The Cryo-EM Structure of the Archaeal 50S Ribosomal Subunit in Complex with Initiation Factor 6
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
| Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
|---|---|---|---|---|---|
| G [auth 6] | SCOP2 Family | L30e/L7ae ribosomal proteins | 8063973 | 4001513 | SCOP2 (2022-06-29) |
| G [auth 6] | SCOP2 Superfamily | L30e-like | 8063974 | 3001739 | SCOP2 (2022-06-29) |
| E [auth 4] | SCOP2B Superfamily | Ribosomal protein L34e-like | 8053546 | 3002203 | SCOP2B (2022-06-29) |
| D [auth 3] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8032610 | 3001320 | SCOP2B (2022-06-29) |
| JA [auth Z] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8032661 | 3001320 | SCOP2B (2022-06-29) |
| HA [auth X] | SCOP2B Superfamily | Ribosomal protein L31e | 8032659 | 3000699 | SCOP2B (2022-06-29) |
| GA [auth W] | SCOP2B Superfamily | Ribosomal protein L30p/L7e | 8032657 | 3001378 | SCOP2B (2022-06-29) |
| FA [auth V] | SCOP2B Superfamily | Ribosomal protein L29 (L29p) | 8032653 | 3000713 | SCOP2B (2022-06-29) |
| EA [auth U] | SCOP2B Superfamily | Glucocorticoid receptor-like (DNA-binding domain) | 8032651 | 3000068 | SCOP2B (2022-06-29) |
| DA [auth T] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8032648 | 3000334 | SCOP2B (2022-06-29) |
| C [auth 2] | SCOP2B Superfamily | Ribosomal protein L39e | 8034428 | 3001756 | SCOP2B (2022-06-29) |
| CA [auth S] | SCOP2B Superfamily | Ribosomal proteins S24e, L23 and L15e | 8032646 | 3000210 | SCOP2B (2022-06-29) |
| BA [auth R] | SCOP2B Superfamily | Ribosomal protein L22 | 8032645 | 3001078 | SCOP2B (2022-06-29) |
| AA [auth Q] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8032644 | 3000334 | SCOP2B (2022-06-29) |
| Z [auth P] | SCOP2B Superfamily | Ribosomal protein L19 (L19e) | 8032641 | 3000890 | SCOP2B (2022-06-29) |
| Y [auth O] | SCOP2B Superfamily | Ribosomal proteins L15p and L18e | 8032640 | 3001045 | SCOP2B (2022-06-29) |
| X [auth N] | SCOP2B Superfamily | Translational machinery components | 8032638 | 3000571 | SCOP2B (2022-06-29) |
| W [auth M] | SCOP2B Superfamily | Ribosomal proteins S24e, L23 and L15e | 8032636 | 3000210 | SCOP2B (2022-06-29) |
| V [auth L] | SCOP2B Superfamily | Ribosomal proteins L15p and L18e | 8032635 | 3001045 | SCOP2B (2022-06-29) |
| U [auth K] | SCOP2B Superfamily | 50S Ribosomal protein L14-like | 8034442 | 3000433 | SCOP2B (2022-06-29) |
| B [auth 1] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8032609 | 3001320 | SCOP2B (2022-06-29) |
| S [auth I] | SCOP2 Family | Ribosome anti-association factor eIF6 (aIF6) | 8084667 | 4001983 | SCOP2 (2022-06-29) |
| S [auth I] | SCOP2 Superfamily | Pentein | 8084668 | 3000640 | SCOP2 (2022-06-29) |
| R [auth H] | SCOP2B Superfamily | Ribosomal protein L16p/L10e | 8035022 | 3000884 | SCOP2B (2022-06-29) |
| Q [auth G] | SCOP2B Superfamily | RplX-like | 8034751 | 3000673 | SCOP2B (2022-06-29) |
| P [auth F] | SCOP2B Superfamily | L30e-like | 8032628 | 3001739 | SCOP2B (2022-06-29) |
| O [auth E] | SCOP2B Superfamily | Ribosomal protein L6 | 8032623 | 3000724 | SCOP2B (2022-06-29) |
| O [auth E] | SCOP2B Superfamily | Ribosomal protein L6 | 8032625 | 3000724 | SCOP2B (2022-06-29) |
| N [auth D] | SCOP2B Superfamily | RL5-like | 8032620 | 3001709 | SCOP2B (2022-06-29) |
| M [auth C] | SCOP2B Superfamily | Ribosomal protein L4 | 8032619 | 3001146 | SCOP2B (2022-06-29) |
| L [auth B] | SCOP2B Superfamily | Translational proteins | 8032615 | 3000811 | SCOP2B (2022-06-29) |
| K [auth A] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8032613 | 3000135 | SCOP2B (2022-06-29) |
| K [auth A] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8032612 | 3000334 | 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) |
