Real space refined coordinates of the 30S and 50S subunits fitted into the low resolution cryo-EM map of the EF-G.GTP state of E. coli 70S ribosome
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
| Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
|---|---|---|---|---|---|
| I [auth AG] | SCOP2B Superfamily | Ribosomal protein L11, C-terminal domain | 8032961 | 3001186 | SCOP2B (2022-06-29) |
| I [auth AG] | SCOP2B Superfamily | Ribosomal L11/L12e N-terminal domain-like | 8032963 | 3000950 | SCOP2B (2022-06-29) |
| H [auth AF] | SCOP2B Superfamily | L9 N-domain-like | 8032960 | 3000338 | SCOP2B (2022-06-29) |
| F [auth AD] | SCOP2B Superfamily | RL5-like | 8096352 | 3001709 | SCOP2B (2022-06-29) |
| SA [auth BS] | SCOP2B Superfamily | Ribosomal protein S19 | 8103915 | 3000686 | SCOP2B (2022-06-29) |
| QA [auth BQ] | SCOP2 Family | Cold shock DNA-binding domain-like | 8102127 | 4001909 | SCOP2 (2022-06-29) |
| QA [auth BQ] | SCOP2 Superfamily | Nucleic acid-binding proteins | 8102128 | 3000135 | SCOP2 (2022-06-29) |
| PA [auth BP] | SCOP2B Superfamily | Ribosomal protein S16 | 8106547 | 3000680 | SCOP2B (2022-06-29) |
| MA [auth BM] | SCOP2B Superfamily | S13-like H2TH domain | 8098358 | 3000053 | SCOP2B (2022-06-29) |
| KA [auth BK] | SCOP2B Superfamily | Translational machinery components | 8035368 | 3000571 | SCOP2B (2022-06-29) |
| JA [auth BJ] | SCOP2B Superfamily | Ribosomal protein S10 | 8102681 | 3001336 | SCOP2B (2022-06-29) |
| HA [auth BH] | SCOP2B Superfamily | Ribosomal protein S8 | 8079059 | 3000709 | SCOP2B (2022-06-29) |
| FA [auth BF] | SCOP2B Superfamily | Ribosomal protein S6 | 8066495 | 3001323 | SCOP2B (2022-06-29) |
| DA [auth BD] | SCOP2 Family | Ribosomal protein S4 | 8083399 | 4001399 | SCOP2 (2022-06-29) |
| DA [auth BD] | SCOP2 Superfamily | Alpha-L RNA-binding motif | 8083400 | 3001473 | SCOP2 (2022-06-29) |
| C [auth AA] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8035394 | 3000135 | SCOP2B (2022-06-29) |
| C [auth AA] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8035393 | 3000334 | SCOP2B (2022-06-29) |
| AA [auth A4] | SCOP2B Superfamily | Ribosomal protein L36 | 8035391 | 3001346 | SCOP2B (2022-06-29) |
| Z [auth A1] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8096362 | 3001320 | SCOP2B (2022-06-29) |
| W [auth AW] | SCOP2B Superfamily | Ribosomal protein L29 (L29p) | 8096370 | 3000713 | SCOP2B (2022-06-29) |
| V [auth AU] | SCOP2B Superfamily | Ribosomal L27 protein-like | 8096338 | 3000539 | SCOP2B (2022-06-29) |
| U [auth AT] | SCOP2B Superfamily | Ribosomal protein L25-like | 8042538 | 3001161 | SCOP2B (2022-06-29) |
| T [auth AS] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8096358 | 3000334 | SCOP2B (2022-06-29) |
| S [auth AR] | SCOP2 Family | L23p | 8105777 | 4000943 | SCOP2 (2022-06-29) |
| S [auth AR] | SCOP2 Superfamily | Ribosomal proteins S24e, L23 and L15e | 8105778 | 3000210 | SCOP2 (2022-06-29) |
| R [auth AQ] | SCOP2B Superfamily | Ribosomal protein L22 | 8096336 | 3001078 | SCOP2B (2022-06-29) |
| P [auth AN] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8096364 | 3000334 | SCOP2B (2022-06-29) |
| O [auth AM] | SCOP2B Superfamily | Translational machinery components | 8032969 | 3000571 | SCOP2B (2022-06-29) |
| J [auth AH] | SCOP2B Superfamily | Ribosomal protein L13 | 8096350 | 3001134 | 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) |
|---|---|---|---|---|---|---|---|---|
| I [auth AG] | P22_portal | e4v47AG1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| H [auth AF] | P22_portal | e4v47AF1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| G [auth AE] | P22_portal | e4v47AE1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| F [auth AD] | P22_portal | e4v47AD1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| E [auth AC] | P22_portal | e4v47AC1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| TA [auth BT] | P22_portal | e4v47BT1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| SA [auth BS] | Cellulase | e4v47BS1 | A: alpha arrays | X: HAD domain-like | H: HAD domain-related | T: PIN domain-like | F: Cellulase | ECOD (v295) |
