8I9W
Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Dbp10-3
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
L [auth CK] | SCOP2B Superfamily | 50S Ribosomal protein L14-like | 8053081 | 3000433 | SCOP2B (2022-06-29) |
O [auth CN] | SCOP2B Superfamily | Pentein | 8084662 | 3000640 | SCOP2B (2022-06-29) |
BA [auth LB] | SCOP2B Superfamily | Translational proteins | 8106162 | 3000811 | SCOP2B (2022-06-29) |
CA [auth LC] | SCOP2B Superfamily | Ribosomal protein L4 | 8077111 | 3001146 | SCOP2B (2022-06-29) |
KA [auth LN] | SCOP2B Superfamily | Ribosomal proteins S24e, L23 and L15e | 8106168 | 3000210 | SCOP2B (2022-06-29) |
QA [auth LV] | SCOP2B Superfamily | 50S Ribosomal protein L14-like | 8106208 | 3000433 | SCOP2B (2022-06-29) |
SA [auth LY] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8106166 | 3000334 | SCOP2B (2022-06-29) |
UA [auth Le] | SCOP2B Superfamily | Ribosomal protein L32e | 8106182 | 3000982 | SCOP2B (2022-06-29) |
VA [auth Lf] | SCOP2B Superfamily | Translational proteins | 8106190 | 3000811 | 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) |
---|---|---|---|---|---|---|---|---|
EA [auth LF] | F_UNCLASSIFIED | e8i9wLF1 | 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) |
N [auth CM] | F_UNCLASSIFIED | e8i9wCM1 | 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) |
O [auth CN] | F_UNCLASSIFIED | e8i9wCN1 | A: a+b duplicates or obligate multimers | X: Pentein (From Topology) | H: Pentein (From Topology) | T: Pentein | F: F_UNCLASSIFIED | ECOD (1.6) |
W [auth CV] | F_UNCLASSIFIED | e8i9wCV1 | A: a+b two layers | X: RPL28 (From Topology) | H: RPL28 (From Topology) | T: RPL28 | F: F_UNCLASSIFIED | ECOD (1.6) |
BA [auth LB] | F_UNCLASSIFIED | e8i9wLB1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: Alanine racemase-C | F: F_UNCLASSIFIED | ECOD (1.6) |
CA [auth LC] | F_UNCLASSIFIED | e8i9wLC1 | 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) |
CA [auth LC] | F_UNCLASSIFIED | e8i9wLC2 | 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) |
C [auth CA] | F_UNCLASSIFIED | e8i9wCA1 | 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) |
DA [auth LE] | F_UNCLASSIFIED | e8i9wLE1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: F_UNCLASSIFIED | ECOD (1.6) |
FA [auth LG] | F_UNCLASSIFIED | e8i9wLG1 | A: a+b three layers | X: Bacillus chorismate mutase-like | H: L30e-like (From Topology) | T: L30e-like | F: F_UNCLASSIFIED | ECOD (1.6) |
GA [auth LH] | F_UNCLASSIFIED | e8i9wLH2 | A: a+b two layers | X: Ribosomal protein L6 (From Topology) | H: Ribosomal protein L6 (From Topology) | T: Ribosomal protein L6 | F: F_UNCLASSIFIED | ECOD (1.6) |
HA [auth LK] | F_UNCLASSIFIED | e8i9wLK1 | A: alpha arrays | X: HTH | H: HTH | T: Ribosomal protein L11, C-terminal domain | F: F_UNCLASSIFIED | ECOD (1.6) |
HA [auth LK] | F_UNCLASSIFIED | e8i9wLK2 | A: a+b two layers | X: Ribosomal protein L11/L12e N-terminal domain-like | H: Ribosomal protein L11/L12e N-terminal domain (From Topology) | T: Ribosomal protein L11/L12e N-terminal domain | F: F_UNCLASSIFIED | ECOD (1.6) |
IA [auth LL] | F_UNCLASSIFIED | e8i9wLL1 | A: extended segments | X: RPL13 (From Topology) | H: RPL13 (From Topology) | T: RPL13 | F: F_UNCLASSIFIED | ECOD (1.6) |
JA [auth LM] | F_UNCLASSIFIED | e8i9wLM1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: F_UNCLASSIFIED | ECOD (1.6) |
KA [auth LN] | F_UNCLASSIFIED | e8i9wLN1 | 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) |
LA [auth LO] | F_UNCLASSIFIED | e8i9wLO1 | 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) |
MA [auth LP] | F_UNCLASSIFIED | e8i9wLP1 | 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) |
NA [auth LQ] | F_UNCLASSIFIED | e8i9wLQ1 | 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) |
OA [auth LS] | F_UNCLASSIFIED | e8i9wLS1 | A: a+b two layers | X: GP2-like | H: RplX-like (From Topology) | T: RplX-like | F: F_UNCLASSIFIED | ECOD (1.6) |
