Structure of the ribosomal 80S-eEF2-sordarin complex from yeast obtained by docking atomic models for RNA and protein components into a 11.7 A cryo-EM map.
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
| Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
|---|---|---|---|---|---|
| G [auth AG] | SCOP2B Superfamily | Ribosomal protein S7 | 8065993 | 3000799 | SCOP2B (2022-06-29) |
| SA [auth BY] | SCOP2 Family | Ribosomal protein L37e | 8080043 | 4003706 | SCOP2 (2022-06-29) |
| SA [auth BY] | SCOP2 Superfamily | Zn-binding ribosomal proteins | 8080044 | 3001320 | SCOP2 (2022-06-29) |
| OA [auth BV] | SCOP2 Family | Ribosomal proteins L15p and L18e | 8077126 | 4003555 | SCOP2 (2022-06-29) |
| OA [auth BV] | SCOP2 Superfamily | Ribosomal proteins L15p and L18e | 8077127 | 3001045 | SCOP2 (2022-06-29) |
| NA [auth BU] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8076760 | 3000334 | SCOP2B (2022-06-29) |
| MA [auth BT] | SCOP2B Superfamily | Ribosomal proteins S24e, L23 and L15e | 8095962 | 3000210 | SCOP2B (2022-06-29) |
| GA [auth BN] | SCOP2 Family | Ribosomal protein L22 | 8076707 | 4001212 | SCOP2 (2022-06-29) |
| GA [auth BN] | SCOP2 Superfamily | Ribosomal protein L22 | 8076708 | 3001078 | SCOP2 (2022-06-29) |
| FA [auth BM] | SCOP2 Family | Ribosomal protein L13 | 8066052 | 4003623 | SCOP2 (2022-06-29) |
| FA [auth BM] | SCOP2 Superfamily | Ribosomal protein L13 | 8066053 | 3001134 | SCOP2 (2022-06-29) |
| EA [auth BL] | SCOP2B Superfamily | Ribosomal proteins S24e, L23 and L15e | 8082481 | 3000210 | SCOP2B (2022-06-29) |
| C [auth AB] | SCOP2B Superfamily | SIS domain/Ribosomal protein S2-like | 8061280 | 3001397 | SCOP2B (2022-06-29) |
| BA [auth BI] | SCOP2B Superfamily | Ribosomal protein L16p/L10e | 8079407 | 3000884 | SCOP2B (2022-06-29) |
| Z [auth BG] | SCOP2 Family | L30e/L7ae ribosomal proteins | 8063961 | 4001513 | SCOP2 (2022-06-29) |
| Z [auth BG] | SCOP2 Superfamily | L30e-like | 8063962 | 3001739 | SCOP2 (2022-06-29) |
| Y [auth BF] | SCOP2B Superfamily | Ribosomal protein L30p/L7e | 8052917 | 3001378 | SCOP2B (2022-06-29) |
| V [auth BC] | SCOP2 Family | Ribosomal protein L3 | 8078362 | 4002103 | SCOP2 (2022-06-29) |
| V [auth BC] | SCOP2 Superfamily | Translational proteins | 8078363 | 3000811 | SCOP2 (2022-06-29) |
| B [auth AT] | SCOP2B Superfamily | Ribosomal protein S5 domain 2-like | 8043947 | 3000100 | SCOP2B (2022-06-29) |
| B [auth AT] | SCOP2B Superfamily | EF-G C-terminal domain-like | 8043948 | 3001287 | SCOP2B (2022-06-29) |
| B [auth AT] | SCOP2B Superfamily | Ras-like P-loop GTPases | 8043945 | 3002022 | SCOP2B (2022-06-29) |
| B [auth AT] | SCOP2B Superfamily | EF-Tu post-G domain-like | 8043943 | 3002024 | SCOP2B (2022-06-29) |
| B [auth AT] | SCOP2B Superfamily | EF-G C-terminal domain-like | 8043949 | 3001287 | SCOP2B (2022-06-29) |
| Q [auth AS] | SCOP2 Family | Ribosomal protein S19 | 8086075 | 4001081 | SCOP2 (2022-06-29) |
| Q [auth AS] | SCOP2 Superfamily | Ribosomal protein S19 | 8086076 | 3000686 | SCOP2 (2022-06-29) |
| N [auth AN] | SCOP2 Family | Ribosomal protein S14p/S29e | 8047591 | 4003647 | SCOP2 (2022-06-29) |
| N [auth AN] | SCOP2 Superfamily | Glucocorticoid receptor-like (DNA-binding domain) | 8052597 | 3000068 | SCOP2 (2022-06-29) |
| K [auth AK] | SCOP2B Superfamily | Translational machinery components | 8095805 | 3000571 | SCOP2B (2022-06-29) |
| J [auth AJ] | SCOP2B Superfamily | Ribosomal protein S10 | 8098648 | 3001336 | 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 AI] | Cellulase | e4v4bAI1 | A: alpha arrays | X: HAD domain-like | H: HAD domain-related | T: PIN domain-like | F: Cellulase | ECOD (v295) |
| H [auth AH] | P22_portal | e4v4bAH1 | 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 AG] | P22_portal | e4v4bAG1 | 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 AE] | P22_portal | e4v4bAE1 | 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 AD] | KAsynt_C_assoc | e4v4bAD1 | A: alpha arrays | X: Type II ABC importer transmembrane domain fold | H: Type II ABC importer transmembrane domain fold | T: Type II ABC importer transmembrane domain fold | F: KAsynt_C_assoc | ECOD (v295) |
