8FZD
Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with apoRF3, RF1, P- and E-site tRNAPhe (Composite state I-B)
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
B [auth b] | SCOP2B Superfamily | SIS domain/Ribosomal protein S2-like | 8063838 | 3001397 | SCOP2B (2022-06-29) |
D [auth d] | SCOP2B Superfamily | Alpha-L RNA-binding motif | 8083400 | 3001473 | SCOP2B (2022-06-29) |
F [auth f] | SCOP2B Superfamily | Ribosomal protein S6 | 8066495 | 3001323 | SCOP2B (2022-06-29) |
G [auth g] | SCOP2B Superfamily | Ribosomal protein S7 | 8077979 | 3000799 | SCOP2B (2022-06-29) |
H [auth h] | SCOP2B Superfamily | Ribosomal protein S8 | 8079059 | 3000709 | SCOP2B (2022-06-29) |
I [auth i] | SCOP2B Superfamily | Ribosomal protein S5 domain 2-like | 8082661 | 3000100 | SCOP2B (2022-06-29) |
J [auth j] | SCOP2B Superfamily | Ribosomal protein S10 | 8102681 | 3001336 | SCOP2B (2022-06-29) |
K [auth k] | SCOP2B Superfamily | Translational machinery components | 8035368 | 3000571 | SCOP2B (2022-06-29) |
L [auth l] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8106545 | 3000135 | SCOP2B (2022-06-29) |
M [auth m] | SCOP2B Superfamily | S13-like H2TH domain | 8098358 | 3000053 | SCOP2B (2022-06-29) |
N [auth n] | SCOP2B Superfamily | Glucocorticoid receptor-like (DNA-binding domain) | 8052568 | 3000068 | SCOP2B (2022-06-29) |
O [auth o] | SCOP2B Superfamily | S15/NS1 RNA-binding domain | 8032375 | 3001284 | SCOP2B (2022-06-29) |
P [auth p] | SCOP2B Superfamily | Ribosomal protein S16 | 8106547 | 3000680 | SCOP2B (2022-06-29) |
Q [auth q] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8059276 | 3000135 | SCOP2B (2022-06-29) |
S [auth s] | SCOP2B Superfamily | Ribosomal protein S19 | 8103915 | 3000686 | SCOP2B (2022-06-29) |
U [auth u] | SCOP2B Superfamily | Ribosomal protein S21 | 8053090 | 3002159 | SCOP2B (2022-06-29) |
Y [auth w] | SCOP2B Superfamily | Release factor N-terminal domain-like | 8032779 | 3001827 | SCOP2B (2022-06-29) |
Y [auth w] | SCOP2B Superfamily | Peptidyl-tRNA hydrolase domain-like | 8054407 | 3001421 | SCOP2B (2022-06-29) |
Y [auth w] | SCOP2B Superfamily | RNA-binding domain, RBD | 8054405 | 3000110 | SCOP2B (2022-06-29) |
Z [auth v] | SCOP2B Superfamily | EF-G C-terminal domain-like | 8092475 | 3001287 | SCOP2B (2022-06-29) |
Z [auth v] | SCOP2B Superfamily | Ras-like P-loop GTPases | 8092476 | 3002022 | SCOP2B (2022-06-29) |
Z [auth v] | SCOP2B Superfamily | EF-Tu post-G domain-like | 8092477 | 3002024 | SCOP2B (2022-06-29) |
Z [auth v] | SCOP2B Superfamily | EF-G C-terminal domain-like | 8092474 | 3001287 | SCOP2B (2022-06-29) |
CA [auth C] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8035394 | 3000135 | SCOP2B (2022-06-29) |
CA [auth C] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8035393 | 3000334 | SCOP2B (2022-06-29) |
DA [auth D] | SCOP2B Superfamily | Translational proteins | 8032955 | 3000811 | SCOP2B (2022-06-29) |
EA [auth E] | SCOP2B Superfamily | Ribosomal protein L4 | 8096356 | 3001146 | SCOP2B (2022-06-29) |
FA [auth F] | SCOP2B Superfamily | RL5-like | 8096352 | 3001709 | SCOP2B (2022-06-29) |
GA [auth G] | SCOP2B Superfamily | Ribosomal protein L6 | 8035398 | 3000724 | SCOP2B (2022-06-29) |
GA [auth G] | SCOP2B Superfamily | Ribosomal protein L6 | 8035397 | 3000724 | SCOP2B (2022-06-29) |
IA [auth I] | SCOP2B Superfamily | Ribosomal protein L10-like | 8079773 | 3000665 | SCOP2B (2022-06-29) |
JA [auth J] | SCOP2B Superfamily | Ribosomal protein L11, C-terminal domain | 8032961 | 3001186 | SCOP2B (2022-06-29) |
