Structural snapshot of cytoplasmic pre-60S ribosomal particles bound with Nmd3, Lsg1, Tif6 and Reh1
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
| Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
|---|---|---|---|---|---|
| I [auth F] | SCOP2B Superfamily | Ribosomal L30p/L7e protein, N-terminal domain-lke | 8052916 | 3002152 | SCOP2B (2022-06-29) |
| I [auth F] | SCOP2B Superfamily | Ribosomal protein L30p/L7e | 8052917 | 3001378 | SCOP2B (2022-06-29) |
| H [auth E] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8053109 | 3000334 | SCOP2B (2022-06-29) |
| G [auth D] | SCOP2B Superfamily | Translational machinery components | 8052875 | 3000571 | SCOP2B (2022-06-29) |
| F [auth C] | SCOP2B Superfamily | Ribosomal protein L4 | 8052816 | 3001146 | SCOP2B (2022-06-29) |
| F [auth C] | SCOP2B Superfamily | 60S ribosomal protein L4 C-terminal domain-like | 8052815 | 3002143 | SCOP2B (2022-06-29) |
| E [auth B] | SCOP2B Superfamily | Translational proteins | 8078363 | 3000811 | SCOP2B (2022-06-29) |
| QA [auth y] | SCOP2B Superfamily | Pentein | 8036230 | 3000640 | SCOP2B (2022-06-29) |
| OA [auth p] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8103126 | 3001320 | SCOP2B (2022-06-29) |
| MA [auth l] | SCOP2B Superfamily | Ribosomal protein L39e | 8078549 | 3001756 | SCOP2B (2022-06-29) |
| LA [auth k] | SCOP2B Superfamily | Ribosomal L38e protein-like | 8053562 | 3002206 | SCOP2B (2022-06-29) |
| KA [auth j] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8080044 | 3001320 | SCOP2B (2022-06-29) |
| JA [auth i] | SCOP2B Superfamily | Ribosomal protein L36e | 8053115 | 3002161 | SCOP2B (2022-06-29) |
| HA [auth g] | SCOP2B Superfamily | Ribosomal protein L34e-like | 8053547 | 3002203 | SCOP2B (2022-06-29) |
| GA [auth f] | SCOP2B Superfamily | Translational proteins | 8087451 | 3000811 | SCOP2B (2022-06-29) |
| DA [auth c] | SCOP2B Superfamily | L30e-like | 8039862 | 3001739 | SCOP2B (2022-06-29) |
| CA [auth b] | SCOP2B Superfamily | Ribosomal protein L29e | 8053045 | 3002157 | SCOP2B (2022-06-29) |
| BA [auth a] | SCOP2B Superfamily | Ribosomal proteins L15p and L18e | 8077127 | 3001045 | SCOP2B (2022-06-29) |
| AA [auth Z] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8053046 | 3000334 | SCOP2B (2022-06-29) |
| Z [auth Y] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8076760 | 3000334 | SCOP2B (2022-06-29) |
| Y [auth X] | SCOP2B Superfamily | Ribosomal proteins S24e, L23 and L15e | 8095962 | 3000210 | SCOP2B (2022-06-29) |
| W [auth V] | SCOP2B Superfamily | 50S Ribosomal protein L14-like | 8103364 | 3000433 | SCOP2B (2022-06-29) |
| V [auth U] | SCOP2B Superfamily | 60S Ribosomal protein L22e | 8053058 | 3002158 | SCOP2B (2022-06-29) |
| S [auth R] | SCOP2B Superfamily | Ribosomal protein L19 (L19e) | 8077485 | 3000890 | SCOP2B (2022-06-29) |
| R [auth Q] | SCOP2B Superfamily | Ribosomal proteins L15p and L18e | 8095970 | 3001045 | SCOP2B (2022-06-29) |
| Q [auth P] | SCOP2B Superfamily | Ribosomal protein L22 | 8076708 | 3001078 | SCOP2B (2022-06-29) |
| P [auth O] | SCOP2B Superfamily | Ribosomal protein L13 | 8066053 | 3001134 | SCOP2B (2022-06-29) |
| O [auth N] | SCOP2B Superfamily | Ribosomal proteins S24e, L23 and L15e | 8082481 | 3000210 | SCOP2B (2022-06-29) |
| M [auth L] | SCOP2B Superfamily | Ribosomal protein L13e-like | 8053159 | 3002162 | SCOP2B (2022-06-29) |
| L [auth J] | SCOP2B Superfamily | RL5-like | 8073884 | 3001709 | SCOP2B (2022-06-29) |
| J [auth G] | SCOP2B Superfamily | L30e-like | 8063962 | 3001739 | 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 F] | PemK_toxin | e5h4pF1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| H [auth E] | PemK_toxin | e5h4pE1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| G [auth D] | PemK_toxin | e5h4pD1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| F [auth C] | PemK_toxin | e5h4pC1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| E [auth B] | PemK_toxin | e5h4pB1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| QA [auth y] | PemK_toxin | e5h4py1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| PA [auth w] | NMD3 | e5h4pw1 | A: beta barrels | X: Ribonuclease H-like | H: Small protein B (SmpB) | T: Small protein B (SmpB) | F: NMD3 | ECOD (v294.2) |
