2YBB
Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876)
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (1) | NADH-QUINONE OXIDOREDUCTASE SUBUNIT 1 | polymer | 438 | 48693.7 | 1 | UniProt (Q56222) Pfam (PF01512) Pfam (PF22461) Pfam (PF10531) Pfam (PF10589) | THERMUS THERMOPHILUS | NADH DEHYDROGENASE I CHAIN 1, NDH-1 SUBUNIT 1 |
| 2 | B (2) | NADH-QUINONE OXIDOREDUCTASE SUBUNIT 2 | polymer | 181 | 20309.2 | 1 | UniProt (Q56221) Pfam (PF01257) | THERMUS THERMOPHILUS | NADH DEHYDROGENASE I CHAIN 2, NDH-1 SUBUNIT 2 |
| 3 | C (3) | NADH-QUINONE OXIDOREDUCTASE SUBUNIT 3 | polymer | 783 | 86656.2 | 1 | UniProt (Q56223) Pfam (PF00384) Pfam (PF01568) Pfam (PF00111) Pfam (PF10588) Pfam (PF22117) Pfam (PF04879) | THERMUS THERMOPHILUS | NADH DEHYDROGENASE I CHAIN 3, NDH-1 SUBUNIT 3 |
| 4 | D (4) | NADH-QUINONE OXIDOREDUCTASE SUBUNIT 4 | polymer | 409 | 46428.0 | 1 | UniProt (Q56220) Pfam (PF00346) | THERMUS THERMOPHILUS | NADH DEHYDROGENASE I CHAIN 4, NDH-1 SUBUNIT 4 |
| 5 | E (5) | NADH-QUINONE OXIDOREDUCTASE SUBUNIT 5 | polymer | 207 | 23893.3 | 1 | UniProt (Q56219) Pfam (PF00329) | THERMUS THERMOPHILUS | NADH DEHYDROGENASE I CHAIN 5, NDH-1 SUBUNIT 5 |
| 6 | F (6) | NADH-QUINONE OXIDOREDUCTASE SUBUNIT 6 | polymer | 181 | 20262.6 | 1 | UniProt (Q56218) Pfam (PF01058) | THERMUS THERMOPHILUS | NADH DEHYDROGENASE I SUBUNIT 6, NDH-1 SUBUNIT 6 |
| 7 | G (7) | NADH-QUINONE OXIDOREDUCTASE SUBUNIT 15 | polymer | 129 | 14812.1 | 1 | UniProt (Q5SKZ7) Pfam (PF11497) | THERMUS THERMOPHILUS | NADH DEHYDROGENASE I CHAIN 15, NDH-1 SUBUNIT 15 |
| 8 | H (8) | NADH-QUINONE OXIDOREDUCTASE SUBUNIT 9 | polymer | 182 | 20106.3 | 1 | UniProt (Q56224) Pfam (PF00037) | THERMUS THERMOPHILUS | NADH DEHYDROGENASE I SUBUNIT 9, NDH-1 SUBUNIT 9 |
| 9 | HA, I (A, a) | CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL | polymer | 446 | 49266.3 | 2 | UniProt (P31800) Pfam (PF00675) Pfam (PF05193) | BOS TAURUS (CATTLE) | COMPLEX III SUBUNIT 1, CORE PROTEIN I, UBIQUINOL-CYTOCHROME- C REDUCTASE COMPLEX CORE PROTEIN 1 |
| 10 | IA, J (B, b) | CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL | polymer | 439 | 46575.5 | 2 | UniProt (P23004) Pfam (PF00675) Pfam (PF05193) | BOS TAURUS (CATTLE) | COMPLEX III SUBUNIT 2, CORE PROTEIN II, UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2 |
| 11 | JA, K (C, c) | CYTOCHROME B | polymer | 379 | 42620.3 | 2 | UniProt (P00157) Pfam (PF00033) Pfam (PF00032) | BOS TAURUS (CATTLE) | COMPLEX III SUBUNIT 3, COMPLEX III SUBUNIT III, CYTOCHROME B-C1 COMPLEX SUBUNIT 3, UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CYTOCHROME B SUBUNIT |
| 12 | KA, L (D, d) | CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL | polymer | 241 | 27323.3 | 2 | UniProt (P00125) Pfam (PF02167) | BOS TAURUS (CATTLE) | COMPLEX III SUBUNIT 4, COMPLEX III SUBUNIT IV, CYTOCHROME B- C1 COMPLEX SUBUNIT 4, UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CYTOCHROME C1 SUBUNIT |