JA [auth J] | SCOP2B Superfamily | Ribosomal L11/L12e N-terminal domain-like | 8032963 | 3000950 | SCOP2B (2022-06-29) |
KA [auth L] | SCOP2B Superfamily | Ribosomal protein L13 | 8096350 | 3001134 | SCOP2B (2022-06-29) |
LA [auth M] | SCOP2B Superfamily | 50S Ribosomal protein L14-like | 8103358 | 3000433 | SCOP2B (2022-06-29) |
MA [auth N] | SCOP2B Superfamily | Ribosomal proteins L15p and L18e | 8070553 | 3001045 | SCOP2B (2022-06-29) |
NA [auth O] | SCOP2B Superfamily | Ribosomal protein L16p/L10e | 8096366 | 3000884 | SCOP2B (2022-06-29) |
OA [auth P] | SCOP2B Superfamily | Prokaryotic ribosomal protein L17 | 8035409 | 3000995 | SCOP2B (2022-06-29) |
PA [auth Q] | SCOP2B Superfamily | Translational machinery components | 8032969 | 3000571 | SCOP2B (2022-06-29) |
QA [auth R] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8096364 | 3000334 | SCOP2B (2022-06-29) |
RA [auth S] | SCOP2B Superfamily | Ribosomal protein L20 | 8096382 | 3000563 | SCOP2B (2022-06-29) |
SA [auth T] | SCOP2B Superfamily | l21p-like | 8096354 | 3002005 | SCOP2B (2022-06-29) |
TA [auth U] | SCOP2B Superfamily | Ribosomal protein L22 | 8096336 | 3001078 | SCOP2B (2022-06-29) |
UA [auth V] | SCOP2B Superfamily | Ribosomal proteins S24e, L23 and L15e | 8035415 | 3000210 | SCOP2B (2022-06-29) |
VA [auth W] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8096358 | 3000334 | SCOP2B (2022-06-29) |
WA [auth X] | SCOP2B Superfamily | Ribosomal protein L25-like | 8042538 | 3001161 | SCOP2B (2022-06-29) |
XA [auth Y] | SCOP2B Superfamily | Ribosomal L27 protein-like | 8096338 | 3000539 | SCOP2B (2022-06-29) |
YA [auth Z] | SCOP2B Superfamily | L28p-like | 8035424 | 3001966 | SCOP2B (2022-06-29) |
ZA [auth 1] | SCOP2B Superfamily | Ribosomal protein L29 (L29p) | 8096370 | 3000713 | SCOP2B (2022-06-29) |
AB [auth 2] | SCOP2B Superfamily | Ribosomal protein L30p/L7e | 8096372 | 3001378 | SCOP2B (2022-06-29) |
BB [auth 3] | SCOP2B Superfamily | L28p-like | 8032740 | 3001966 | SCOP2B (2022-06-29) |
CB [auth 4] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8096380 | 3001320 | SCOP2B (2022-06-29) |
DB [auth 5] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8096362 | 3001320 | SCOP2B (2022-06-29) |
FB [auth 7] | SCOP2B Superfamily | L35p-like | 8035388 | 3000790 | SCOP2B (2022-06-29) |
GB [auth 8] | SCOP2B Superfamily | Ribosomal protein L36 | 8035391 | 3001346 | SCOP2B (2022-06-29) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
BA [auth B] | PF00318 | Ribosomal protein S2 (Ribosomal_S2) | Ribosomal protein S2 | - | Family |
CA [auth C] | PF03947 | Ribosomal Proteins L2, C-terminal domain (Ribosomal_L2_C) | Ribosomal Proteins L2, C-terminal domain | Domain | |
CA [auth C] | PF00181 | Ribosomal Proteins L2, RNA binding domain (Ribosomal_L2) | Ribosomal Proteins L2, RNA binding domain | Domain | |
CA [auth C] | PF07650 | KH domain (KH_2) | KH domain | Domain | |
CA [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 |
DA [auth D] | PF00163 | Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4) | Ribosomal protein S4/S9 N-terminal domain | - | Family |
DA [auth D] | PF00297 | Ribosomal protein L3 (Ribosomal_L3) | Ribosomal protein L3 | - | Family |
DA [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 |
EA [auth E] | PF03719 | Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C) | Ribosomal protein S5, C-terminal domain | Domain | |
EA [auth E] | PF00573 | Ribosomal protein L4/L1 family (Ribosomal_L4) | Ribosomal protein L4/L1 family | - | Family |