| PA [auth w] | NMD_SH3 | e5h4pw2 | A: beta barrels | X: Ribonuclease H-like | H: Small protein B (SmpB) | T: Small protein B (SmpB) | F: NMD_SH3 | ECOD (v294.2) |
| PA [auth w] | Thymidylat_synt | e5h4pw3 | A: beta barrels | X: Ribonuclease H-like | H: Small protein B (SmpB) | T: Small protein B (SmpB) | F: Thymidylat_synt | ECOD (v294.2) |
| OA [auth p] | PemK_toxin | e5h4pp1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| NA [auth o] | PemK_toxin | e5h4po1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| D [auth A] | Ribosomal_L2_C | e5h4pA1 | A: beta barrels | X: TIM beta/alpha-barrel | H: TIM barrels | T: TIM barrels | F: Ribosomal_L2_C | ECOD (v294.2) |
| MA [auth l] | PemK_toxin | e5h4pl1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| LA [auth k] | PemK_toxin | e5h4pk1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| KA [auth j] | PemK_toxin | e5h4pj1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| JA [auth i] | PemK_toxin | e5h4pi1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| IA [auth h] | PemK_toxin | e5h4ph1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| HA [auth g] | PemK_toxin | e5h4pg1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| GA [auth f] | PemK_toxin | e5h4pf1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| FA [auth e] | PemK_toxin | e5h4pe1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| EA [auth d] | PemK_toxin | e5h4pd1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| DA [auth c] | PemK_toxin | e5h4pc1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| CA [auth b] | PemK_toxin | e5h4pb1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| BA [auth a] | MORF_dom | e5h4pa1 | A: beta barrels | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: MORF_dom | ECOD (v294.2) |
| AA [auth Z] | PemK_toxin | e5h4pZ1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| Z [auth Y] | PemK_toxin | e5h4pY1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| Y [auth X] | PemK_toxin | e5h4pX1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| X [auth W] | PemK_toxin | e5h4pW1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| W [auth V] | PemK_toxin | e5h4pV1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| V [auth U] | PemK_toxin | e5h4pU1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| U [auth T] | PemK_toxin | e5h4pT1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| T [auth S] | PemK_toxin | e5h4pS1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| S [auth R] | PemK_toxin | e5h4pR1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| R [auth Q] | PemK_toxin | e5h4pQ1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| Q [auth P] | PemK_toxin | e5h4pP1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| P [auth O] | PemK_toxin | e5h4pO1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| O [auth N] | PemK_toxin | e5h4pN1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| N [auth M] | PemK_toxin | e5h4pM1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| M [auth L] | PemK_toxin | e5h4pL1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| L [auth J] | PemK_toxin | e5h4pJ1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| K [auth H] | PemK_toxin | e5h4pH1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
| J [auth G] | PemK_toxin | e5h4pG1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PemK_toxin | ECOD (v294.2) |
Protein Family Annotation Pfam Database Homepage
| Chains | Accession | Name | Description | Comments | Source |
|---|---|---|---|---|---|
| I [auth F] | PF00327 | Ribosomal protein L30p/L7e (Ribosomal_L30) | Ribosomal protein L30p/L7e | This family includes prokaryotic L30 and eukaryotic L7. | Domain |
| I [auth F] | PF01247 | Ribosomal protein L35Ae (Ribosomal_L35Ae) | Ribosomal protein L35Ae | This entry represents the ribosomal eL33 previously known as L35A, eukaryotic and archaebacterial ribosomal proteins. | Domain |
| H [auth E] | PF01655 | Ribosomal protein L32 (Ribosomal_L32e) | Ribosomal protein L32 | - | Family |
| H [auth E] | PF01159 | Ribosomal protein L6e (Ribosomal_L6e) | Ribosomal protein L6e | - | Family |
| G [auth D] | PF17144 | Ribosomal large subunit proteins 60S L5, and 50S L18 (Ribosomal_L5e) | Ribosomal large subunit proteins 60S L5, and 50S L18 | - | Family |
| G [auth D] | PF01198 | Ribosomal protein L31e (Ribosomal_L31e) | Ribosomal protein L31e | - | Family |
