Cryo-EM structure of the wild-type Thermus thermophilus 70S ribosome in complex with mRNA, A-site Q230-N5-methylated Release Factor 1, and P-site 2'-deoxy-A76-fMEAAAKC-peptidyl-tRNAcys at 2.13A resolution
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
C [auth D] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8033194 | 3000334 | SCOP2B (2022-06-29) |
C [auth D] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8033195 | 3000135 | SCOP2B (2022-06-29) |
D [auth E] | SCOP2B Superfamily | Translational proteins | 8033197 | 3000811 | SCOP2B (2022-06-29) |
E [auth F] | SCOP2B Superfamily | Ribosomal protein L4 | 8033198 | 3001146 | SCOP2B (2022-06-29) |
G [auth H] | SCOP2B Superfamily | Ribosomal protein L6 | 8033202 | 3000724 | SCOP2B (2022-06-29) |
G [auth H] | SCOP2B Superfamily | Ribosomal protein L6 | 8033203 | 3000724 | SCOP2B (2022-06-29) |
H [auth I] | SCOP2B Superfamily | L9 N-domain-like | 8042935 | 3000338 | SCOP2B (2022-06-29) |
H [auth I] | SCOP2B Superfamily | Ribosomal protein L9 C-domain | 8042934 | 3000329 | SCOP2B (2022-06-29) |
I [auth N] | SCOP2B Superfamily | Ribosomal protein L13 | 8033205 | 3001134 | SCOP2B (2022-06-29) |
J [auth O] | SCOP2B Superfamily | 50S Ribosomal protein L14-like | 8042936 | 3000433 | SCOP2B (2022-06-29) |
K [auth P] | SCOP2B Superfamily | Ribosomal proteins L15p and L18e | 8033207 | 3001045 | SCOP2B (2022-06-29) |
L [auth Q] | SCOP2B Superfamily | Ribosomal protein L16p/L10e | 8043627 | 3000884 | SCOP2B (2022-06-29) |
M [auth R] | SCOP2B Superfamily | Prokaryotic ribosomal protein L17 | 8032744 | 3000995 | SCOP2B (2022-06-29) |
N [auth S] | SCOP2B Superfamily | Translational machinery components | 8033211 | 3000571 | SCOP2B (2022-06-29) |
O [auth T] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8033214 | 3000334 | SCOP2B (2022-06-29) |
P [auth U] | SCOP2B Superfamily | Ribosomal protein L20 | 8033216 | 3000563 | SCOP2B (2022-06-29) |
Q [auth V] | SCOP2B Superfamily | l21p-like | 8033218 | 3002005 | SCOP2B (2022-06-29) |
R [auth W] | SCOP2B Superfamily | Ribosomal protein L22 | 8033220 | 3001078 | SCOP2B (2022-06-29) |
S [auth X] | SCOP2B Superfamily | Ribosomal proteins S24e, L23 and L15e | 8033219 | 3000210 | SCOP2B (2022-06-29) |
T [auth Y] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8033223 | 3000334 | SCOP2B (2022-06-29) |
V [auth 0] | SCOP2B Superfamily | Ribosomal L27 protein-like | 8041210 | 3000539 | SCOP2B (2022-06-29) |
W [auth 1] | SCOP2B Superfamily | L28p-like | 8042932 | 3001966 | SCOP2B (2022-06-29) |
X [auth 2] | SCOP2B Superfamily | Ribosomal protein L29 (L29p) | 8042933 | 3000713 | SCOP2B (2022-06-29) |
Z [auth 4] | SCOP2B Superfamily | L28p-like | 8033189 | 3001966 | SCOP2B (2022-06-29) |
AA [auth 5] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8033190 | 3001320 | SCOP2B (2022-06-29) |
BA [auth 6] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8033191 | 3001320 | SCOP2B (2022-06-29) |
DA [auth 8] | SCOP2B Superfamily | L35p-like | 8033192 | 3000790 | SCOP2B (2022-06-29) |
GA [auth b] | SCOP2B Superfamily | SIS domain/Ribosomal protein S2-like | 8044010 | 3001397 | SCOP2B (2022-06-29) |
HA [auth c] | SCOP2B Superfamily | Ribosomal protein S3 C-terminal domain | 8044012 | 3001053 | SCOP2B (2022-06-29) |
HA [auth c] | SCOP2B Superfamily | Prokaryotic type KH domain (KH-domain type II) | 8044011 | 3001043 | SCOP2B (2022-06-29) |
IA [auth d] | SCOP2B Superfamily | Alpha-L RNA-binding motif | 8044014 | 3001473 | SCOP2B (2022-06-29) |
JA [auth e] | SCOP2B Superfamily | dsRNA-binding domain-like | 8044017 | 3000985 | SCOP2B (2022-06-29) |
JA [auth e] | SCOP2B Superfamily | Ribosomal protein S5 domain 2-like | 8044015 | 3000100 | SCOP2B (2022-06-29) |
LA [auth g] | SCOP2B Superfamily | Ribosomal protein S7 | 8033523 | 3000799 | SCOP2B (2022-06-29) |
NA [auth i] | SCOP2B Superfamily | Ribosomal protein S5 domain 2-like | 8037678 | 3000100 | SCOP2B (2022-06-29) |