EA [auth E] | PF00333 | Ribosomal protein S5, N-terminal domain (Ribosomal_S5) | Ribosomal protein S5, N-terminal domain | Domain | |
FA [auth F] | PF00281 | Ribosomal protein L5 (Ribosomal_L5) | Ribosomal protein L5 | Domain | |
FA [auth F] | PF01250 | Ribosomal protein S6 (Ribosomal_S6) | Ribosomal protein S6 | Domain | |
FA [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 |
GA [auth G] | PF00347 | Ribosomal protein L6 (Ribosomal_L6) | Ribosomal protein L6 | Domain | |
HA [auth H] | PF01281 | Ribosomal protein L9, N-terminal domain (Ribosomal_L9_N) | Ribosomal protein L9, N-terminal domain | Domain | |
HA [auth H] | PF00410 | Ribosomal protein S8 (Ribosomal_S8) | Ribosomal protein S8 | Domain | |
IA [auth I] | PF00380 | Ribosomal protein S9/S16 (Ribosomal_S9) | Ribosomal protein S9/S16 | - | Family |
IA [auth I] | PF00466 | Ribosomal protein L10 (Ribosomal_L10) | Ribosomal protein L10 | - | Family |
JA [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 |
JA [auth J] | PF00338 | Ribosomal protein S10p/S20e (Ribosomal_S10) | Ribosomal protein S10p/S20e | This family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes. | Domain |
JA [auth J] | PF00298 | Ribosomal protein L11, RNA binding domain (Ribosomal_L11) | Ribosomal protein L11, RNA binding domain | Domain | |
KA [auth L] | PF00164 | Ribosomal protein S12/S23 (Ribosom_S12_S23) | Ribosomal protein S12/S23 | This protein is known as S12 in bacteria and archaea and S23 in eukaryotes. | Domain |
KA [auth L] | PF00572 | Ribosomal protein L13 (Ribosomal_L13) | Ribosomal protein L13 | - | Family |
LA [auth M] | PF00238 | Ribosomal protein L14p/L23e (Ribosomal_L14) | Ribosomal protein L14p/L23e | Domain | |
LA [auth M] | PF00416 | Ribosomal protein S13/S18 (Ribosomal_S13) | Ribosomal protein S13/S18 | - | Family |
MA [auth N] | PF00828 | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A (Ribosomal_L27A) | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A | This family includes higher eukaryotic ribosomal 60S L27A, archaeal 50S L18e, prokaryotic 50S L15, fungal mitochondrial L10, plant L27A, mitochondrial L15 and chloroplast L18-3 proteins. | Domain |
MA [auth N] | PF00253 | Ribosomal protein S14p/S29e (Ribosomal_S14) | Ribosomal protein S14p/S29e | - | Family |
NA [auth O] | PF00252 | Ribosomal protein L16p/L10e (Ribosomal_L16) | Ribosomal protein L16p/L10e | Domain | |
NA [auth O] | PF00312 | Ribosomal protein S15 (Ribosomal_S15) | Ribosomal protein S15 | Domain | |
OA [auth P] | PF00886 | Ribosomal protein S16 (Ribosomal_S16) | Ribosomal protein S16 | - | Family |
OA [auth P] | PF01196 | Ribosomal protein L17 (Ribosomal_L17) | Ribosomal protein L17 | - | Family |
PA [auth Q] | PF00366 | Ribosomal protein S17 (Ribosomal_S17) | Ribosomal protein S17 | Domain | |
QA [auth R] | PF01245 | Ribosomal protein L19 (Ribosomal_L19) | Ribosomal protein L19 | - | Family |
RA [auth S] | PF00453 | Ribosomal protein L20 (Ribosomal_L20) | Ribosomal protein L20 | - | Family |
RA [auth S] | PF00203 | Ribosomal protein S19 (Ribosomal_S19) | Ribosomal protein S19 | Domain | |
SA [auth T] | PF01649 | Ribosomal protein S20 (Ribosomal_S20p) | Ribosomal protein S20 | - | Family |
SA [auth T] | PF00829 | Ribosomal prokaryotic L21 protein (Ribosomal_L21p) | Ribosomal prokaryotic L21 protein | - | Family |
TA [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 |
TA [auth U] | PF01165 | Ribosomal protein S21 (Ribosomal_S21) | Ribosomal protein S21 | - | Family |
UA [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 |
UA [auth V] | PF00276 | Ribosomal protein L23 (Ribosomal_L23) | Ribosomal protein L23 | - | Family |
