Cryo-EM Structure of the Mammalian Oligosaccharyltransferase Bound to Sec61 and the Programmed 80S Ribosome
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
| Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
|---|---|---|---|---|---|
| I | SCOP2B Superfamily | Ribosomal protein L16p/L10e | 8097320 | 3000884 | SCOP2B (2022-06-29) |
| XA [auth y] | SCOP2B Superfamily | Protein translocase subunit SecE-like | 8053309 | 3002174 | SCOP2B (2022-06-29) |
| E | SCOP2B Superfamily | Ribosomal protein L6e, N-terminal domain | 8053101 | 3002160 | SCOP2B (2022-06-29) |
| E | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8053102 | 3000334 | SCOP2B (2022-06-29) |
| WA [auth x] | SCOP2B Superfamily | SecY-like | 8056967 | 3000333 | SCOP2B (2022-06-29) |
| OA [auth p] | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8101435 | 3001320 | SCOP2B (2022-06-29) |
| KA [auth l] | SCOP2B Superfamily | Ribosomal protein L39e | 8095595 | 3001756 | SCOP2B (2022-06-29) |
| HA [auth i] | SCOP2B Superfamily | Ribosomal protein L36e | 8053119 | 3002161 | SCOP2B (2022-06-29) |
| FA [auth g] | SCOP2B Superfamily | Ribosomal protein L34e-like | 8103328 | 3002203 | SCOP2B (2022-06-29) |
| EA [auth f] | SCOP2B Superfamily | Translational proteins | 8093714 | 3000811 | SCOP2B (2022-06-29) |
| DA [auth e] | SCOP2B Superfamily | Ribosomal protein L32e | 8102088 | 3000982 | SCOP2B (2022-06-29) |
| C | SCOP2B Superfamily | Ribosomal protein L4 | 8052829 | 3001146 | SCOP2B (2022-06-29) |
| C | SCOP2B Superfamily | 60S ribosomal protein L4 C-terminal domain-like | 8052828 | 3002143 | SCOP2B (2022-06-29) |
| Z [auth a] | SCOP2B Superfamily | Ribosomal proteins L15p and L18e | 8097818 | 3001045 | SCOP2B (2022-06-29) |
| Y [auth Z] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8053047 | 3000334 | SCOP2B (2022-06-29) |
| X [auth Y] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8076754 | 3000334 | SCOP2B (2022-06-29) |
| W [auth X] | SCOP2B Superfamily | Ribosomal proteins S24e, L23 and L15e | 8095966 | 3000210 | SCOP2B (2022-06-29) |
| U [auth V] | SCOP2B Superfamily | 50S Ribosomal protein L14-like | 8072048 | 3000433 | SCOP2B (2022-06-29) |
| B | SCOP2B Superfamily | Translational proteins | 8078357 | 3000811 | SCOP2B (2022-06-29) |
| M [auth N] | SCOP2B Superfamily | Ribosomal proteins S24e, L23 and L15e | 8082477 | 3000210 | SCOP2B (2022-06-29) |
| J | SCOP2B Superfamily | RL5-like | 8073894 | 3001709 | 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 | V-set | e6ftiI1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| H | V-set | e6ftiH1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| G | V-set | e6ftiG1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| F | V-set | e6ftiF1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| DB [auth 5] | V-set | e6fti51 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| CB [auth 4] | V-set | e6fti41 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| YA [auth z] | V-set | e6ftiz1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| XA [auth y] | V-set | e6ftiy1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| E | V-set | e6ftiE1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| WA [auth x] | V-set | e6ftix1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| RA [auth t] | V-set | e6ftit1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| QA [auth s] | V-set | e6ftis1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| PA [auth r] | V-set | e6ftir1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| OA [auth p] | V-set | e6ftip1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| NA [auth o] | V-set | e6ftio1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| D | V-set | e6ftiD1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| MA [auth n] | V-set | e6ftin1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| LA [auth m] | V-set | e6ftim1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| KA [auth l] | V-set | e6ftil1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| JA [auth k] | V-set | e6ftik1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| IA [auth j] | V-set | e6ftij1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| HA [auth i] | V-set | e6ftii1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| GA [auth h] | V-set | e6ftih1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| FA [auth g] | V-set | e6ftig1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| EA [auth f] | V-set | e6ftif1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| DA [auth e] | V-set | e6ftie1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| C | Ald_deCOase | e6ftiC1 | A: a/b three-layered sandwiches | X: Rubredoxin-like | H: Ferritin/Heme oxygenase | T: Heme oxygenase/Ribonucleotide reductase | F: Ald_deCOase | ECOD (v294.1) |
| CA [auth d] | V-set | e6ftid1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| BA [auth c] | V-set | e6ftic1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| AA [auth b] | V-set | e6ftib1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| Z [auth a] | V-set | e6ftia1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| Y [auth Z] | V-set | e6ftiZ1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| X [auth Y] | V-set | e6ftiY1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| W [auth X] | V-set | e6ftiX1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| V [auth W] | V-set | e6ftiW1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| U [auth V] | V-set | e6ftiV1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| T [auth U] | V-set | e6ftiU1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| B | V-set | e6ftiB1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| S [auth T] | V-set | e6ftiT1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| R [auth S] | V-set | e6ftiS1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| Q [auth R] | V-set | e6ftiR1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| P [auth Q] | V-set | e6ftiQ1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| O [auth P] | V-set | e6ftiP1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| N [auth O] | V-set | e6ftiO1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| M [auth N] | V-set | e6ftiN1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| L [auth M] | V-set | e6ftiM1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| K [auth L] | V-set | e6ftiL1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| J | V-set | e6ftiJ1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
| A | V-set | e6ftiA1 | A: a/b three-layered sandwiches | X: Periplasmic binding protein-like II | H: Rubredoxin-related | T: Tetrapyrrole methylase C-terminal domain | F: V-set | ECOD (v294.1) |
Protein Family Annotation Pfam Database Homepage
| Chains | Accession | Name | Description | Comments | Source |
|---|---|---|---|---|---|
| PF00252 | Ribosomal protein L16p/L10e (Ribosomal_L16) | Ribosomal protein L16p/L10e | Domain | ||
| PF01158 | Ribosomal protein L36e (Ribosomal_L36e) | Ribosomal protein L36e | - | Family | |
| PF00831 | Ribosomal L29 protein (Ribosomal_L29) | Ribosomal L29 protein | - | Family | |
| PF00347 | Ribosomal protein L6 (Ribosomal_L6) | Ribosomal protein L6 | Domain | ||
| 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 | |
| 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 | |
| PF00327 | Ribosomal protein L30p/L7e (Ribosomal_L30) | Ribosomal protein L30p/L7e | This family includes prokaryotic L30 and eukaryotic L7. | Domain | |
| DB [auth 5] | PF02516 | Oligosaccharyl transferase STT3, N-terminal (STT3) | Oligosaccharyl transferase STT3, N-terminal | This entry consists of the oligosaccharyl transferase STT3 subunit and related proteins. The STT3 subunit is part of the oligosaccharyl transferase (OTase) complex of proteins and is required for its activity [2]. In eukaryotes, OTase transfers a l ... | Domain |
| DB [auth 5] | PF22627 | AglB core domain (AglB_core-like) | AglB core domain | This entry represents the C-terminal core domain of archaeal oligosaccharyltransferase AglB that transfers oligosaccharide chain from a lipid-linked oligosaccharide (LLO) donor to the asparagine residues in the N-glycosylation sequon, Asn-X-Ser/Thr ( ... | Domain |