OA [auth j] | SCOP2B Superfamily | Ribosomal protein S10 | 8044019 | 3001336 | SCOP2B (2022-06-29) |
PA [auth k] | SCOP2B Superfamily | Translational machinery components | 8044020 | 3000571 | SCOP2B (2022-06-29) |
QA [auth l] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8044021 | 3000135 | SCOP2B (2022-06-29) |
RA [auth m] | SCOP2B Superfamily | S13-like H2TH domain | 8003708 | 3000053 | SCOP2B (2022-06-29) |
SA [auth n] | SCOP2B Superfamily | Glucocorticoid receptor-like (DNA-binding domain) | 8052585 | 3000068 | SCOP2B (2022-06-29) |
UA [auth p] | SCOP2B Superfamily | Ribosomal protein S16 | 8044025 | 3000680 | SCOP2B (2022-06-29) |
VA [auth q] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8044026 | 3000135 | SCOP2B (2022-06-29) |
WA [auth r] | SCOP2B Superfamily | Ribosomal protein S18 | 8044028 | 3001191 | SCOP2B (2022-06-29) |
XA [auth s] | SCOP2B Superfamily | Ribosomal protein S19 | 8044027 | 3000686 | SCOP2B (2022-06-29) |
YA [auth t] | SCOP2B Superfamily | Ribosomal protein S20 | 8044029 | 3001362 | SCOP2B (2022-06-29) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF00318 | Ribosomal protein S2 (Ribosomal_S2) | Ribosomal protein S2 | - | Family | |
C [auth D] | PF03947 | Ribosomal Proteins L2, C-terminal domain (Ribosomal_L2_C) | Ribosomal Proteins L2, C-terminal domain | Domain | |
C [auth D] | PF00181 | Ribosomal Proteins L2, RNA binding N-terminal domain (Ribosomal_L2_N) | Ribosomal Proteins L2, RNA binding N-terminal domain | Domain | |
C [auth D] | PF00163 | Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4) | Ribosomal protein S4/S9 N-terminal domain | - | Family |
C [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 |
D [auth E] | PF03719 | Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C) | Ribosomal protein S5, C-terminal domain | Domain | |
D [auth E] | PF00297 | Ribosomal protein L3 (Ribosomal_L3) | Ribosomal protein L3 | - | Family |
D [auth E] | PF00333 | Ribosomal protein S5, N-terminal domain (Ribosomal_S5) | Ribosomal protein S5, N-terminal domain | Domain | |
E [auth F] | PF01250 | Ribosomal protein S6 (Ribosomal_S6) | Ribosomal protein S6 | Domain | |
E [auth F] | PF00573 | Ribosomal protein L4/L1 family (Ribosomal_L4) | Ribosomal protein L4/L1 family | - | Family |
F [auth G] | PF00281 | Ribosomal protein L5 (Ribosomal_L5) | Ribosomal protein L5 | Domain | |
F [auth G] | PF00673 | ribosomal L5P family C-terminus (Ribosomal_L5_C) | ribosomal L5P family C-terminus | This region is found associated with Pfam:PF00281. | Domain |
G [auth H] | PF00347 | Ribosomal protein L6 (Ribosomal_L6) | Ribosomal protein L6 | Domain | |
G [auth H] | PF00410 | Ribosomal protein S8 (Ribosomal_S8) | Ribosomal protein S8 | Domain | |
H [auth I] | PF00380 | Ribosomal protein S9/S16 (Ribosomal_S9) | Ribosomal protein S9/S16 | - | Family |
H [auth I] | PF01281 | Ribosomal protein L9, N-terminal domain (Ribosomal_L9_N) | Ribosomal protein L9, N-terminal domain | Domain | |
H [auth I] | PF03948 | Ribosomal protein L9, C-terminal domain (Ribosomal_L9_C) | Ribosomal protein L9, C-terminal domain | Domain | |
I [auth N] | PF00253 | Ribosomal protein S14p/S29e (Ribosomal_S14) | Ribosomal protein S14p/S29e | - | Family |
I [auth N] | PF00572 | Ribosomal protein L13 (Ribosomal_L13) | Ribosomal protein L13 | - | Family |
J [auth O] | PF00238 | Ribosomal protein L14p/L23e (Ribosomal_L14) | Ribosomal protein L14p/L23e | Domain | |
J [auth O] | PF00312 | Ribosomal protein S15 (Ribosomal_S15) | Ribosomal protein S15 | Domain | |
K [auth P] | PF00886 | Ribosomal protein S16 (Ribosomal_S16) | Ribosomal protein S16 | - | Family |
K [auth P] | 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 |
L [auth Q] | PF00252 | Ribosomal protein L16p/L10e (Ribosomal_L16) | Ribosomal protein L16p/L10e | Domain | |
L [auth Q] | PF00366 | Ribosomal protein S17 (Ribosomal_S17) | Ribosomal protein S17 | Domain | |
