8FZI
Cryo-EM structure of an E. coli rotated ribosome bound with RF3-GDPCP and p/E-tRNAPhe (Composite state II-B)
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
M [auth m] | SCOP2B Superfamily | S13-like H2TH domain | 8106110 | 3000053 | SCOP2B (2022-06-29) |
P [auth p] | SCOP2B Superfamily | Ribosomal protein S16 | 8097402 | 3000680 | SCOP2B (2022-06-29) |
B [auth b] | SCOP2B Superfamily | SIS domain/Ribosomal protein S2-like | 8107572 | 3001397 | SCOP2B (2022-06-29) |
U [auth u] | SCOP2B Superfamily | Ribosomal protein S21 | 8093436 | 3002159 | SCOP2B (2022-06-29) |
X [auth v] | SCOP2B Superfamily | EF-G C-terminal domain-like | 8092474 | 3001287 | SCOP2B (2022-06-29) |
X [auth v] | SCOP2B Superfamily | EF-Tu post-G domain-like | 8092477 | 3002024 | SCOP2B (2022-06-29) |
X [auth v] | SCOP2B Superfamily | Ras-like P-loop GTPases | 8092476 | 3002022 | SCOP2B (2022-06-29) |
X [auth v] | SCOP2B Superfamily | EF-G C-terminal domain-like | 8092475 | 3001287 | SCOP2B (2022-06-29) |
AA [auth C] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8035394 | 3000135 | SCOP2B (2022-06-29) |
AA [auth C] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8035393 | 3000334 | SCOP2B (2022-06-29) |
DA [auth F] | SCOP2B Superfamily | RL5-like | 8107414 | 3001709 | SCOP2B (2022-06-29) |
FA [auth I] | SCOP2B Superfamily | Ribosomal protein L10-like | 8079773 | 3000665 | SCOP2B (2022-06-29) |
GA [auth J] | SCOP2B Superfamily | Ribosomal protein L11, C-terminal domain | 8032961 | 3001186 | SCOP2B (2022-06-29) |
GA [auth J] | SCOP2B Superfamily | Ribosomal L11/L12e N-terminal domain-like | 8032963 | 3000950 | SCOP2B (2022-06-29) |
IA [auth M] | SCOP2B Superfamily | 50S Ribosomal protein L14-like | 8106350 | 3000433 | SCOP2B (2022-06-29) |
D [auth d] | SCOP2B Superfamily | Alpha-L RNA-binding motif | 8083400 | 3001473 | SCOP2B (2022-06-29) |
QA [auth U] | SCOP2B Superfamily | Ribosomal protein L22 | 8096336 | 3001078 | SCOP2B (2022-06-29) |
UA [auth Y] | SCOP2B Superfamily | Ribosomal L27 protein-like | 8096338 | 3000539 | SCOP2B (2022-06-29) |
VA [auth Z] | SCOP2B Superfamily | L28p-like | 8106038 | 3001966 | SCOP2B (2022-06-29) |
CB [auth 7] | SCOP2B Superfamily | L35p-like | 8035388 | 3000790 | SCOP2B (2022-06-29) |
DB [auth 8] | SCOP2B Superfamily | Ribosomal protein L36 | 8093434 | 3001346 | SCOP2B (2022-06-29) |
F [auth f] | SCOP2B Superfamily | Ribosomal protein S6 | 8107228 | 3001323 | SCOP2B (2022-06-29) |
G [auth g] | SCOP2B Superfamily | Ribosomal protein S7 | 8077979 | 3000799 | SCOP2B (2022-06-29) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
Z [auth B] | PF00318 | Ribosomal protein S2 (Ribosomal_S2) | Ribosomal protein S2 | - | Family |
AA [auth C] | PF03947 | Ribosomal Proteins L2, C-terminal domain (Ribosomal_L2_C) | Ribosomal Proteins L2, C-terminal domain | - | Domain |
AA [auth C] | PF00181 | Ribosomal Proteins L2, RNA binding domain (Ribosomal_L2) | Ribosomal Proteins L2, RNA binding domain | - | Domain |
AA [auth C] | PF07650 | KH domain (KH_2) | KH domain | - | Domain |
AA [auth C] | PF00189 | Ribosomal protein S3, C-terminal domain (Ribosomal_S3_C) | Ribosomal protein S3, C-terminal domain | This family contains a central domain Pfam:PF00013, hence the amino and carboxyl terminal domains are stored separately. This is a minimal carboxyl-terminal domain. Some are much longer. | Domain |
BA [auth D] | PF00163 | Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4) | Ribosomal protein S4/S9 N-terminal domain | - | Family |
BA [auth D] | PF01479 | S4 domain (S4) | S4 domain | 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 pro ... | Domain |
CA [auth E] | PF03719 | Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C) | Ribosomal protein S5, C-terminal domain | - | Domain |
CA [auth E] | PF00573 | Ribosomal protein L4/L1 family (Ribosomal_L4) | Ribosomal protein L4/L1 family | - | Family |
CA [auth E] | PF00333 | Ribosomal protein S5, N-terminal domain (Ribosomal_S5) | Ribosomal protein S5, N-terminal domain | - | Domain |
DA [auth F] | PF00281 | Ribosomal protein L5 (Ribosomal_L5) | Ribosomal protein L5 | - | Domain |