|---|---|---|---|---|---|---|---|---|
| H [auth 7] | zf-MYND | e4adx71 | A: a/b three-layered sandwiches | X: jelly-roll | H: Double-stranded beta-helix | T: Double-stranded beta-helix | F: zf-MYND | ECOD (v294.1) |
| G [auth 6] | I-set | e4adx61 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| F [auth 5] | HLH | e4adx51 | A: a/b three-layered sandwiches | X: Ribonuclease H-like | H: Ribonuclease H-like | T: Ribonuclease H-like | F: HLH | ECOD (v294.1) |
| E [auth 4] | BAH | e4adx41 | A: a/b three-layered sandwiches | X: Alpha-beta plaits | H: SH3 | T: SH3 | F: BAH | ECOD (v294.1) |
| D [auth 3] | I-set | e4adx31 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| JA [auth Z] | I-set | e4adxZ1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| IA [auth Y] | HLH | e4adxY1 | A: a/b three-layered sandwiches | X: Ribonuclease H-like | H: Ribonuclease H-like | T: Ribonuclease H-like | F: HLH | ECOD (v294.1) |
| HA [auth X] | I-set | e4adxX1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| GA [auth W] | I-set | e4adxW1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| FA [auth V] | I-set | e4adxV1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| EA [auth U] | I-set | e4adxU1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| DA [auth T] | I-set | e4adxT1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| C [auth 2] | I-set | e4adx21 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| CA [auth S] | I-set | e4adxS1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| BA [auth R] | I-set | e4adxR1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| AA [auth Q] | I-set | e4adxQ1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| Z [auth P] | I-set | e4adxP1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| Y [auth O] | I-set | e4adxO1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| X [auth N] | I-set | e4adxN1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| W [auth M] | I-set | e4adxM1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| V [auth L] | I-set | e4adxL1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| U [auth K] | I-set | e4adxK1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| T [auth J] | I-set | e4adxJ1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| B [auth 1] | I-set | e4adx11 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| S [auth I] | I-set | e4adxI1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| R [auth H] | I-set | e4adxH1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| Q [auth G] | I-set | e4adxG1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| P [auth F] | I-set | e4adxF1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| O [auth E] | I-set | e4adxE1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| N [auth D] | I-set | e4adxD1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| M [auth C] | I-set | e4adxC1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| L [auth B] | I-set | e4adxB1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
| K [auth A] | I-set | e4adxA1 | A: a/b three-layered sandwiches | X: cradle loop barrel | H: RIFT-related | T: acid protease | F: I-set | ECOD (v294.1) |
Protein Family Annotation Pfam Database Homepage
| Chains | Accession | Name | Description | Comments | Source |
|---|---|---|---|---|---|
| H [auth 7] | PF01929 | Ribosomal protein L14 (Ribosomal_L14e) | Ribosomal protein L14 | - | Family |
| H [auth 7] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
| G [auth 6] | PF01248 | Ribosomal protein L7Ae/L30e/S12e/Gadd45 family (Ribosomal_L7Ae) | Ribosomal protein L7Ae/L30e/S12e/Gadd45 family | This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD11 ... | Domain |
