5LMQ
Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex, open form (state-2A)
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
J | SCOP2B Superfamily | Ribosomal protein S10 | 8044019 | 3001336 | SCOP2B (2022-06-29) |
K | SCOP2B Superfamily | Translational machinery components | 8044020 | 3000571 | SCOP2B (2022-06-29) |
L | SCOP2B Superfamily | Nucleic acid-binding proteins | 8044021 | 3000135 | SCOP2B (2022-06-29) |
M | SCOP2B Superfamily | S13-like H2TH domain | 8003708 | 3000053 | SCOP2B (2022-06-29) |
N | SCOP2B Superfamily | Glucocorticoid receptor-like (DNA-binding domain) | 8052585 | 3000068 | SCOP2B (2022-06-29) |
P | SCOP2B Superfamily | Ribosomal protein S16 | 8044025 | 3000680 | SCOP2B (2022-06-29) |
Q | SCOP2B Superfamily | Nucleic acid-binding proteins | 8044026 | 3000135 | SCOP2B (2022-06-29) |
R | SCOP2B Superfamily | Ribosomal protein S18 | 8044028 | 3001191 | SCOP2B (2022-06-29) |
S | SCOP2B Superfamily | Ribosomal protein S19 | 8044027 | 3000686 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | SIS domain/Ribosomal protein S2-like | 8044010 | 3001397 | SCOP2B (2022-06-29) |
T | SCOP2B Superfamily | Ribosomal protein S20 | 8044029 | 3001362 | SCOP2B (2022-06-29) |
V [auth W] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8041946 | 3000135 | SCOP2B (2022-06-29) |
W [auth X] | SCOP2B Superfamily | Translation initiation factor IF3, C-terminal domain | 8033780 | 3001514 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | Ribosomal protein S3 C-terminal domain | 8044012 | 3001053 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | Prokaryotic type KH domain (KH-domain type II) | 8044011 | 3001043 | SCOP2B (2022-06-29) |
D | SCOP2B Superfamily | Alpha-L RNA-binding motif | 8044014 | 3001473 | SCOP2B (2022-06-29) |
E | SCOP2B Superfamily | dsRNA-binding domain-like | 8044017 | 3000985 | SCOP2B (2022-06-29) |
E | SCOP2B Superfamily | Ribosomal protein S5 domain 2-like | 8044015 | 3000100 | SCOP2B (2022-06-29) |
G | SCOP2B Superfamily | Ribosomal protein S7 | 8033523 | 3000799 | SCOP2B (2022-06-29) |
I | SCOP2B Superfamily | Ribosomal protein S5 domain 2-like | 8037678 | 3000100 | 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) |
---|---|---|---|---|---|---|---|---|
J | Ribosomal_S10 | e5lmqJ1 | A: a+b two layers | X: Alpha-beta plaits | H: Ribosomal protein S10 (From Topology) | T: Ribosomal protein S10 | F: Ribosomal_S10 | ECOD (1.6) |
K | Ribosomal_S11 | e5lmqK1 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: Ribonuclease H-like (From Topology) | T: Ribonuclease H-like | F: Ribosomal_S11 | ECOD (1.6) |
L | Ribosom_S12_S23 | e5lmqL1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: Ribosom_S12_S23 | ECOD (1.6) |
M | Ribosomal_S13_1 | e5lmqM1 | A: alpha arrays | X: HhH/H2TH | H: H2TH (From Topology) | T: H2TH | F: Ribosomal_S13_1 | ECOD (1.6) |
N | Ribosomal_S14 | e5lmqN1 | A: few secondary structure elements | X: Glucocorticoid receptor-like | H: LIM domain-like | T: LIM domain-like | F: Ribosomal_S14 | ECOD (1.6) |
O | Ribosomal_S15_1 | e5lmqO1 | 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: Ribosomal_S15_1 | ECOD (1.6) |
P | Ribosomal_S16_1 | e5lmqP1 | A: a+b two layers | X: Ribosomal protein S16 (From Topology) | H: Ribosomal protein S16 (From Topology) | T: Ribosomal protein S16 | F: Ribosomal_S16_1 | ECOD (1.6) |
Q | Ribosomal_S17_1 | e5lmqQ1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: Ribosomal_S17_1 | ECOD (1.6) |
R | Ribosomal_S18 | e5lmqR1 | A: alpha arrays | X: HTH | H: HTH | T: tri-helical | F: Ribosomal_S18 | ECOD (1.6) |
S | Ribosomal_S19 | e5lmqS1 | A: a+b two layers | X: Ribosomal protein S19 (From Topology) | H: Ribosomal protein S19 (From Topology) | T: Ribosomal protein S19 | F: Ribosomal_S19 | ECOD (1.6) |
B | Ribosomal_S2 | e5lmqB1 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Ribosomal protein S2/SIS domain (From Topology) | T: Ribosomal protein S2/SIS domain | F: Ribosomal_S2 | ECOD (1.6) |
T | Ribosomal_S20p | e5lmqT1 | A: alpha bundles | X: Spectrin repeat-like | H: Ribosomal protein S20 (From Topology) | T: Ribosomal protein S20 | F: Ribosomal_S20p | ECOD (1.6) |
V [auth W] | eIF-1a | e5lmqW1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: eIF-1a | ECOD (1.6) |