| BB [auth 3] | PF04756 | OST3 / OST6 family, transporter family (OST3_OST6) | OST3 / OST6 family, transporter family | - | Family |
| PF03868 | Ribosomal protein L6, N-terminal domain (Ribosomal_L6e_N) | Ribosomal protein L6, N-terminal domain | Domain | ||
| PF01159 | Ribosomal protein L6e (Ribosomal_L6e) | Ribosomal protein L6e | - | Family | |
| PF17144 | Ribosomal large subunit proteins 60S L5, and 50S L18 (Ribosomal_L5e) | Ribosomal large subunit proteins 60S L5, and 50S L18 | - | Family | |
| PF01198 | Ribosomal protein L31e (Ribosomal_L31e) | Ribosomal protein L31e | - | Family | |
| 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 | |
| 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 | |
| PF00573 | Ribosomal protein L4/L1 family (Ribosomal_L4) | Ribosomal protein L4/L1 family | - | Family | |
| Y [auth Z] | PF01777 | Ribosomal L27e protein family (Ribosomal_L27e) | Ribosomal L27e protein family | - | Family |
| Y [auth Z] | PF03911 | Sec61beta family (Sec61_beta) | Sec61beta family | - | Family |
| Y [auth Z] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
| X [auth Y] | PF16906 | Ribosomal proteins L26 eukaryotic, L24P archaeal (Ribosomal_L26) | Ribosomal proteins L26 eukaryotic, L24P archaeal | - | Family |
| X [auth Y] | PF00584 | SecE/Sec61-gamma subunits of protein translocation complex (SecE) | SecE/Sec61-gamma subunits of protein translocation complex | - | Family |
| X [auth Y] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
| W [auth X] | PF03939 | Ribosomal protein L23, N-terminal domain (Ribosomal_L23eN) | Ribosomal protein L23, N-terminal domain | - | Family |
| W [auth X] | 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 |
| W [auth X] | PF00276 | Ribosomal protein L23 (Ribosomal_L23) | Ribosomal protein L23 | - | Family |
| W [auth X] | PF00344 | SecY (SecY) | SecY | - | Family |
| V [auth W] | PF01246 | Ribosomal protein L24e (Ribosomal_L24e) | Ribosomal protein L24e | Domain | |
| U [auth V] | PF00238 | Ribosomal protein L14p/L23e (Ribosomal_L14) | Ribosomal protein L14p/L23e | Domain | |
| PF01779 | Ribosomal L29e protein family (Ribosomal_L29e) | Ribosomal L29e protein family | - | Family | |
| PF00297 | Ribosomal protein L3 (Ribosomal_L3) | Ribosomal protein L3 | - | Family | |
| S [auth T] | 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 |
| S [auth T] | PF00298 | Ribosomal protein L11, RNA binding domain (Ribosomal_L11) | Ribosomal protein L11, RNA binding domain | Domain | |
| S [auth T] | PF01157 | Ribosomal protein L21e (Ribosomal_L21e) | Ribosomal protein L21e | - | Family |
| Q [auth R] | PF01778 | Ribosomal L28e protein family (Ribosomal_L28e) | Ribosomal L28e protein family | - | Family |
| O [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 |
| O [auth P] | PF01780 | Ribosomal L37ae protein family (Ribosomal_L37ae) | Ribosomal L37ae protein family | - | Family |
| N [auth O] | PF00935 | Ribosomal protein L44 (Ribosomal_L44) | Ribosomal protein L44 | - | Family |
| M [auth N] | PF05162 | Ribosomal protein L41 (Ribosomal_L41) | Ribosomal protein L41 | - | Family |
| M [auth N] | PF00827 | Ribosomal L15 (Ribosomal_L15e) | Ribosomal L15 | - | Family |
| L [auth M] | PF01929 | Ribosomal protein L14 (Ribosomal_L14e) | Ribosomal protein L14 | - | Family |
| K [auth L] | PF00832 | Ribosomal L39 protein (Ribosomal_L39) | Ribosomal L39 protein | - | Family |
| PF00281 | Ribosomal protein L5 (Ribosomal_L5) | Ribosomal protein L5 | Domain | ||
| PF00673 | ribosomal L5P family C-terminus (Ribosomal_L5_C) | ribosomal L5P family C-terminus | This region is found associated with Pfam:PF00281. | Domain | |
| PF03947 | Ribosomal Proteins L2, C-terminal domain (Ribosomal_L2_C) | Ribosomal Proteins L2, C-terminal domain | Domain | ||
| PF00181 | Ribosomal Proteins L2, RNA binding N-terminal domain (Ribosomal_L2_N) | Ribosomal Proteins L2, RNA binding N-terminal domain | Domain | ||
| 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 |














