F_UNCLASSIFIED | ECOD (1.6) |
SA [auth Cx] | F_UNCLASSIFIED | e8i9rCx1 | A: a+b two layers | X: Rrs1 (From Topology) | H: Rrs1 (From Topology) | T: Rrs1 | F: F_UNCLASSIFIED | ECOD (1.6) |
TA [auth LJ] | F_UNCLASSIFIED | e8i9rLJ1 | A: a+b two layers | X: Ribosomal protein L5 (From Topology) | H: Ribosomal protein L5 (From Topology) | T: Ribosomal protein L5 | F: F_UNCLASSIFIED | ECOD (1.6) |
UA [auth LD] | F_UNCLASSIFIED | e8i9rLD1 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: Ribonuclease H-like (From Topology) | T: Ribonuclease H-like | F: F_UNCLASSIFIED | ECOD (1.6) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
C [auth CA] | PF04427 | Brix domain (Brix) | Brix domain | - | Domain |
D [auth CB] | PF00687 | Ribosomal protein L1p/L10e family (Ribosomal_L1) | Ribosomal protein L1p/L10e family | This family includes prokaryotic L1 and eukaryotic L10. | Domain |
E [auth CC] | PF08145 | BOP1NT (NUC169) domain (BOP1NT) | BOP1NT (NUC169) domain | This N terminal domain is found in BOP1-like WD40 proteins [1]. | Domain |
E [auth CC] | PF05997 | Nucleolar protein,Nop52 (Nop52) | Nucleolar protein,Nop52 | - | Family |
F [auth CE] | PF01778 | Ribosomal L28e protein family (Ribosomal_L28e) | Ribosomal L28e protein family | - | Family |
F [auth CE] | PF00270 | DEAD/DEAH box helicase (DEAD) | DEAD/DEAH box helicase | Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome ... | Domain |
F [auth CE] | PF13959 | Domain of unknown function (DUF4217) (DUF4217) | Domain of unknown function (DUF4217) | This short domain is found at the C-terminus of many helicase proteins. | Domain |
F [auth CE] | PF00271 | Helicase conserved C-terminal domain (Helicase_C) | Helicase conserved C-terminal domain | The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. | Domain |
F [auth CE] | PF04874 | Mak16 protein C-terminal region (Mak16) | Mak16 protein C-terminal region | - | Family |
G [auth CH] | PF08155 | NOGCT (NUC087) domain (NOGCT) | NOGCT (NUC087) domain | This C terminal domain is found in the NOG subfamily of nucleolar GTP-binding proteins [1]. | Domain |
H [auth CI] | PF00076 | RNA recognition motif (RRM_1) | RNA recognition motif | The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and pro ... | Domain |
I [auth CJ] | PF06732 | Pescadillo N-terminus (Pescadillo_N) | Pescadillo N-terminus | - | Family |
I [auth CJ] | PF00533 | BRCA1 C Terminus (BRCT) domain (BRCT) | BRCA1 C Terminus (BRCT) domain | - | Family |
J [auth CM], S [auth LF] | PF08079 | Ribosomal L30 N-terminal domain (Ribosomal_L30_N) | Ribosomal L30 N-terminal domain | This presumed domain is found at the N-terminus of Ribosomal L30 proteins and has been termed RL30NT or NUC018 [1]. | Domain |
J [auth CM], S [auth LF] | PF00327 | Ribosomal protein L30p/L7e (Ribosomal_L30) | Ribosomal protein L30p/L7e | This family includes prokaryotic L30 and eukaryotic L7. | Domain |
J [auth CM], S [auth LF] | PF01247 | Ribosomal protein L35Ae (Ribosomal_L35Ae) | Ribosomal protein L35Ae | - | Domain |
K [auth CN] | PF01912 | eIF-6 family (eIF-6) | eIF-6 family | - | Family |
L [auth CQ] | PF01246 | Ribosomal protein L24e (Ribosomal_L24e) | Ribosomal protein L24e | - | Domain |
M [auth CR] | PF09420 | Ribosome biogenesis protein Nop16 (Nop16) | Ribosome biogenesis protein Nop16 | - | Family |
N [auth CU] | PF05890 | Eukaryotic rRNA processing protein EBP2 (Ebp2) | Eukaryotic rRNA processing protein EBP2 | - | Family |