| UA [auth B9] | P22_portal | e4v4bB91 | 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 BZ] | P22_portal | e4v4bBZ1 | 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 BY] | P22_portal | e4v4bBY1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| RA [auth BX] | P22_portal | e4v4bBX1 | 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 BW] | P22_portal | e4v4bBW1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| PA [auth B0] | P22_portal | e4v4bB01 | 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 BV] | CE2_N | e4v4bBV1 | A: alpha arrays | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: CE2_N | ECOD (v295) |
| NA [auth BU] | P22_portal | e4v4bBU1 | 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 AC] | P22_portal | e4v4bAC1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| MA [auth BT] | P22_portal | e4v4bBT1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| LA [auth BS] | P22_portal | e4v4bBS1 | 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 BR] | P22_portal | e4v4bBR1 | 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 BQ] | P22_portal | e4v4bBQ1 | 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 BP] | P22_portal | e4v4bBP1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| HA [auth BO] | P22_portal | e4v4bBO1 | 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 BN] | P22_portal | e4v4bBN1 | 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 BM] | P22_portal | e4v4bBM1 | 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 BL] | P22_portal | e4v4bBL1 | 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 BK] | P22_portal | e4v4bBK1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| C [auth AB] | FlaF_Ig-like | e4v4bAB1 | 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) |
| CA [auth BJ] | P22_portal | e4v4bBJ1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| BA [auth BI] | P22_portal | e4v4bBI1 | 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 BH] | P22_portal | e4v4bBH1 | 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 BG] | P22_portal | e4v4bBG1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| Y [auth BF] | P22_portal | e4v4bBF1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| X [auth BE] | P22_portal | e4v4bBE1 | 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 BD] | P22_portal | e4v4bBD1 | 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 BC] | P22_portal | e4v4bBC1 | 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 BB] | AAA_16 | e4v4bBB1 | A: alpha arrays | X: Trefoil/Plexin domain-like | H: P-loop domains-related | T: P-loop containing nucleoside triphosphate hydrolases | F: AAA_16 | ECOD (v295) |
| T [auth BA] | P22_portal | e4v4bBA1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| B [auth AT] | P22_portal | e4v4bAT1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| B [auth AT] | Ribosomal_S18 | e4v4bAT6 | A: alpha arrays | X: HTH | H: HTH | T: Three-helical HTH | F: Ribosomal_S18 | ECOD (v295) |
| Q [auth AS] | Ribosomal_S17,Ribosomal_S17_N | e4v4bAS1 | A: alpha arrays | X: OB-fold | H: Nucleic acid-binding protein | T: Nucleic acid-binding protein | F: Ribosomal_S17,Ribosomal_S17_N | ECOD (v295) |
| P [auth AQ] | Cellulase | e4v4bAQ1 | A: alpha arrays | X: HAD domain-like | H: HAD domain-related | T: PIN domain-like | F: Cellulase | ECOD (v295) |
| O [auth AO] | P22_portal | e4v4bAO1 | A: alpha arrays | X: VP4 membrane interaction domain | H: VP4 membrane interaction domain | T: VP4 membrane interaction domain | F: P22_portal | ECOD (v295) |
| N [auth AN] | P22_portal | e4v4bAN1 | 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 AM] | FlaF_Ig-like | e4v4bAM1 | 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) |
| L [auth AL] | P22_portal | e4v4bAL1 | 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 AK] | P22_portal | e4v4bAK1 | 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 AJ] | P22_portal | e4v4bAJ1 | 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 |
|---|---|---|---|---|---|