| RA [auth BR] | P22_portal | e4v47BR1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| QA [auth BQ] | Cellulase | e4v47BQ1 | A: alpha arrays | X: HAD domain-like | H: HAD domain-related | T: PIN domain-like | F: Cellulase | ECOD (v295) |
| PA [auth BP] | P22_portal | e4v47BP1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| OA [auth BO] | P22_portal | e4v47BO1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| NA [auth BN] | P22_portal | e4v47BN1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| D [auth AB] | AP_endonuc_2 | e4v47AB1 | A: alpha arrays | X: Cytochrome P450 | H: Cytochrome P450 | T: Cytochrome P450 | F: AP_endonuc_2 | ECOD (v295) |
| MA [auth BM] | Cellulase | e4v47BM1 | A: alpha arrays | X: HAD domain-like | H: HAD domain-related | T: PIN domain-like | F: Cellulase | ECOD (v295) |
| LA [auth BL] | P22_portal | e4v47BL1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| KA [auth BK] | P22_portal | e4v47BK1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| JA [auth BJ] | P22_portal | e4v47BJ1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| IA [auth BI] | FlaF_Ig-like | e4v47BI1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: FlaF_Ig-like | ECOD (v295) |
| HA [auth BH] | P22_portal | e4v47BH1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| GA [auth BG] | P22_portal | e4v47BG1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| FA [auth BF] | P22_portal | e4v47BF1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| EA [auth BE] | P22_portal | e4v47BE1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| DA [auth BD] | FlaF_Ig-like | e4v47BD1 | A: alpha arrays | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: FlaF_Ig-like | ECOD (v295) |
| C [auth AA] | P22_portal | e4v47AA1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| CA [auth BC] | P22_portal | e4v47BC1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| AA [auth A4] | P22_portal | e4v47A41 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| Z [auth A1] | AP_endonuc_2 | e4v47A11 | A: alpha arrays | X: Cytochrome P450 | H: Cytochrome P450 | T: Cytochrome P450 | F: AP_endonuc_2 | ECOD (v295) |
| Y [auth AZ] | Internalin_N | e4v47AZ1 | A: alpha arrays | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Internalin_N | ECOD (v295) |
| X [auth AX] | P22_portal | e4v47AX1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| W [auth AW] | P22_portal | e4v47AW1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| V [auth AU] | P22_portal | e4v47AU1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| U [auth AT] | P22_portal | e4v47AT1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| T [auth AS] | P22_portal | e4v47AS1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| S [auth AR] | P22_portal | e4v47AR1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| R [auth AQ] | P22_portal | e4v47AQ1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| Q [auth AO] | AP_endonuc_2 | e4v47AO1 | A: alpha arrays | X: Cytochrome P450 | H: Cytochrome P450 | T: Cytochrome P450 | F: AP_endonuc_2 | ECOD (v295) |
| P [auth AN] | AP_endonuc_2 | e4v47AN1 | A: alpha arrays | X: Cytochrome P450 | H: Cytochrome P450 | T: Cytochrome P450 | F: AP_endonuc_2 | ECOD (v295) |
| O [auth AM] | AP_endonuc_2 | e4v47AM1 | A: alpha arrays | X: Cytochrome P450 | H: Cytochrome P450 | T: Cytochrome P450 | F: AP_endonuc_2 | ECOD (v295) |
