6TC3
Cryo-EM structure of an Escherichia coli ribosome-SpeFL complex stalled in response to L-ornithine (Replicate 1)
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
B [auth S021] | SCOP2B Superfamily | SIS domain/Ribosomal protein S2-like | 8063838 | 3001397 | SCOP2B (2022-06-29) |
D [auth S041] | SCOP2B Superfamily | Alpha-L RNA-binding motif | 8083400 | 3001473 | SCOP2B (2022-06-29) |
H [auth S081] | SCOP2B Superfamily | Ribosomal protein S8 | 8079059 | 3000709 | SCOP2B (2022-06-29) |
I [auth S091] | SCOP2B Superfamily | Ribosomal protein S5 domain 2-like | 8082661 | 3000100 | SCOP2B (2022-06-29) |
K [auth S111] | SCOP2B Superfamily | Translational machinery components | 8035368 | 3000571 | SCOP2B (2022-06-29) |
M [auth S131] | SCOP2B Superfamily | S13-like H2TH domain | 8098358 | 3000053 | SCOP2B (2022-06-29) |
N [auth S141] | SCOP2B Superfamily | Glucocorticoid receptor-like (DNA-binding domain) | 8052568 | 3000068 | SCOP2B (2022-06-29) |
O [auth S151] | SCOP2B Superfamily | S15/NS1 RNA-binding domain | 8032375 | 3001284 | SCOP2B (2022-06-29) |
P [auth S161] | SCOP2B Superfamily | Ribosomal protein S16 | 8106547 | 3000680 | SCOP2B (2022-06-29) |
Q [auth S171] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8059276 | 3000135 | SCOP2B (2022-06-29) |
Y [auth L031] | SCOP2B Superfamily | Translational proteins | 8032955 | 3000811 | SCOP2B (2022-06-29) |
Z [auth L041] | SCOP2B Superfamily | Ribosomal protein L4 | 8096356 | 3001146 | SCOP2B (2022-06-29) |
CA [auth L091] | SCOP2B Superfamily | L9 N-domain-like | 8032960 | 3000338 | SCOP2B (2022-06-29) |
CA [auth L091] | SCOP2B Superfamily | Ribosomal protein L9 C-domain | 8032958 | 3000329 | SCOP2B (2022-06-29) |
DA [auth L311] | SCOP2B Superfamily | L28p-like | 8032740 | 3001966 | SCOP2B (2022-06-29) |
FA [auth L141] | SCOP2B Superfamily | 50S Ribosomal protein L14-like | 8103358 | 3000433 | SCOP2B (2022-06-29) |
GA [auth L151] | SCOP2B Superfamily | Ribosomal proteins L15p and L18e | 8070553 | 3001045 | SCOP2B (2022-06-29) |
HA [auth L161] | SCOP2B Superfamily | Ribosomal protein L16p/L10e | 8096366 | 3000884 | SCOP2B (2022-06-29) |
KA [auth L191] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8096364 | 3000334 | SCOP2B (2022-06-29) |
LA [auth L201] | SCOP2B Superfamily | Ribosomal protein L20 | 8096382 | 3000563 | SCOP2B (2022-06-29) |
MA [auth L211] | SCOP2B Superfamily | l21p-like | 8096354 | 3002005 | SCOP2B (2022-06-29) |
NA [auth L221] | SCOP2B Superfamily | Ribosomal protein L22 | 8096336 | 3001078 | SCOP2B (2022-06-29) |
OA [auth L231] | SCOP2B Superfamily | Ribosomal proteins S24e L23 and L15e | 8035415 | 3000210 | SCOP2B (2022-06-29) |
PA [auth L241] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8096358 | 3000334 | SCOP2B (2022-06-29) |
RA [auth L271] | SCOP2B Superfamily | Ribosomal L27 protein-like | 8096338 | 3000539 | SCOP2B (2022-06-29) |
TA [auth L291] | SCOP2B Superfamily | Ribosomal protein L29 (L29p) | 8096370 | 3000713 | SCOP2B (2022-06-29) |
UA [auth L301] | SCOP2B Superfamily | Ribosomal protein L30p/L7e | 8096372 | 3001378 | SCOP2B (2022-06-29) |
VA [auth L321] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8096380 | 3001320 | SCOP2B (2022-06-29) |
WA [auth L331] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8096362 | 3001320 | SCOP2B (2022-06-29) |