| 13 | LA, M (E, e) | CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL | polymer | 196 | 21640.6 | 2 | UniProt (P13272) Pfam (PF02921) Pfam (PF00355) | BOS TAURUS (CATTLE) | COMPLEX III SUBUNIT 5, CYTOCHROME B-C1 COMPLEX SUBUNIT 5, RIESKE IRON-SULFUR PROTEIN, UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT |
| 14 | MA, N (F, f) | CYTOCHROME B-C1 COMPLEX SUBUNIT 7 | polymer | 110 | 13371.2 | 2 | UniProt (P00129) Pfam (PF02271) | BOS TAURUS (CATTLE) | COMPLEX III SUBUNIT 7, UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KDA PROTEIN, COMPLEX III SUBUNIT VII |
| 15 | NA, O (G, g) | CYTOCHROME B-C1 COMPLEX SUBUNIT 8 | polymer | 81 | 9606.0 | 2 | UniProt (P13271) Pfam (PF02939) | BOS TAURUS (CATTLE) | COMPLEX III SUBUNIT 8, COMPLEX III SUBUNIT VIII, UBIQUINOL- CYTOCHROME C REDUCTASE COMPLEX 9.5 KDA PROTEIN, UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C |
| 16 | OA, P (H, h) | CYTOCHROME B-C1 COMPLEX SUBUNIT 6, MITOCHONDRIAL | polymer | 78 | 9189.1 | 2 | UniProt (P00126) Pfam (PF02320) | BOS TAURUS (CATTLE) | COMPLEX III SUBUNIT 6, COMPLEX III SUBUNIT VIII, CYTOCHROME C1 NON-HEME 11 KDA PROTEIN, MITOCHONDRIAL HINGE PROTEIN, UBIQUINOL- CYTOCHROME C REDUCTASE COMPLEX 11 KDA PROTEIN |
| 17 | PA, Q (I, i) | CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL | polymer | 65 | 6677.7 | 2 | UniProt (P13272) Pfam (PF09165) | BOS TAURUS (CATTLE) | COMPLEX III SUBUNIT 5, CYTOCHROME B-C1 COMPLEX SUBUNIT 5, RIESKE IRON-SULFUR PROTEIN, UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, CYTOCHROME B-C1 COMPLEX SUBUNIT 11, COMPLEX III SUBUNIT IX, UBIQUINOL-CYTOCHROME C REDUCTASE 8 KDA PROTEIN, RISP |
| 18 | QA, R (J, j) | CYTOCHROME B-C1 COMPLEX SUBUNIT 9 | polymer | 62 | 7209.3 | 2 | UniProt (P00130) Pfam (PF05365) | BOS TAURUS (CATTLE) | COMPLEX III SUBUNIT 9, COMPLEX III SUBUNIT X, CYTOCHROME C1 NON-HEME 7 KDA PROTEIN, UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.2 KDA PROTEIN |
| 19 | RA, S (K, k) | CYTOCHROME B-C1 COMPLEX SUBUNIT 10 | polymer | 56 | 6370.4 | 2 | UniProt (P07552) Pfam (PF08997) | BOS TAURUS (CATTLE) | COMPLEX III SUBUNIT 10, COMPLEX III SUBUNIT XI, UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 6.4 KDA PROTEIN |
| 20 | T (L) | CYTOCHROME C OXIDASE SUBUNIT 1 | polymer | 514 | 57065.8 | 1 | UniProt (P00396) Pfam (PF00115) | BOS TAURUS (CATTLE) | CYTOCHROME C OXIDASE POLYPEPTIDE I |
| 21 | U (M) | CYTOCHROME C OXIDASE SUBUNIT 2 | polymer | 227 | 26040.4 | 1 | UniProt (P68530) Pfam (PF02790) Pfam (PF00116) | BOS TAURUS (CATTLE) | CYTOCHROME C OXIDASE POLYPEPTIDE II |
| 22 | V (N) | CYTOCHROME C OXIDASE SUBUNIT 3 | polymer | 261 | 29957.6 | 1 | UniProt (P00415) Pfam (PF00510) | BOS TAURUS (CATTLE) | CYTOCHROME C OXIDASE POLYPEPTIDE III |