Q [auth LC] | PF14374 | 60S ribosomal protein L4 C-terminal domain (Ribos_L4_asso_C) | 60S ribosomal protein L4 C-terminal domain | This family is found at the very C-terminal of 60 ribosomal L4 proteins. | Domain |
Q [auth LC] | PF00573 | Ribosomal protein L4/L1 family (Ribosomal_L4) | Ribosomal protein L4/L1 family | - | Family |
R [auth LE] | PF01655 | Ribosomal protein L32 (Ribosomal_L32e) | Ribosomal protein L32 | - | Family |
R [auth LE] | PF01159 | Ribosomal protein L6e (Ribosomal_L6e) | Ribosomal protein L6e | - | Family |
T [auth LG] | PF01248 | Ribosomal protein L7Ae/L30e/S12e/Gadd45 family (Ribosomal_L7Ae) | Ribosomal protein L7Ae/L30e/S12e/Gadd45 family | 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 MyD11 ... | Domain |
V [auth LM] | PF01929 | Ribosomal protein L14 (Ribosomal_L14e) | Ribosomal protein L14 | - | Family |
W [auth LN] | PF00827 | Ribosomal L15 (Ribosomal_L15e) | Ribosomal L15 | - | Family |
X [auth LO] | PF00572 | Ribosomal protein L13 (Ribosomal_L13) | Ribosomal protein L13 | - | Family |
Y [auth LP] | PF00237 | Ribosomal protein L22p/L17e (Ribosomal_L22) | Ribosomal protein L22p/L17e | This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. | Domain |
Z [auth LQ] | PF00687 | Ribosomal protein L1p/L10e family (Ribosomal_L1) | Ribosomal protein L1p/L10e family | This family includes prokaryotic L1 and eukaryotic L10. | Domain |
AA [auth LS] | PF01775 | Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A (Ribosomal_L18A) | Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A | This family includes: archaeal 50S ribosomal protein L18Ae, often referred to as L20e or LX; fungal 60S ribosomal protein L20; and higher eukaryote 60S ribosomal protein L18A. | Domain |
CA [auth LV] | PF00238 | Ribosomal protein L14p/L23e (Ribosomal_L14) | Ribosomal protein L14p/L23e | - | Domain |
DA [auth LY] | PF16906 | Ribosomal proteins L26 eukaryotic, L24P archaeal (Ribosomal_L26) | Ribosomal proteins L26 eukaryotic, L24P archaeal | - | Family |
DA [auth LY] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
PA [auth CP] | PF01189 | 16S rRNA methyltransferase RsmB/F (Methyltr_RsmB-F) | 16S rRNA methyltransferase RsmB/F | - | Family |
PA [auth CP] | PF22458 | Methyltr_RsmF/B-like, ferredoxin-like domain (RsmF-B_ferredox) | Methyltr_RsmF/B-like, ferredoxin-like domain | This entry represents a ferredoxin-like domain found in methyltransferases RsmB, RsmF and related sequences [1-5]. | Domain |
QA [auth CG] | PF04427 | Brix domain (Brix) | Brix domain | - | Domain |
QA [auth CG] | PF03657 | UPF0113 PUA domain (UPF0113) | UPF0113 PUA domain | - | Domain |
QA [auth CG] | PF17833 | UPF0113 Pre-PUA domain (UPF0113_N) | UPF0113 Pre-PUA domain | - | Domain |
TA [auth LJ] | PF00281 | Ribosomal protein L5 (Ribosomal_L5) | Ribosomal protein L5 | - | Domain |
TA [auth LJ] | PF00673 | ribosomal L5P family C-terminus (Ribosomal_L5_C) | ribosomal L5P family C-terminus | This region is found associated with Pfam:PF00281. | Domain |
UA [auth LD] | PF17144 | Ribosomal large subunit proteins 60S L5, and 50S L18 (Ribosomal_L5e) | Ribosomal large subunit proteins 60S L5, and 50S L18 | - | Family |
UA [auth LD] | PF14204 | Ribosomal L18 C-terminal region (Ribosomal_L18_c) | Ribosomal L18 C-terminal region | This domain is the C-terminal end of ribosomal L18/L5 proteins. | Domain |
WA [auth CX] | PF04939 | Ribosome biogenesis regulatory protein (RRS1) (RRS1) | Ribosome biogenesis regulatory protein (RRS1) | - | Family |