YA [auth L351] | SCOP2B Superfamily | L35p-like | 8035388 | 3000790 | SCOP2B (2022-06-29) |
ZA [auth L361] | SCOP2B Superfamily | Ribosomal protein L36 | 8035391 | 3001346 | SCOP2B (2022-06-29) |
J [auth S101] | SCOP2B Superfamily | Ribosomal protein S10 | 8102681 | 3001336 | SCOP2B (2022-06-29) |
L [auth S121] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8106545 | 3000135 | SCOP2B (2022-06-29) |
S [auth S191] | SCOP2B Superfamily | Ribosomal protein S19 | 8103915 | 3000686 | SCOP2B (2022-06-29) |
U [auth S211] | SCOP2B Superfamily | Ribosomal protein S21 | 8053090 | 3002159 | SCOP2B (2022-06-29) |
X [auth L021] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8035393 | 3000334 | SCOP2B (2022-06-29) |
X [auth L021] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8035394 | 3000135 | SCOP2B (2022-06-29) |
AA [auth L051] | SCOP2B Superfamily | RL5-like | 8096352 | 3001709 | SCOP2B (2022-06-29) |
BA [auth L061] | SCOP2B Superfamily | Ribosomal protein L6 | 8035398 | 3000724 | SCOP2B (2022-06-29) |
BA [auth L061] | SCOP2B Superfamily | Ribosomal protein L6 | 8035397 | 3000724 | SCOP2B (2022-06-29) |
EA [auth L131] | SCOP2B Superfamily | Ribosomal protein L13 | 8096350 | 3001134 | SCOP2B (2022-06-29) |
IA [auth L171] | SCOP2B Superfamily | Prokaryotic ribosomal protein L17 | 8035409 | 3000995 | SCOP2B (2022-06-29) |
JA [auth L181] | SCOP2B Superfamily | Translational machinery components | 8032969 | 3000571 | SCOP2B (2022-06-29) |
QA [auth L251] | SCOP2B Superfamily | Ribosomal protein L25-like | 8042538 | 3001161 | SCOP2B (2022-06-29) |
SA [auth L281] | SCOP2B Superfamily | L28p-like | 8035424 | 3001966 | SCOP2B (2022-06-29) |
F [auth S061] | SCOP2B Superfamily | Ribosomal protein S6 | 8066495 | 3001323 | SCOP2B (2022-06-29) |
G [auth S071] | SCOP2B Superfamily | Ribosomal protein S7 | 8077979 | 3000799 | 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) |
---|---|---|---|---|---|---|---|---|
B [auth S021] | PF00318 | e6tc3S0211 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Ribosomal protein S2/SIS domain (From Topology) | T: Ribosomal protein S2/SIS domain | F: PF00318 | ECOD (1.6) |
D [auth S041] | PF00163,PF01479 | e6tc3S0411 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Alpha-L RNA-binding motif | F: PF00163,PF01479 | ECOD (1.6) |
E [auth S051] | PF03719 | e6tc3S0512 | A: a+b two layers | X: Ribosomal protein S5 domain 2-like (From Topology) | H: Ribosomal protein S5 domain 2-like (From Topology) | T: Ribosomal protein S5 domain 2-like | F: PF03719 | ECOD (1.6) |
E [auth S051] | PF00333 | e6tc3S0511 | A: a+b two layers | X: dsRBD-like | H: dsRNA-binding domain-like (From Topology) | T: dsRNA-binding domain-like | F: PF00333 | ECOD (1.6) |
H [auth S081] | PF00410 | e6tc3S0811 | A: a+b two layers | X: R3H domain-like | H: Ribosomal protein S8, N-terminal domain (From Topology) | T: Ribosomal protein S8, N-terminal domain | F: PF00410 | ECOD (1.6) |
H [auth S081] | PF00410 | e6tc3S0812 | A: a+b two layers | X: Ribosomal protein S8, C-terminal domain (From Topology) | H: Ribosomal protein S8, C-terminal domain (From Topology) | T: Ribosomal protein S8, C-terminal domain | F: PF00410 | ECOD (1.6) |
