Cryo-EM structure of Chaetomium thermophilum ribosome-bound SND3 translocon
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
| Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
|---|---|---|---|---|---|
| I [auth LC] | SCOP2B Superfamily | Ribosomal protein L4 | 8077111 | 3001146 | SCOP2B (2022-06-29) |
| H [auth LB] | SCOP2B Superfamily | Translational proteins | 8106162 | 3000811 | SCOP2B (2022-06-29) |
| TA [auth Lp] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8106178 | 3001320 | SCOP2B (2022-06-29) |
| PA [auth Ll] | SCOP2B Superfamily | Ribosomal protein L39e | 8106282 | 3001756 | SCOP2B (2022-06-29) |
| KA [auth Lg] | SCOP2B Superfamily | Ribosomal protein L34e-like | 8106200 | 3002203 | SCOP2B (2022-06-29) |
| JA [auth Lf] | SCOP2B Superfamily | Translational proteins | 8106190 | 3000811 | SCOP2B (2022-06-29) |
| IA [auth Le] | SCOP2B Superfamily | Ribosomal protein L32e | 8106182 | 3000982 | SCOP2B (2022-06-29) |
| GA [auth Lc] | SCOP2B Superfamily | L30e-like | 8106196 | 3001739 | SCOP2B (2022-06-29) |
| CA [auth LY] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8106166 | 3000334 | SCOP2B (2022-06-29) |
| AA [auth LV] | SCOP2B Superfamily | 50S Ribosomal protein L14-like | 8106208 | 3000433 | SCOP2B (2022-06-29) |
| Z [auth LU] | SCOP2B Superfamily | 60S Ribosomal protein L22e | 8106192 | 3002158 | SCOP2B (2022-06-29) |
| W [auth LR] | SCOP2B Superfamily | Ribosomal protein L19 (L19e) | 8106186 | 3000890 | SCOP2B (2022-06-29) |
| S [auth LN] | SCOP2B Superfamily | Ribosomal proteins S24e, L23 and L15e | 8106168 | 3000210 | SCOP2B (2022-06-29) |
| P [auth LJ] | SCOP2B Superfamily | RL5-like | 8077505 | 3001709 | SCOP2B (2022-06-29) |
| O [auth LI] | SCOP2B Superfamily | Ribosomal protein L16p/L10e | 8106198 | 3000884 | SCOP2B (2022-06-29) |
| J [auth LD] | SCOP2B Superfamily | Translational machinery components | 8106194 | 3000571 | 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 LC] | e9i78LC1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: | ECOD (v295.2) | |
| H [auth LB] | IBR | e9i78LB1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: IBR | ECOD (v295.2) |
| G [auth LA] | RVT_1 | e9i78LA1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: RVT_1 | ECOD (v295.2) |
| UA [auth Lq] | e9i78Lq1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: | ECOD (v295.2) | |
| TA [auth Lp] | RVT_1 | e9i78Lp1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: RVT_1 | ECOD (v295.2) |
| SA [auth Lo] | e9i78Lo1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: | ECOD (v295.2) | |
| RA [auth Ln] | PAD_N | e9i78Ln1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: PAD_N | ECOD (v295.2) |
| QA [auth Lm] | IBR | e9i78Lm1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: IBR | ECOD (v295.2) |
| PA [auth Ll] | PAD_N | e9i78Ll1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: PAD_N | ECOD (v295.2) |
| OA [auth Lk] | e9i78Lk1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: | ECOD (v295.2) | |
| NA [auth Lj] | RVT_1 | e9i78Lj1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: RVT_1 | ECOD (v295.2) |
| D [auth 4] | e9i7842 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: Hypothetical protein YqbG-like | F: | ECOD (v295.2) | |
| MA [auth Li] | Beta-Casp | e9i78Li1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: Beta-Casp | ECOD (v295.2) |
| LA [auth Lh] | Beta-Casp | e9i78Lh1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: Beta-Casp | ECOD (v295.2) |
| KA [auth Lg] | RVT_1 | e9i78Lg1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: RVT_1 | ECOD (v295.2) |
| JA [auth Lf] | RVT_1 | e9i78Lf1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: RVT_1 | ECOD (v295.2) |
| IA [auth Le] | e9i78Le1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: | ECOD (v295.2) | |
| HA [auth Ld] | e9i78Ld1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: | ECOD (v295.2) | |
| GA [auth Lc] | IBR | e9i78Lc1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: IBR | ECOD (v295.2) |