| G [auth AG] | PF00177 | Ribosomal protein S7p/S5e (Ribosomal_S7) | Ribosomal protein S7p/S5e | This family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes. | Domain |
| F [auth AE] | PF03719 | Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C) | Ribosomal protein S5, C-terminal domain | Domain | |
| F [auth AE] | PF00333 | Ribosomal protein S5, N-terminal domain (Ribosomal_S5) | Ribosomal protein S5, N-terminal domain | Domain | |
| E [auth AD] | PF00163 | Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4) | Ribosomal protein S4/S9 N-terminal domain | - | Family |
| E [auth AD] | 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 |
| SA [auth BY] | PF01907 | Ribosomal protein L37e (Ribosomal_L37e) | Ribosomal protein L37e | - | Family |
| PA [auth B0] | PF01655 | Ribosomal protein L32 (Ribosomal_L32e) | Ribosomal protein L32 | - | Family |
| OA [auth BV] | 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 |
| NA [auth BU] | PF16906 | Ribosomal proteins L26 eukaryotic, L24P archaeal (Ribosomal_L26) | Ribosomal proteins L26 eukaryotic, L24P archaeal | - | Family |
| NA [auth BU] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
| D [auth AC] | PF07650 | KH domain (KH_2) | KH domain | Domain | |
| D [auth AC] | 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 |
| MA [auth BT] | PF00276 | Ribosomal protein L23 (Ribosomal_L23) | Ribosomal protein L23 | - | Family |
| GA [auth BN] | PF00237 | Ribosomal protein L22p/L17e (Ribosomal_L22) | Ribosomal protein L22p/L17e | This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. | Domain |
| FA [auth BM] | PF00572 | Ribosomal protein L13 (Ribosomal_L13) | Ribosomal protein L13 | - | Family |
| C [auth AB] | PF00318 | Ribosomal protein S2 (Ribosomal_S2) | Ribosomal protein S2 | - | Family |
| BA [auth BI] | PF00252 | Ribosomal protein L16p/L10e (Ribosomal_L16) | Ribosomal protein L16p/L10e | Domain | |
| AA [auth BH] | PF00347 | Ribosomal protein L6 (Ribosomal_L6) | Ribosomal protein L6 | Domain | |
| Z [auth BG] | 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 |
| Y [auth BF] | PF00327 | Ribosomal protein L30p/L7e (Ribosomal_L30) | Ribosomal protein L30p/L7e | This family includes prokaryotic L30 and eukaryotic L7. | Domain |
| X [auth BE] | PF17144 | Ribosomal large subunit proteins 60S L5, and 50S L18 (Ribosomal_L5e) | Ribosomal large subunit proteins 60S L5, and 50S L18 | - | Family |
| W [auth BD] | PF00573 | Ribosomal protein L4/L1 family (Ribosomal_L4) | Ribosomal protein L4/L1 family | - | Family |
| B [auth AT] | PF00679 | Elongation factor G C-terminus (EFG_C) | Elongation factor G C-terminus | This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold. | Domain |
| B [auth AT] | PF00009 | Elongation factor Tu GTP binding domain (GTP_EFTU) | Elongation factor Tu GTP binding domain | This domain contains a P-loop motif, also found in several other families such as Pfam:PF00071, Pfam:PF00025 and Pfam:PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains. | Domain |
| B [auth AT] | PF14492 | Elongation Factor G, domain III (EFG_III) | Elongation Factor G, domain III | This domain is found in Elongation Factor G. It shares a similar structure with domain V (Pfam:PF00679). Structural studies in drosophila indicate this is domain 3 [1]. | Domain |
| B [auth AT] | PF03144 | Elongation factor Tu domain 2 (GTP_EFTU_D2) | Elongation factor Tu domain 2 | Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as e ... | Domain |
| B [auth AT] | PF03764 | Elongation factor G, domain IV (EFG_IV) | Elongation factor G, domain IV | This domain is found in elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopts a ribosomal protein S5 domain 2-like fold. | Domain |
| Q [auth AS] | PF00203 | Ribosomal protein S19 (Ribosomal_S19) | Ribosomal protein S19 | Domain | |
| O [auth AO] | PF00312 | Ribosomal protein S15 (Ribosomal_S15) | Ribosomal protein S15 | Domain | |
| N [auth AN] | PF00253 | Ribosomal protein S14p/S29e (Ribosomal_S14) | Ribosomal protein S14p/S29e | - | Family |
| K [auth AK] | PF00411 | Ribosomal protein S11 (Ribosomal_S11) | Ribosomal protein S11 | - | Family |
| J [auth AJ] | 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 |