| N [auth AL] | P22_portal | e4v47AL1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| M [auth AK] | AP_endonuc_2 | e4v47AK1 | A: alpha arrays | X: Cytochrome P450 | H: Cytochrome P450 | T: Cytochrome P450 | F: AP_endonuc_2 | ECOD (v295) |
| L [auth AJ] | P22_portal | e4v47AJ1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| K [auth AI] | P22_portal | e4v47AI1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| J [auth AH] | P22_portal | e4v47AH1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
Protein Family Annotation Pfam Database Homepage
| Chains | Accession | Name | Description | Comments | Source |
|---|---|---|---|---|---|
| I [auth AG] | 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 |
| I [auth AG] | PF00298 | Ribosomal protein L11, RNA binding domain (Ribosomal_L11) | Ribosomal protein L11, RNA binding domain | Domain | |
| H [auth AF] | PF01281 | Ribosomal protein L9, N-terminal domain (Ribosomal_L9_N) | Ribosomal protein L9, N-terminal domain | Domain | |
| H [auth AF] | PF03948 | Ribosomal protein L9, C-terminal domain (Ribosomal_L9_C) | Ribosomal protein L9, C-terminal domain | Domain | |
| F [auth AD] | PF00281 | Ribosomal protein L5 (Ribosomal_L5) | Ribosomal protein L5 | Domain | |
| F [auth AD] | PF00673 | ribosomal L5P family C-terminus (Ribosomal_L5_C) | ribosomal L5P family C-terminus | This region is found associated with Pfam:PF00281. | Domain |
| E [auth AC] | PF00573 | Ribosomal protein L4/L1 family (Ribosomal_L4) | Ribosomal protein L4/L1 family | - | Family |
| PA [auth BP] | PF00886 | Ribosomal protein S16 (Ribosomal_S16) | Ribosomal protein S16 | - | Family |
| D [auth AB] | PF00297 | Ribosomal protein L3 (Ribosomal_L3) | Ribosomal protein L3 | - | Family |
| MA [auth BM] | PF00416 | Ribosomal protein S13/S18 (Ribosomal_S13) | Ribosomal protein S13/S18 | - | Family |
| KA [auth BK] | PF00411 | Ribosomal protein S11 (Ribosomal_S11) | Ribosomal protein S11 | - | Family |
| JA [auth BJ] | 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 |
| IA [auth BI] | PF00380 | Ribosomal protein S9/S16 (Ribosomal_S9) | Ribosomal protein S9/S16 | - | Family |
| HA [auth BH] | PF00410 | Ribosomal protein S8 (Ribosomal_S8) | Ribosomal protein S8 | Domain | |
| FA [auth BF] | PF01250 | Ribosomal protein S6 (Ribosomal_S6) | Ribosomal protein S6 | Domain | |
| EA [auth BE] | PF03719 | Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C) | Ribosomal protein S5, C-terminal domain | Domain | |
| EA [auth BE] | PF00333 | Ribosomal protein S5, N-terminal domain (Ribosomal_S5) | Ribosomal protein S5, N-terminal domain | Domain | |
| DA [auth BD] | PF00163 | Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4) | Ribosomal protein S4/S9 N-terminal domain | - | Family |
| DA [auth BD] | 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 |
| C [auth AA] | PF03947 | Ribosomal Proteins L2, C-terminal domain (Ribosomal_L2_C) | Ribosomal Proteins L2, C-terminal domain | Domain | |
| CA [auth BC] | PF07650 | KH domain (KH_2) | KH domain | Domain | |
| CA [auth BC] | 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 |
| Z [auth A1] | PF00471 | Ribosomal protein L33 (Ribosomal_L33) | Ribosomal protein L33 | - | Family |
| W [auth AW] | PF00831 | Ribosomal L29 protein (Ribosomal_L29) | Ribosomal L29 protein | - | Family |
| U [auth AT] | 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 |
| T [auth AS] | 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 AS] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
| R [auth AQ] | PF00237 | Ribosomal protein L22p/L17e (Ribosomal_L22) | Ribosomal protein L22p/L17e | This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. | Domain |
| P [auth AN] | PF01245 | Ribosomal protein L19 (Ribosomal_L19) | Ribosomal protein L19 | - | Family |
| J [auth AH] | PF00572 | Ribosomal protein L13 (Ribosomal_L13) | Ribosomal protein L13 | - | Family |