| FA [auth Lb] | RVT_1 | e9i78Lb1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: RVT_1 | ECOD (v295.2) |
| EA [auth La] | RVT_1 | e9i78La1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: RVT_1 | ECOD (v295.2) |
| DA [auth LZ] | e9i78LZ1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: | ECOD (v295.2) | |
| C [auth 3] | e9i7831 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: | ECOD (v295.2) | |
| CA [auth LY] | e9i78LY1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: | ECOD (v295.2) | |
| BA [auth LX] | RVT_1 | e9i78LX1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: RVT_1 | ECOD (v295.2) |
| AA [auth LV] | IBR | e9i78LV1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: IBR | ECOD (v295.2) |
| Z [auth LU] | e9i78LU1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: | ECOD (v295.2) | |
| Y [auth LT] | e9i78LT1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: | ECOD (v295.2) | |
| X [auth LS] | IBR | e9i78LS1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: IBR | ECOD (v295.2) |
| W [auth LR] | RVT_1 | e9i78LR1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: RVT_1 | ECOD (v295.2) |
| V [auth LQ] | e9i78LQ1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: | ECOD (v295.2) | |
| U [auth LP] | e9i78LP1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: | ECOD (v295.2) | |
| S [auth LN] | IBR | e9i78LN1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: IBR | ECOD (v295.2) |
| R [auth LM] | e9i78LM1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: | ECOD (v295.2) | |
| Q [auth LL] | e9i78LL1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: | ECOD (v295.2) | |
| P [auth LJ] | e9i78LJ1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: | ECOD (v295.2) | |
| O [auth LI] | IBR | e9i78LI1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: IBR | ECOD (v295.2) |
| N [auth LH] | e9i78LH1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: | ECOD (v295.2) | |
| M [auth LG] | RVT_1 | e9i78LG1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: RVT_1 | ECOD (v295.2) |
| L [auth LF] | Beta-Casp | e9i78LF1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: Beta-Casp | ECOD (v295.2) |
| K [auth LE] | Beta-Casp | e9i78LE1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: Beta-Casp | ECOD (v295.2) |
| J [auth LD] | e9i78LD1 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: | ECOD (v295.2) | |
| A [auth 1] | e9i7811 | A: alpha arrays | X: Hypothetical protein YqbG-like | H: Hypothetical protein YqbG-like | T: alpha/beta-Hydrolases | F: | ECOD (v295.2) |
Protein Family Annotation Pfam Database Homepage
| Chains | Accession | Name | Description | Comments | Source |
|---|---|---|---|---|---|
| I [auth LC] | 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 |
| I [auth LC] | PF00573 | Ribosomal protein L4/L1 family (Ribosomal_L4) | Ribosomal protein L4/L1 family | - | Family |
| I [auth LC] | 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 |
| H [auth LB] | PF01779 | Ribosomal L29e protein family (Ribosomal_L29e) | Ribosomal L29e protein family | - | Family |
| G [auth LA] | PF03947 | Ribosomal Proteins L2, C-terminal domain (Ribosomal_L2_C) | Ribosomal Proteins L2, C-terminal domain | Domain | |
| DA [auth LZ] | 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 |
| C [auth 3] | PF00584 | SecE/Sec61-gamma subunits of protein translocation complex (SecE) | SecE/Sec61-gamma subunits of protein translocation complex | - | Family |
| CA [auth LY] | PF16906 | Ribosomal proteins L26 eukaryotic, L24P archaeal (Ribosomal_L26) | Ribosomal proteins L26 eukaryotic, L24P archaeal | - | Family |
| CA [auth LY] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
| BA [auth LX] | PF00276 | Ribosomal protein L23 (Ribosomal_L23) | Ribosomal protein L23 | - | Family |
| AA [auth LV] | PF00238 | Ribosomal protein L14p/L23e (Ribosomal_L14) | Ribosomal protein L14p/L23e | Domain | |
| Z [auth LU] | PF01776 | Ribosomal L22e protein family (Ribosomal_L22e) | Ribosomal L22e protein family | - | Family |