| D [auth 3] | PF00935 | Ribosomal protein L44 (Ribosomal_L44) | Ribosomal protein L44 | - | Family |
| IA [auth Y] | PF01655 | Ribosomal protein L32 (Ribosomal_L32e) | Ribosomal protein L32 | - | Family |
| GA [auth W] | PF00327 | Ribosomal protein L30p/L7e (Ribosomal_L30) | Ribosomal protein L30p/L7e | This family includes prokaryotic L30 and eukaryotic L7. | Domain |
| FA [auth V] | PF00831 | Ribosomal L29 protein (Ribosomal_L29) | Ribosomal L29 protein | - | Family |
| DA [auth T] | PF16906 | Ribosomal proteins L26 eukaryotic, L24P archaeal (Ribosomal_L26) | Ribosomal proteins L26 eukaryotic, L24P archaeal | - | Family |
| DA [auth T] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
| C [auth 2] | PF00832 | Ribosomal L39 protein (Ribosomal_L39) | Ribosomal L39 protein | - | Family |
| CA [auth S] | PF00276 | Ribosomal protein L23 (Ribosomal_L23) | Ribosomal protein L23 | - | Family |
| BA [auth R] | PF00237 | Ribosomal protein L22p/L17e (Ribosomal_L22) | Ribosomal protein L22p/L17e | This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. | Domain |
| Z [auth P] | PF01280 | Ribosomal protein L19e, N-terminal domain (Ribosomal_L19e) | Ribosomal protein L19e, N-terminal domain | This domain is found at the N-terminal end of the large ribosomal subunit protein eL19 found in eukaryotes and archaea. This is an helical domain that assumes an orthogonal bundle topology. | Domain |
| Z [auth P] | PF25476 | Ribosomal protein L19e, C-terminal domain (Ribosomal_L19e_C) | Ribosomal protein L19e, C-terminal domain | This domain is found at the C-terminal end of the large ribosomal subunit protein eL19 found in eukaryotes and archaea. This is an helical domain that assumes an orthogonal bundle topology. | Domain |
| Y [auth O] | 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 |
| X [auth N] | PF17144 | Ribosomal large subunit proteins 60S L5, and 50S L18 (Ribosomal_L5e) | Ribosomal large subunit proteins 60S L5, and 50S L18 | - | Family |
| V [auth L] | 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 |
| U [auth K] | PF00238 | Ribosomal protein L14p/L23e (Ribosomal_L14) | Ribosomal protein L14p/L23e | Domain | |
| B [auth 1] | PF01907 | Ribosomal protein L37e (Ribosomal_L37e) | Ribosomal protein L37e | - | Family |
| S [auth I] | PF01912 | eIF-6 family (eIF-6) | eIF-6 family | - | Family |
| R [auth H] | PF00252 | Ribosomal protein L16p/L10e (Ribosomal_L16) | Ribosomal protein L16p/L10e | Domain | |
| Q [auth G] | PF01775 | Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A (Ribosomal_L18A) | Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A | This family includes: archaeal 50S ribosomal protein L18Ae, often referred to as L20e or LX; fungal 60S ribosomal protein L20; and higher eukaryote 60S ribosomal protein L18A. | Domain |
| P [auth F] | PF01248 | Ribosomal protein L7Ae/L30e/S12e/Gadd45 family (Ribosomal_L7Ae) | Ribosomal protein L7Ae/L30e/S12e/Gadd45 family | This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD11 ... | Domain |
| O [auth E] | PF00347 | Ribosomal protein L6 (Ribosomal_L6) | Ribosomal protein L6 | Domain | |
| N [auth D] | PF00281 | Ribosomal protein L5 (Ribosomal_L5) | Ribosomal protein L5 | Domain | |
| N [auth D] | PF00673 | ribosomal L5P family C-terminus (Ribosomal_L5_C) | ribosomal L5P family C-terminus | This region is found associated with Pfam:PF00281. | Domain |
| M [auth C] | PF00573 | Ribosomal protein L4/L1 family (Ribosomal_L4) | Ribosomal protein L4/L1 family | - | Family |
| K [auth A] | PF03947 | Ribosomal Proteins L2, C-terminal domain (Ribosomal_L2_C) | Ribosomal Proteins L2, C-terminal domain | Domain | |