DA [auth F] | PF01250 | Ribosomal protein S6 (Ribosomal_S6) | Ribosomal protein S6 | - | Domain |
DA [auth F] | PF00673 | ribosomal L5P family C-terminus (Ribosomal_L5_C) | ribosomal L5P family C-terminus | This region is found associated with Pfam:PF00281. | Domain |
EA [auth G] | PF00347 | Ribosomal protein L6 (Ribosomal_L6) | Ribosomal protein L6 | - | Domain |
FA [auth I] | PF00466 | Ribosomal protein L10 (Ribosomal_L10) | Ribosomal protein L10 | - | Family |
GA [auth J] | 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 |
GA [auth J] | PF00298 | Ribosomal protein L11, RNA binding domain (Ribosomal_L11) | Ribosomal protein L11, RNA binding domain | - | Domain |
HA [auth L] | PF00164 | Ribosomal protein S12/S23 (Ribosom_S12_S23) | Ribosomal protein S12/S23 | - | Family |
IA [auth M] | PF00238 | Ribosomal protein L14p/L23e (Ribosomal_L14) | Ribosomal protein L14p/L23e | - | Domain |
IA [auth M] | PF00416 | Ribosomal protein S13/S18 (Ribosomal_S13) | Ribosomal protein S13/S18 | - | Family |
JA [auth N] | PF00828 | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A (Ribosomal_L27A) | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A | - | Family |
LA [auth P] | PF00886 | Ribosomal protein S16 (Ribosomal_S16) | Ribosomal protein S16 | - | Family |
OA [auth S] | PF00453 | Ribosomal protein L20 (Ribosomal_L20) | Ribosomal protein L20 | - | Family |
PA [auth T] | PF01649 | Ribosomal protein S20 (Ribosomal_S20p) | Ribosomal protein S20 | - | Family |
PA [auth T] | PF00829 | Ribosomal prokaryotic L21 protein (Ribosomal_L21p) | Ribosomal prokaryotic L21 protein | - | Family |
QA [auth U] | PF00237 | Ribosomal protein L22p/L17e (Ribosomal_L22) | Ribosomal protein L22p/L17e | This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. | Domain |
QA [auth U] | PF01165 | Ribosomal protein S21 (Ribosomal_S21) | Ribosomal protein S21 | - | Family |
RA [auth V] | PF00009 | Elongation factor Tu GTP binding domain (GTP_EFTU) | Elongation factor Tu GTP binding domain | This domain contains a P-loop motif, also found in several other families such as Pfam:PF00071, Pfam:PF00025 and Pfam:PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains. | Domain |
VA [auth Z] | PF00830 | Ribosomal L28 family (Ribosomal_L28) | Ribosomal L28 family | - | Family |
YA [auth 3] | PF01197 | Ribosomal protein L31 (Ribosomal_L31) | Ribosomal protein L31 | - | Family |
BB [auth 6] | PF00468 | Ribosomal protein L34 (Ribosomal_L34) | Ribosomal protein L34 | - | Family |
CB [auth 7] | PF01632 | Ribosomal protein L35 (Ribosomal_L35p) | Ribosomal protein L35 | - | Family |
DB [auth 8] | PF00444 | Ribosomal protein L36 (Ribosomal_L36) | Ribosomal protein L36 | - | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Protein Modification Annotation
Modified Residue(s) | ||
---|---|---|
Chain | Residue(s) | Description |
A [auth a] | 2MG | Parent Component: G |
A [auth a] | 4OC | Parent Component: C |
A [auth a] | 5MC | Parent Component: C |
A [auth a] | G7M | Parent Component: G |
A [auth a] | MA6 | Parent Component: A |
A [auth a] | PSU | Parent Component: U |
A [auth a] | UR3 | Parent Component: U |
K [auth k] | IAS | |
L [auth l] | D2T | Parent Component: ASP |
V [auth x] | 4SU | Parent Component: U |
V [auth x] | 5MU | Parent Component: U |
V [auth x] | G7M | Parent Component: G |
V [auth x] | MIA | Parent Component: A |
V [auth x] | PSU | Parent Component: U |
Y [auth A] | 1MG | Parent Component: G |
Y [auth A] | 2MA | Parent Component: A |
Y [auth A] | 2MG | Parent Component: G |
Y [auth A] | 3TD | Parent Component: U |
Y [auth A] | 5MC | Parent Component: C |
Y [auth A] | 5MU | Parent Component: U |
Y [auth A] | 6MZ | Parent Component: A |
Y [auth A] | G7M | Parent Component: G |
Y [auth A] | H2U | Parent Component: U |
Y [auth A] | OMC | Parent Component: C |
Y [auth A] | OMG | Parent Component: G |
Y [auth A] | OMU | Parent Component: U |
Y [auth A] | PSU | Parent Component: U |
BA [auth D] | MEQ | Parent Component: GLN :  AA0071 :  N5-methyl-L-glutamine MOD:00080 |
KA [auth O] | 4D4 | Parent Component: ARG :  AA0071 |
KA [auth O] | MS6 | AA0071 | :