| G [auth D] | PF14204 | Ribosomal L18 C-terminal region (Ribosomal_L18_c) | Ribosomal L18 C-terminal region | This domain is the C-terminal end of ribosomal L18/L5 proteins. | Domain |
| F [auth C] | PF14374 | 60S ribosomal protein L4 C-terminal domain (Ribos_L4_asso_C) | 60S ribosomal protein L4 C-terminal domain | This family is found at the very C-terminal of 60 ribosomal L4 proteins. | Domain |
| F [auth C] | PF00573 | Ribosomal protein L4/L1 family (Ribosomal_L4) | Ribosomal protein L4/L1 family | - | Family |
| E [auth B] | PF01779 | Ribosomal L29e protein family (Ribosomal_L29e) | Ribosomal L29e protein family | - | Family |
| D [auth A] | PF03947 | Ribosomal Proteins L2, C-terminal domain (Ribosomal_L2_C) | Ribosomal Proteins L2, C-terminal domain | Domain | |
| D [auth A] | PF00181 | Ribosomal Proteins L2, RNA binding N-terminal domain (Ribosomal_L2_N) | Ribosomal Proteins L2, RNA binding N-terminal domain | Domain | |
| D [auth A] | 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 |
| AA [auth Z] | PF01777 | Ribosomal L27e protein family (Ribosomal_L27e) | Ribosomal L27e protein family | The N-terminal region of the eukaryotic ribosomal L27 has the KOW motif. C-terminal region is represented by this family. | Domain |
| Z [auth Y] | PF01912 | eIF-6 family (eIF-6) | eIF-6 family | This family includes eukaryotic translation initiation factor 6 as well as presumed archaebacterial homologues. | Domain |
| Z [auth Y] | PF16906 | Ribosomal proteins L26 eukaryotic, L24P archaeal (Ribosomal_L26) | Ribosomal proteins L26 eukaryotic, L24P archaeal | - | Family |
| Z [auth Y] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
| Y [auth X] | PF00276 | Ribosomal protein L23 (Ribosomal_L23) | Ribosomal protein L23 | - | Family |
| X [auth W] | PF04981 | NMD3, second domain (NMD3) | NMD3, second domain | The NMD3 protein is involved in nonsense mediated mRNA decay. This amino terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p ... | Domain |
| X [auth W] | PF01246 | Ribosomal protein L24e (Ribosomal_L24e) | Ribosomal protein L24e | Domain | |
| W [auth V] | PF00238 | Ribosomal protein L14p/L23e (Ribosomal_L14) | Ribosomal protein L14p/L23e | Domain | |
| V [auth U] | PF01776 | Ribosomal L22e protein family (Ribosomal_L22e) | Ribosomal L22e protein family | - | Family |
| T [auth S] | 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 |
| S [auth R] | 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 |
| S [auth R] | 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 |
| R [auth Q] | PF17135 | Ribosomal protein 60S L18 and 50S L18e (Ribosomal_L18) | Ribosomal protein 60S L18 and 50S L18e | - | Family |
| Q [auth P] | PF00237 | Ribosomal protein L22p/L17e (Ribosomal_L22) | Ribosomal protein L22p/L17e | This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. | Domain |
| Q [auth P] | PF01780 | Ribosomal L37ae protein family (Ribosomal_L37ae) | Ribosomal L37ae protein family | - | Family |
| P [auth O] | PF00935 | Ribosomal protein L44 (Ribosomal_L44) | Ribosomal protein L44 | - | Family |
| P [auth O] | PF00572 | Ribosomal protein L13 (Ribosomal_L13) | Ribosomal protein L13 | - | Family |
| O [auth N] | PF00827 | Ribosomal L15 (Ribosomal_L15e) | Ribosomal L15 | - | Family |
| N [auth M] | PF01929 | Ribosomal protein L14 (Ribosomal_L14e) | Ribosomal protein L14 | - | Family |
| N [auth M] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
| M [auth L] | PF00832 | Ribosomal L39 protein (Ribosomal_L39) | Ribosomal L39 protein | - | Family |
| M [auth L] | PF01294 | Ribosomal protein L13e (Ribosomal_L13e) | Ribosomal protein L13e | - | Family |
| L [auth J] | PF00281 | Ribosomal protein L5 (Ribosomal_L5) | Ribosomal protein L5 | Domain | |
| L [auth J] | PF01907 | Ribosomal protein L37e (Ribosomal_L37e) | Ribosomal protein L37e | - | Family |
| L [auth J] | PF00673 | ribosomal L5P family C-terminus (Ribosomal_L5_C) | ribosomal L5P family C-terminus | This region is found associated with Pfam:PF00281. | Domain |
| K [auth H] | PF00831 | Ribosomal L29 protein (Ribosomal_L29) | Ribosomal L29 protein | - | Family |
| K [auth H] | PF00347 | Ribosomal protein L6 (Ribosomal_L6) | Ribosomal protein L6 | Domain | |
| J [auth G] | 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 |