I [auth S091] | PF00380 | e6tc3S0911 | A: a+b two layers | X: Ribosomal protein S5 domain 2-like (From Topology) | H: Ribosomal protein S5 domain 2-like (From Topology) | T: Ribosomal protein S5 domain 2-like | F: PF00380 | ECOD (1.6) |
K [auth S111] | PF00411 | e6tc3S1111 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: Ribonuclease H-like (From Topology) | T: Ribonuclease H-like | F: PF00411 | ECOD (1.6) |
M [auth S131] | PF00416 | e6tc3S1311 | A: alpha arrays | X: HhH/H2TH | H: H2TH (From Topology) | T: H2TH | F: PF00416 | ECOD (1.6) |
N [auth S141] | PF00253 | e6tc3S1411 | A: few secondary structure elements | X: Glucocorticoid receptor-like | H: LIM domain-like | T: LIM domain-like | F: PF00253 | ECOD (1.6) |
O [auth S151] | PF00312 | e6tc3S1511 | A: alpha arrays | X: S15/NS1 RNA-binding domain (From Topology) | H: S15/NS1 RNA-binding domain (From Topology) | T: S15/NS1 RNA-binding domain | F: PF00312 | ECOD (1.6) |
P [auth S161] | PF00886 | e6tc3S1611 | A: a+b two layers | X: Ribosomal protein S16 (From Topology) | H: Ribosomal protein S16 (From Topology) | T: Ribosomal protein S16 | F: PF00886 | ECOD (1.6) |
Q [auth S171] | PF00366 | e6tc3S1711 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: PF00366 | ECOD (1.6) |
Y [auth L031] | PF00297 | e6tc3L0311 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: Alanine racemase-C | F: PF00297 | ECOD (1.6) |
Z [auth L041] | PF00573 | e6tc3L0411 | A: a/b three-layered sandwiches | X: Ribosomal protein L4 (From Topology) | H: Ribosomal protein L4 (From Topology) | T: Ribosomal protein L4 | F: PF00573 | ECOD (1.6) |
CA [auth L091] | PF01281 | e6tc3L0911 | A: a+b two layers | X: L9 N-domain-like | H: L9 N-domain-like (From Topology) | T: L9 N-domain-like | F: PF01281 | ECOD (1.6) |
CA [auth L091] | PF03948 | e6tc3L0912 | A: a+b two layers | X: Ribosomal protein L9 C-domain (From Topology) | H: Ribosomal protein L9 C-domain (From Topology) | T: Ribosomal protein L9 C-domain | F: PF03948 | ECOD (1.6) |
DA [auth L311] | PF01197 | e6tc3L3111 | A: few secondary structure elements | X: Ribosomal protein L31p (From Topology) | H: Ribosomal protein L31p (From Topology) | T: Ribosomal protein L31p | F: PF01197 | ECOD (1.6) |
FA [auth L141] | PF00238 | e6tc3L1411 | A: beta barrels | X: Ribosomal protein L14-like | H: Ribosomal protein L14-related (From Topology) | T: Ribosomal protein L14-related | F: PF00238 | ECOD (1.6) |
GA [auth L151] | PF00828 | e6tc3L1511 | 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: PF00828 | ECOD (1.6) |
HA [auth L161] | PF00252 | e6tc3L1611 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Ribosomal protein L10e | F: PF00252 | ECOD (1.6) |
KA [auth L191] | PF01245 | e6tc3L1911 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PF01245 | ECOD (1.6) |
LA [auth L201] | PF00453 | e6tc3L2011 | A: alpha arrays | X: PABP domain-like | H: Ribosomal protein L20 (From Topology) | T: Ribosomal protein L20 | F: PF00453 | ECOD (1.6) |
MA [auth L211] | PF00829 | e6tc3L2111 | A: beta barrels | X: Ribosomal protein L21p (From Topology) | H: Ribosomal protein L21p (From Topology) | T: Ribosomal protein L21p | F: PF00829 | ECOD (1.6) |
NA [auth L221] | PF00237 | e6tc3L2211 | A: a+b two layers | X: Enolase-N/ribosomal protein | H: Ribosomal protein L22 (From Topology) | T: Ribosomal protein L22 | F: PF00237 | ECOD (1.6) |