| X [auth LS] | 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 |
| W [auth LR] | 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 |
| W [auth LR] | 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 |
| V [auth LQ] | PF01778 | Ribosomal L28e protein family (Ribosomal_L28e) | Ribosomal L28e protein family | - | Family |
| V [auth LQ] | PF17135 | Ribosomal protein 60S L18 and 50S L18e (Ribosomal_L18) | Ribosomal protein 60S L18 and 50S L18e | - | Family |
| U [auth LP] | PF00237 | Ribosomal protein L22p/L17e (Ribosomal_L22) | Ribosomal protein L22p/L17e | This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. | Domain |
| U [auth LP] | PF01780 | Ribosomal L37ae protein family (Ribosomal_L37ae) | Ribosomal L37ae protein family | - | Family |
| T [auth LO] | PF00935 | Ribosomal protein L44 (Ribosomal_L44) | Ribosomal protein L44 | - | Family |
| T [auth LO] | PF00572 | Ribosomal protein L13 (Ribosomal_L13) | Ribosomal protein L13 | - | Family |
| S [auth LN] | PF05162 | Ribosomal protein L41 (Ribosomal_L41) | Ribosomal protein L41 | - | Family |
| S [auth LN] | PF00827 | Ribosomal L15 (Ribosomal_L15e) | Ribosomal L15 | - | Family |
| R [auth LM] | PF01929 | Ribosomal protein L14 (Ribosomal_L14e) | Ribosomal protein L14 | - | Family |
| Q [auth LL] | PF00832 | Ribosomal L39 protein (Ribosomal_L39) | Ribosomal L39 protein | - | Family |
| Q [auth LL] | PF01294 | Ribosomal protein L13e (Ribosomal_L13e) | Ribosomal protein L13e | - | Family |
| P [auth LJ] | PF00281 | Ribosomal protein L5 (Ribosomal_L5) | Ribosomal protein L5 | Domain | |
| P [auth LJ] | PF00673 | ribosomal L5P family C-terminus (Ribosomal_L5_C) | ribosomal L5P family C-terminus | This region is found associated with Pfam:PF00281. | Domain |
| O [auth LI] | PF00252 | Ribosomal protein L16p/L10e (Ribosomal_L16) | Ribosomal protein L16p/L10e | Domain | |
| O [auth LI] | PF01158 | Ribosomal protein L36e (Ribosomal_L36e) | Ribosomal protein L36e | - | Family |
| N [auth LH] | PF00347 | Ribosomal protein L6 (Ribosomal_L6) | Ribosomal protein L6 | Domain | |
| N [auth LH] | PF00831 | Ribosomal L29 protein (Ribosomal_L29) | Ribosomal L29 protein | - | Family |
| M [auth LG] | 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 |
| L [auth LF] | PF08079 | Ribosomal L30 N-terminal domain (Ribosomal_L30_N) | Ribosomal L30 N-terminal domain | This presumed domain is found at the N-terminus of Ribosomal L30 proteins and has been termed RL30NT or NUC018 [1]. | Domain |
| L [auth LF] | PF00327 | Ribosomal protein L30p/L7e (Ribosomal_L30) | Ribosomal protein L30p/L7e | This family includes prokaryotic L30 and eukaryotic L7. | Domain |
| L [auth LF] | 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 |
| K [auth LE] | PF01655 | Ribosomal protein L32 (Ribosomal_L32e) | Ribosomal protein L32 | - | Family |
| K [auth LE] | PF01159 | Ribosomal protein L6e (Ribosomal_L6e) | Ribosomal protein L6e | - | Family |
| J [auth LD] | PF17144 | Ribosomal large subunit proteins 60S L5, and 50S L18 (Ribosomal_L5e) | Ribosomal large subunit proteins 60S L5, and 50S L18 | - | Family |
| J [auth LD] | PF01198 | Ribosomal protein L31e (Ribosomal_L31e) | Ribosomal protein L31e | - | Family |
| J [auth LD] | 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 |
| A [auth 1] | PF10559 | Plug domain of Sec61p (Plug_translocon) | Plug domain of Sec61p | The Sec61/SecY translocon mediates translocation of proteins across the membrane and integration of membrane proteins into the lipid bilayer. The structure of the translocon revealed a plug domain blocking the pore on the lumenal side.The plug is unl ... | Domain |
| A [auth 1] | PF00344 | SecY (SecY) | SecY | - | Family |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Protein Modification Annotation
| Modified Residue(s) | ||
|---|---|---|
| Chain | Residue(s) | Description |
| VA [auth L1] | OMG | Parent Component: G |
| T [auth LO] | ACE | :  AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 :  N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359 |