VA [auth W] | PF03462 | PCRF domain (PCRF) | PCRF domain | This domain is found in peptide chain release factors. | Domain |
VA [auth W] | PF17136 | Ribosomal proteins 50S L24/mitochondrial 39S L24 (ribosomal_L24) | Ribosomal proteins 50S L24/mitochondrial 39S L24 | - | Family |
VA [auth W] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
WA [auth X] | PF01386 | Ribosomal L25p family (Ribosomal_L25p) | Ribosomal L25p family | Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. This family includes Ctc from B. subtilis Swiss:P14194, which is induced by stress. | Domain |
YA [auth Z] | PF00830 | Ribosomal L28 family (Ribosomal_L28) | Ribosomal L28 family | - | Family |
ZA [auth 1] | PF00831 | Ribosomal L29 protein (Ribosomal_L29) | Ribosomal L29 protein | - | Family |
AB [auth 2] | PF00327 | Ribosomal protein L30p/L7e (Ribosomal_L30) | Ribosomal protein L30p/L7e | This family includes prokaryotic L30 and eukaryotic L7. | Domain |
BB [auth 3] | PF01197 | Ribosomal protein L31 (Ribosomal_L31) | Ribosomal protein L31 | - | Family |
CB [auth 4] | PF01783 | Ribosomal L32p protein family (Ribosomal_L32p) | Ribosomal L32p protein family | - | Family |
DB [auth 5] | PF00471 | Ribosomal protein L33 (Ribosomal_L33) | Ribosomal protein L33 | - | Family |
EB [auth 6] | PF00468 | Ribosomal protein L34 (Ribosomal_L34) | Ribosomal protein L34 | - | Family |
FB [auth 7] | PF01632 | Ribosomal protein L35 (Ribosomal_L35p) | Ribosomal protein L35 | - | Family |
GB [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 |
W [auth y] | 4SU | Parent Component: U |
W [auth y] | 5MU | Parent Component: U |
W [auth y] | AMP | AA0203 , AA0227 , AA0371 , AA0511 : O4'-(phospho-5'-adenosine)-L-tyrosine MOD:00208 , N6-(phospho-5'-adenosine)-L-lysine MOD:00232 , 1'-(phospho-5'-adenosine)-L-histidine MOD:00376 , glycyl phospho-5'-adenosine MOD:01614 | :
W [auth y] | G7M | Parent Component: G : AA0203 , AA0227 , AA0371 , AA0511 |
W [auth y] | PSU | Parent Component: U : AA0203 , AA0227 , AA0371 , AA0511 |
AA [auth A] | 1MG | Parent Component: G : AA0203 , AA0227 , AA0371 , AA0511 |
AA [auth A] | 2MA | Parent Component: A : AA0203 , AA0227 , AA0371 , AA0511 |
AA [auth A] | 2MG | Parent Component: G : AA0203 , AA0227 , AA0371 , AA0511 |
AA [auth A] | 3TD | Parent Component: U : AA0203 , AA0227 , AA0371 , AA0511 |
AA [auth A] | 5MC | Parent Component: C : AA0203 , AA0227 , AA0371 , AA0511 |
AA [auth A] | 5MU | Parent Component: U : AA0203 , AA0227 , AA0371 , AA0511 |
AA [auth A] | 6MZ | Parent Component: A : AA0203 , AA0227 , AA0371 , AA0511 |
AA [auth A] | G7M | Parent Component: G : AA0203 , AA0227 , AA0371 , AA0511 |
AA [auth A] | H2U | Parent Component: U : AA0203 , AA0227 , AA0371 , AA0511 |
AA [auth A] | OMC | Parent Component: C : AA0203 , AA0227 , AA0371 , AA0511 |
AA [auth A] | OMG | Parent Component: G : AA0203 , AA0227 , AA0371 , AA0511 |
AA [auth A] | OMU | Parent Component: U : AA0203 , AA0227 , AA0371 , AA0511 |
AA [auth A] | PSU | Parent Component: U : AA0203 , AA0227 , AA0371 , AA0511 |
DA [auth D] | MEQ | Parent Component: GLN : AA0203 , AA0227 , AA0371 , AA0511 , AA0071 : O4'-(phospho-5'-adenosine)-L-tyrosine MOD:00208 , N6-(phospho-5'-adenosine)-L-lysine MOD:00232 , 1'-(phospho-5'-adenosine)-L-histidine MOD:00376 , glycyl phospho-5'-adenosine MOD:01614 , N5-methyl-L-glutamine MOD:00080 |
NA [auth O] | 4D4 | Parent Component: ARG : AA0203 , AA0227 , AA0371 , AA0511 , AA0071 |
NA [auth O] | MS6 | AA0203 , AA0227 , AA0371 , AA0511 , AA0071 | :