OA [auth L231] | PF00276 | e6tc3L2311 | 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: PF00276 | ECOD (1.6) |
PA [auth L241] | PF00467,PF17136 | e6tc3L2411 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PF00467,PF17136 | ECOD (1.6) |
RA [auth L271] | PF01016 | e6tc3L2711 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Ribosomal L27 protein | F: PF01016 | ECOD (1.6) |
TA [auth L291] | PF00831 | e6tc3L2911 | A: alpha bundles | X: Long alpha-hairpin | H: Ribosomal protein L29 (L29p) (From Topology) | T: Ribosomal protein L29 (L29p) | F: PF00831 | ECOD (1.6) |
UA [auth L301] | PF00327 | e6tc3L3011 | 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: PF00327 | ECOD (1.6) |
VA [auth L321] | PF01783 | e6tc3L3211 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: PF01783 | ECOD (1.6) |
WA [auth L331] | PF00471 | e6tc3L3311 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: PF00471 | ECOD (1.6) |
XA [auth L341] | PF00468 | e6tc3L3411 | A: extended segments | X: 50S ribosomal protein L34 (From Topology) | H: 50S ribosomal protein L34 (From Topology) | T: 50S ribosomal protein L34 | F: PF00468 | ECOD (1.6) |
YA [auth L351] | PF01632 | e6tc3L3511 | A: a+b two layers | X: Ribosomal protein L35p (From Topology) | H: Ribosomal protein L35p (From Topology) | T: Ribosomal protein L35p | F: PF01632 | ECOD (1.6) |
ZA [auth L361] | PF00444 | e6tc3L3611 | A: few secondary structure elements | X: Ribosomal protein L36 (From Topology) | H: Ribosomal protein L36 (From Topology) | T: Ribosomal protein L36 | F: PF00444 | ECOD (1.6) |
J [auth S101] | PF00338 | e6tc3S1011 | A: a+b two layers | X: Alpha-beta plaits | H: Ribosomal protein S10 (From Topology) | T: Ribosomal protein S10 | F: PF00338 | ECOD (1.6) |
L [auth S121] | PF00164 | e6tc3S1211 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: PF00164 | ECOD (1.6) |
R [auth S181] | PF01084 | e6tc3S1811 | A: alpha arrays | X: HTH | H: HTH | T: tri-helical | F: PF01084 | ECOD (1.6) |
S [auth S191] | PF00203 | e6tc3S1911 | A: a+b two layers | X: Ribosomal protein S19 (From Topology) | H: Ribosomal protein S19 (From Topology) | T: Ribosomal protein S19 | F: PF00203 | ECOD (1.6) |
T [auth S201] | PF01649 | e6tc3S2011 | A: alpha bundles | X: Spectrin repeat-like | H: Ribosomal protein S20 (From Topology) | T: Ribosomal protein S20 | F: PF01649 | ECOD (1.6) |
U [auth S211] | PF01165 | e6tc3S2111 | A: extended segments | X: 30S ribosomal protein S21 (From Topology) | H: 30S ribosomal protein S21 (From Topology) | T: 30S ribosomal protein S21 | F: PF01165 | ECOD (1.6) |
X [auth L021] | PF00181 | e6tc3L0212 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: PF00181 | ECOD (1.6) |
X [auth L021] | PF03947 | e6tc3L0211 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PF03947 | ECOD (1.6) |
AA [auth L051] | PF00281,PF00673 | e6tc3L0511 | A: a+b two layers | X: Ribosomal protein L5 (From Topology) | H: Ribosomal protein L5 (From Topology) | T: Ribosomal protein L5 | F: PF00281,PF00673 | ECOD (1.6) |
BA [auth L061] | PF00347 | e6tc3L0611 | A: a+b two layers | X: Ribosomal protein L6 (From Topology) | H: Ribosomal protein L6 (From Topology) | T: Ribosomal protein L6 | F: PF00347 | ECOD (1.6) |