M [auth R] | PF01084 | Ribosomal protein S18 (Ribosomal_S18) | Ribosomal protein S18 | - | Family |
M [auth R] | PF01196 | Ribosomal protein L17 (Ribosomal_L17) | Ribosomal protein L17 | - | Family |
N [auth S] | PF00203 | Ribosomal protein S19 (Ribosomal_S19) | Ribosomal protein S19 | Domain | |
O [auth T] | PF01245 | Ribosomal protein L19 (Ribosomal_L19) | Ribosomal protein L19 | - | Family |
P [auth U] | PF00453 | Ribosomal protein L20 (Ribosomal_L20) | Ribosomal protein L20 | - | Family |
Q [auth V] | PF00829 | Ribosomal prokaryotic L21 protein (Ribosomal_L21p) | Ribosomal prokaryotic L21 protein | - | Family |
R [auth W] | PF00237 | Ribosomal protein L22p/L17e (Ribosomal_L22) | Ribosomal protein L22p/L17e | This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. | Domain |
S [auth X] | PF00276 | Ribosomal protein L23 (Ribosomal_L23) | Ribosomal protein L23 | - | Family |
T [auth Y] | PF17136 | Large ribosomal subunit protein uL24, C-terminal domain (ribosomal_L24) | Large ribosomal subunit protein uL24, C-terminal domain | This entry describes the C-terminal domain in large ribosomal subunit protein uL24 (also known as RPL26). RPL26 is one of the proteins from the large ribosomal subunit. In their mature form, these proteins have 103 to 150 amino-acid residues. RPL26 m ... | Domain |
T [auth Y] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
U [auth Z] | PF14693 | Ribosomal protein TL5, C-terminal domain (Ribosomal_TL5_C) | Ribosomal protein TL5, C-terminal domain | This family contains the C-terminal domain of ribosomal protein TL5. The N-terminal domain, which binds to 5S rRNA, is contained in family Ribosomal_L25p, Pfam:PF01386. Full length (N- and C-terminal domain) homologues of TL5 are also known as CTC pr ... | Domain |
U [auth Z] | 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 |
W [auth 1] | PF00830 | Ribosomal L28 family (Ribosomal_L28) | Ribosomal L28 family | - | Family |
X [auth 2] | PF00831 | Ribosomal L29 protein (Ribosomal_L29) | Ribosomal L29 protein | - | Family |
Y [auth 3] | PF00327 | Ribosomal protein L30p/L7e (Ribosomal_L30) | Ribosomal protein L30p/L7e | This family includes prokaryotic L30 and eukaryotic L7. | Domain |
Z [auth 4] | PF01197 | Ribosomal protein L31 (Ribosomal_L31) | Ribosomal protein L31 | - | Family |
AA [auth 5] | PF01783 | Ribosomal L32p protein family (Ribosomal_L32p) | Ribosomal L32p protein family | - | Family |
BA [auth 6] | PF00471 | Ribosomal protein L33 (Ribosomal_L33) | Ribosomal protein L33 | - | Family |
CA [auth 7] | PF00468 | Ribosomal protein L34 (Ribosomal_L34) | Ribosomal protein L34 | - | Family |
DA [auth 8] | PF01632 | Ribosomal protein L35 (Ribosomal_L35p) | Ribosomal protein L35 | - | Family |
EA [auth 9] | 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 |
2MA | Parent Component: A | |
5MC | Parent Component: C | |
5MU | Parent Component: U | |
OMC | Parent Component: C | |
OMG | Parent Component: G | |
OMU | Parent Component: U | |
PSU | Parent Component: U | |
FA [auth a] | 2MG | Parent Component: G |
FA [auth a] | 4OC | Parent Component: C |
FA [auth a] | 5MC | Parent Component: C |
FA [auth a] | G7M | Parent Component: G |
FA [auth a] | M2G | Parent Component: G |
FA [auth a] | MA6 | Parent Component: A |
FA [auth a] | PSU | Parent Component: U |
FA [auth a] | UR3 | Parent Component: U |
QA [auth l] | 0TD | Parent Component: ASP |
BB [auth w] | MEQ | Parent Component: GLN :  AA0071 :  N5-methyl-L-glutamine MOD:00080 |
CB [auth x] | 4SU | Parent Component: U :  AA0071 |
CB [auth x] | 5MU | Parent Component: U :  AA0071 |
CB [auth x] | H2U | Parent Component: U :  AA0071 |
CB [auth x] | MIA | Parent Component: A :  AA0071 |
CB [auth x] | PSU | Parent Component: U :  AA0071 |
DB [auth z] | FME | Parent Component: MET :  AA0071 , AA0021 , AA0566 :  N5-methyl-L-glutamine MOD:00080 , N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891 |