PA [auth LT] | F_UNCLASSIFIED | e8i9wLT1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: F_UNCLASSIFIED | ECOD (1.6) |
QA [auth LV] | F_UNCLASSIFIED | e8i9wLV1 | 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) |
SA [auth LY] | F_UNCLASSIFIED | e8i9wLY1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: F_UNCLASSIFIED | ECOD (1.6) |
TA [auth Ld] | F_UNCLASSIFIED | e8i9wLd1 | A: a+b two layers | X: Ribosomal protein L31e-like | H: Ribosomal protein L31e/gp120 outer domain (From Topology) | T: Ribosomal protein L31e/gp120 outer domain | F: F_UNCLASSIFIED | ECOD (1.6) |
UA [auth Le] | F_UNCLASSIFIED | e8i9wLe1 | 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) |
VA [auth Lf] | F_UNCLASSIFIED | e8i9wLf1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: Alanine racemase-C | F: F_UNCLASSIFIED | ECOD (1.6) |
WA [auth Lh] | F_UNCLASSIFIED | e8i9wLh1 | 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) |
XA [auth Li] | F_UNCLASSIFIED | e8i9wLi1 | 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) |
YA [auth Lj] | F_UNCLASSIFIED | e8i9wLj1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: F_UNCLASSIFIED | ECOD (1.6) |
ZA [auth Lq] | F_UNCLASSIFIED | e8i9wLq2 | 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) |
ZA [auth Lq] | F_UNCLASSIFIED | e8i9wLq1 | 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) |
G [auth CF] | F_UNCLASSIFIED | e8i9wCF1 | A: a+b two layers | X: Alpha-beta plaits | H: Ribosomal protein L10-like (From Topology) | T: Ribosomal protein L10-like | F: F_UNCLASSIFIED | ECOD (1.6) |
G [auth CF] | F_UNCLASSIFIED | e8i9wCF2 | A: a+b two layers | X: Insertion domain in 60S ribosomal protein rpP0 (L10P) (From Topology) | H: Insertion domain in 60S ribosomal protein rpP0 (L10P) (From Topology) | T: Insertion domain in 60S ribosomal protein rpP0 (L10P) | F: F_UNCLASSIFIED | ECOD (1.6) |
H [auth CG] | F_UNCLASSIFIED | e8i9wCG1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: PUA domain | F: F_UNCLASSIFIED | ECOD (1.6) |
H [auth CG] | F_UNCLASSIFIED | e8i9wCG2 | A: a+b two layers | X: Cystatin-like | H: Pre-PUA domain (From Topology) | T: Pre-PUA domain | F: F_UNCLASSIFIED | ECOD (1.6) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
J [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 |
K [auth CJ] | PF06732 | Pescadillo N-terminus (Pescadillo_N) | Pescadillo N-terminus | - | Family |
K [auth CJ] | PF00533 | BRCA1 C Terminus (BRCT) domain (BRCT) | BRCA1 C Terminus (BRCT) domain | - | Family |
L [auth CK] | PF01201 | Ribosomal protein S8e (Ribosomal_S8e) | Ribosomal protein S8e | - | Family |
M [auth CL] | PF01926 | 50S ribosome-binding GTPase (MMR_HSR1) | 50S ribosome-binding GTPase | - | Family |
M [auth CL] | PF08701 | GNL3L/Grn1 putative GTPase (GN3L_Grn1) | GNL3L/Grn1 putative GTPase | - | Family |
EA [auth LF], N [auth CM] | 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 |
EA [auth LF], N [auth CM] | PF00327 | Ribosomal protein L30p/L7e (Ribosomal_L30) | Ribosomal protein L30p/L7e | This family includes prokaryotic L30 and eukaryotic L7. | Domain |
EA [auth LF], N [auth CM] | PF01247 | Ribosomal protein L35Ae (Ribosomal_L35Ae) | Ribosomal protein L35Ae | - | Domain |
O [auth CN] | PF01912 | eIF-6 family (eIF-6) | eIF-6 family | - | Family |
Q [auth CP] | PF01189 | 16S rRNA methyltransferase RsmB/F (Methyltr_RsmB-F) | 16S rRNA methyltransferase RsmB/F | - | Family |
Q [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 |
R [auth CQ] | PF01246 | Ribosomal protein L24e (Ribosomal_L24e) | Ribosomal protein L24e | - | Domain |
S [auth CR] | PF09420 | Ribosome biogenesis protein Nop16 (Nop16) | Ribosome biogenesis protein Nop16 | - | Family |
U [auth CT] | PF03914 | CBF/Mak21 family (CBF) | CBF/Mak21 family | - | Repeat |