C [auth S031] | PF00189 | e6tc3S0312 | A: a+b two layers | X: T-fold | H: Ribosomal protein S3-C (From Topology) | T: Ribosomal protein S3-C | F: PF00189 | ECOD (1.6) |
C [auth S031] | PF07650 | e6tc3S0311 | A: a+b two layers | X: Alpha-lytic protease prodomain-like | H: KH-domains | T: Prokaryotic type KH domain (KH-domain type II) | F: PF07650 | ECOD (1.6) |
EA [auth L131] | PF00572 | e6tc3L1311 | 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: PF00572 | ECOD (1.6) |
IA [auth L171] | PF01196 | e6tc3L1711 | A: a+b two layers | X: Enolase-N/ribosomal protein | H: Prokaryotic ribosomal protein L17 (From Topology) | T: Prokaryotic ribosomal protein L17 | F: PF01196 | ECOD (1.6) |
JA [auth L181] | PF00861 | e6tc3L1811 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: Ribonuclease H-like (From Topology) | T: Ribonuclease H-like | F: PF00861 | ECOD (1.6) |
QA [auth L251] | PF01386 | e6tc3L2511 | A: beta barrels | X: Ribosomal protein L25-like | H: Ribosomal protein L25-like (From Topology) | T: Ribosomal protein L25-like | F: PF01386 | ECOD (1.6) |
SA [auth L281] | PF00830 | e6tc3L2811 | A: few secondary structure elements | X: Ribosomal protein bL28-related (From Homology) | H: Ribosomal protein bL28-related | T: Ribosomal protein L28 | F: PF00830 | ECOD (1.6) |
F [auth S061] | PF01250 | e6tc3S0611 | A: a+b two layers | X: Alpha-beta plaits | H: Ribosomal protein S6 (From Topology) | T: Ribosomal protein S6 | F: PF01250 | ECOD (1.6) |
G [auth S071] | PF00177 | e6tc3S0711 | A: alpha arrays | X: Ribosomal protein S7 (From Topology) | H: Ribosomal protein S7 (From Topology) | T: Ribosomal protein S7 | F: PF00177 | ECOD (1.6) |
Protein Family Annotation Pfam Database Homepage
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 16S1] | 2MG | Parent Component: G |
A [auth 16S1] | 4OC | Parent Component: C |
A [auth 16S1] | 5MC | Parent Component: C |
A [auth 16S1] | G7M | Parent Component: G |
A [auth 16S1] | MA6 | Parent Component: A |
A [auth 16S1] | PSU | Parent Component: U |
A [auth 16S1] | UR3 | Parent Component: U |
V [auth 23S1] | 1MG | Parent Component: G |
V [auth 23S1] | 2MA | Parent Component: A |
V [auth 23S1] | 2MG | Parent Component: G |
V [auth 23S1] | 3TD | Parent Component: U |
V [auth 23S1] | 5MC | Parent Component: C |
V [auth 23S1] | 5MU | Parent Component: U |
V [auth 23S1] | 6MZ | Parent Component: A |
V [auth 23S1] | G7M | Parent Component: G |
V [auth 23S1] | OMC | Parent Component: C |
V [auth 23S1] | OMG | Parent Component: G |
V [auth 23S1] | OMU | Parent Component: U |
V [auth 23S1] | PSU | Parent Component: U |
Y [auth L031] | MEQ | Parent Component: GLN :  AA0071 :  N5-methyl-L-glutamine MOD:00080 |
HA [auth L161] | 4D4 | Parent Component: ARG :  AA0071 |
L [auth S121] | D2T | Parent Component: ASP :  AA0071 |
AB [auth SPE1] | 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 |
CB [auth PTR1] | 2MG | Parent Component: G :  AA0071 , AA0021 , AA0566 |
CB [auth PTR1] | 4SU | Parent Component: U :  AA0071 , AA0021 , AA0566 |
CB [auth PTR1] | 5MU | Parent Component: U :  AA0071 , AA0021 , AA0566 |
CB [auth PTR1] | G7M | Parent Component: G :  AA0071 , AA0021 , AA0566 |
CB [auth PTR1] | PSU | Parent Component: U :  AA0071 , AA0021 , AA0566 |
CB [auth PTR1] | RSP | Parent Component: C :  AA0071 , AA0021 , AA0566 |