W [auth X] | IF3_N | e5lmqX2 | A: a+b two layers | X: beta-Grasp | H: IF3-N (From Topology) | T: IF3-N | F: IF3_N | ECOD (1.6) |
W [auth X] | IF3_C | e5lmqX1 | A: a+b two layers | X: IF3-like | H: Translation initiation factor IF3, C-terminal domain (From Topology) | T: Translation initiation factor IF3, C-terminal domain | F: IF3_C | ECOD (1.6) |
C | Ribosomal_S3_C | e5lmqC2 | A: a+b two layers | X: T-fold | H: Ribosomal protein S3-C (From Topology) | T: Ribosomal protein S3-C | F: Ribosomal_S3_C | ECOD (1.6) |
C | KH_2_1 | e5lmqC1 | A: a+b two layers | X: Alpha-lytic protease prodomain-like | H: KH-domains | T: Prokaryotic type KH domain (KH-domain type II) | F: KH_2_1 | ECOD (1.6) |
D | S4 | e5lmqD1 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Alpha-L RNA-binding motif | F: S4 | ECOD (1.6) |
E | Ribosomal_S5_C | e5lmqE2 | 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: Ribosomal_S5_C | ECOD (1.6) |
E | Ribosomal_S5 | e5lmqE1 | A: a+b two layers | X: dsRBD-like | H: dsRNA-binding domain-like (From Topology) | T: dsRNA-binding domain-like | F: Ribosomal_S5 | ECOD (1.6) |
F | Ribosomal_S6 | e5lmqF1 | A: a+b two layers | X: Alpha-beta plaits | H: Ribosomal protein S6 (From Topology) | T: Ribosomal protein S6 | F: Ribosomal_S6 | ECOD (1.6) |
G | Ribosomal_S7_1 | e5lmqG1 | A: alpha arrays | X: Ribosomal protein S7 (From Topology) | H: Ribosomal protein S7 (From Topology) | T: Ribosomal protein S7 | F: Ribosomal_S7_1 | ECOD (1.6) |
H | Ribosomal_S8_N | e5lmqH1 | 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: Ribosomal_S8_N | ECOD (1.6) |
H | Ribosomal_S8_C | e5lmqH2 | 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: Ribosomal_S8_C | ECOD (1.6) |
I | Ribosomal_S9 | e5lmqI1 | 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: Ribosomal_S9 | ECOD (1.6) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
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 | |
PF00411 | Ribosomal protein S11 (Ribosomal_S11) | Ribosomal protein S11 | - | Family | |
PF00164 | Ribosomal protein S12/S23 (Ribosom_S12_S23) | Ribosomal protein S12/S23 | - | Family | |
PF00416 | Ribosomal protein S13/S18 (Ribosomal_S13) | Ribosomal protein S13/S18 | - | Family | |
PF00253 | Ribosomal protein S14p/S29e (Ribosomal_S14) | Ribosomal protein S14p/S29e | - | Family | |
PF00312 | Ribosomal protein S15 (Ribosomal_S15) | Ribosomal protein S15 | - | Domain | |
PF00886 | Ribosomal protein S16 (Ribosomal_S16) | Ribosomal protein S16 | - | Family | |
PF00366 | Ribosomal protein S17 (Ribosomal_S17) | Ribosomal protein S17 | - | Domain | |
PF01084 | Ribosomal protein S18 (Ribosomal_S18) | Ribosomal protein S18 | - | Family | |
PF00203 | Ribosomal protein S19 (Ribosomal_S19) | Ribosomal protein S19 | - | Domain | |
PF00318 | Ribosomal protein S2 (Ribosomal_S2) | Ribosomal protein S2 | - | Family | |
V [auth W] | PF01176 | Translation initiation factor 1A / IF-1 (eIF-1a) | Translation initiation factor 1A / IF-1 | This family includes both the eukaryotic translation factor eIF-1A and the bacterial translation initiation factor IF-1. | Domain |
W [auth X] | PF05198 | Translation initiation factor IF-3, N-terminal domain (IF3_N) | Translation initiation factor IF-3, N-terminal domain | - | Domain |
W [auth X] | PF00707 | Translation initiation factor IF-3, C-terminal domain (IF3_C) | Translation initiation factor IF-3, C-terminal domain | - | Domain |
PF07650 | KH domain (KH_2) | KH domain | - | Domain | |
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 | |
PF00163 | Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4) | Ribosomal protein S4/S9 N-terminal domain | - | Family | |
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 | |
PF03719 | Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C) | Ribosomal protein S5, C-terminal domain | - | Domain | |
PF00333 | Ribosomal protein S5, N-terminal domain (Ribosomal_S5) | Ribosomal protein S5, N-terminal domain | - | Domain | |
PF01250 | Ribosomal protein S6 (Ribosomal_S6) | Ribosomal protein S6 | - | Domain | |
PF00410 | Ribosomal protein S8 (Ribosomal_S8) | Ribosomal protein S8 | - | Domain | |
PF00380 | Ribosomal protein S9/S16 (Ribosomal_S9) | Ribosomal protein S9/S16 | - | Family |