U [auth CT] | PF07540 | Nucleolar complex-associated protein (NOC3p) | Nucleolar complex-associated protein | - | Family |
V [auth CU] | PF05890 | Eukaryotic rRNA processing protein EBP2 (Ebp2) | Eukaryotic rRNA processing protein EBP2 | - | Family |
W [auth CV] | PF01778 | Ribosomal L28e protein family (Ribosomal_L28e) | Ribosomal L28e protein family | - | Family |
Y [auth CY] | PF03715 | Noc2p family (Noc2) | Noc2p family | - | Family |
CA [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 |
CA [auth LC] | PF00573 | Ribosomal protein L4/L1 family (Ribosomal_L4) | Ribosomal protein L4/L1 family | - | Family |
C [auth CA] | PF04427 | Brix domain (Brix) | Brix domain | - | Domain |
DA [auth LE] | PF01655 | Ribosomal protein L32 (Ribosomal_L32e) | Ribosomal protein L32 | - | Family |
DA [auth LE] | PF01159 | Ribosomal protein L6e (Ribosomal_L6e) | Ribosomal protein L6e | - | Family |
FA [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 |
GA [auth LH] | PF00831 | Ribosomal L29 protein (Ribosomal_L29) | Ribosomal L29 protein | - | Family |
GA [auth LH] | PF00347 | Ribosomal protein L6 (Ribosomal_L6) | Ribosomal protein L6 | - | Domain |
HA [auth LK] | PF03946 | Ribosomal protein L11, N-terminal domain (Ribosomal_L11_N) | Ribosomal protein L11, N-terminal domain | The N-terminal domain of Ribosomal protein L11 adopts an alpha/beta fold and is followed by the RNA binding C-terminal domain. | Domain |
HA [auth LK] | PF00298 | Ribosomal protein L11, RNA binding domain (Ribosomal_L11) | Ribosomal protein L11, RNA binding domain | - | Domain |
JA [auth LM] | PF01929 | Ribosomal protein L14 (Ribosomal_L14e) | Ribosomal protein L14 | - | Family |
KA [auth LN] | PF00827 | Ribosomal L15 (Ribosomal_L15e) | Ribosomal L15 | - | Family |
LA [auth LO] | PF00572 | Ribosomal protein L13 (Ribosomal_L13) | Ribosomal protein L13 | - | Family |
MA [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 |
NA [auth LQ] | PF00687 | Ribosomal protein L1p/L10e family (Ribosomal_L1) | Ribosomal protein L1p/L10e family | This family includes prokaryotic L1 and eukaryotic L10. | Domain |
D [auth CB] | 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 |
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 |
OA [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 |
QA [auth LV] | PF00238 | Ribosomal protein L14p/L23e (Ribosomal_L14) | Ribosomal protein L14p/L23e | - | Domain |
RA [auth LX] | PF03939 | Ribosomal protein L23, N-terminal domain (Ribosomal_L23eN) | Ribosomal protein L23, N-terminal domain | - | Family |
SA [auth LY] | PF16906 | Ribosomal proteins L26 eukaryotic, L24P archaeal (Ribosomal_L26) | Ribosomal proteins L26 eukaryotic, L24P archaeal | - | Family |
SA [auth LY] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
E [auth CC] | PF08145 | BOP1NT (NUC169) domain (BOP1NT) | BOP1NT (NUC169) domain | This N terminal domain is found in BOP1-like WD40 proteins [1]. | Domain |
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 |
G [auth CF] | PF17777 | Insertion domain in 60S ribosomal protein L10P (RL10P_insert) | Insertion domain in 60S ribosomal protein L10P | This domain is found in prokaryotic and archaeal ribosomal L10 protein [1]. | Domain |
G [auth CF] | PF00466 | Ribosomal protein L10 (Ribosomal_L10) | Ribosomal protein L10 | - | Family |
H [auth CG] | PF03657 | UPF0113 PUA domain (UPF0113) | UPF0113 PUA domain | - | Domain |
H [auth CG] | PF17833 | UPF0113 Pre-PUA domain (UPF0113_N) | UPF0113 Pre-PUA domain | - | Domain |
I [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 |
I [auth CH] | PF06858 | Nucleolar GTP-binding protein 1 (NOG1) (NOG1) | Nucleolar GTP-binding protein 1 (NOG1) | - | Family |
I [auth CH] | PF17835 | NOG1 N-terminal helical domain (NOG1_N) | NOG1 N-terminal helical domain | This domain is found at the N-terminus of NOG1 GTPase proteins. | Domain |