| 23 | W (O) | CYTOCHROME C OXIDASE SUBUNIT 4 ISOFORM 1, MITOCHONDRIAL | polymer | 147 | 17179.6 | 1 | UniProt (P00423) Pfam (PF02936) | BOS TAURUS (CATTLE) | CYTOCHROME C OXIDASE POLYPEPTIDE IV, CYTOCHROME C OXIDASE SUBUNIT IV ISOFORM 1, COX IV-1 |
| 24 | X (P) | CYTOCHROME C OXIDASE SUBUNIT 5A, MITOCHONDRIAL | polymer | 109 | 12453.1 | 1 | UniProt (P00426) Pfam (PF02284) | BOS TAURUS (CATTLE) | CYTOCHROME C OXIDASE POLYPEPTIDE VA |
| 25 | Y (Q) | CYTOCHROME C OXIDASE SUBUNIT 5B, MITOCHONDRIAL | polymer | 98 | 10684.0 | 1 | UniProt (P00428) Pfam (PF01215) | BOS TAURUS (CATTLE) | CYTOCHROME C OXIDASE POLYPEPTIDE VIA, CYTOCHROME C OXIDASE POLYPEPTIDE VB |
| 26 | Z (R) | CYTOCHROME C OXIDASE POLYPEPTIDE VIA, CYTOCHROME C OXIDASE POLYPEPTIDE VB | polymer | 84 | 9452.7 | 1 | UniProt (P07471) Pfam (PF02046) | BOS TAURUS (CATTLE) | CYTOCHROME C OXIDASE POLYPEPTIDE VIA-HEART, CYTOCHROME C OXIDASE POLYPEPTIDE VIB, COXVIAH |
| 27 | AA (S) | CYTOCHROME C OXIDASE SUBUNIT 6B1 | polymer | 85 | 10039.2 | 1 | UniProt (P00429) Pfam (PF02297) | BOS TAURUS (CATTLE) | CYTOCHROME C OXIDASE POLYPEPTIDE VII, CYTOCHROME C OXIDASE SUBUNIT AED, CYTOCHROME C OXIDASE SUBUNIT VIB ISOFORM 1, COX VIB-1 |
| 28 | BA (T) | CYTOCHROME C OXIDASE SUBUNIT 6C | polymer | 73 | 8495.0 | 1 | UniProt (P04038) Pfam (PF02937) | BOS TAURUS (CATTLE) | CYTOCHROME C OXIDASE POLYPEPTIDE VIC, CYTOCHROME C OXIDASE SUBUNIT STA |
| 29 | CA (U) | CYTOCHROME C OXIDASE SUBUNIT 7A1, MITOCHONDRIAL | polymer | 59 | 6682.7 | 1 | UniProt (P07470) Pfam (PF02238) | BOS TAURUS (CATTLE) | CYTOCHROME C OXIDASE SUBUNIT VIIIC, CYTOCHROME C OXIDASE SUBUNIT VIIA-HEART, CYTOCHROME C OXIDASE SUBUNIT VIIA-MUSCLE, VIIIC, CYTOCHROME C OXIDASE SUBUNIT VIIA-H, CYTOCHROME C OXIDASE SUBUNIT VIIA-M |
| 30 | DA (V) | CYTOCHROME C OXIDASE SUBUNIT 7B, MITOCHONDRIAL | polymer | 56 | 6365.2 | 1 | UniProt (P13183) Pfam (PF05392) | BOS TAURUS (CATTLE) | CYTOCHROME C OXIDASE POLYPEPTIDE VIIB, IHQ |
| 31 | EA (W) | CYTOCHROME C OXIDASE SUBUNIT 7C, MITOCHONDRIAL | polymer | 47 | 5449.4 | 1 | UniProt (P00430) Pfam (PF02935) | BOS TAURUS (CATTLE) | CYTOCHROME C OXIDASE POLYPEPTIDE VIIIA, CYTOCHROME C OXIDASE POLYPEPTIDE VIIC |
| 32 | FA (X) | CYTOCHROME C OXIDASE SUBUNIT 8B, MITOCHONDRIAL | polymer | 46 | 4967.8 | 1 | UniProt (P10175) Pfam (PF02285) | BOS TAURUS (CATTLE) | CYTOCHROME C OXIDASE POLYPEPTIDE VIII-HEART, CYTOCHROME C OXIDASE SUBUNIT 8-1, CYTOCHROME C OXIDASE SUBUNIT 8H, IX, VIIIB |
| 33 | GA (Y) | CYTOCHROME C | polymer | 104 | 11595.4 | 1 | UniProt (P62894) Pfam (PF00034) | BOS TAURUS (CATTLE) | |
| 34 | SA (m) | NADH\: UBIQUINONE OXIDOREDUCTASE, MEMBRANE SUBUNIT L, | polymer | 474 | 40357.7 | 1 | ESCHERICHIA COLI | ||
| 35 | TA (n) | NADH\: UBIQUINONE OXIDOREDUCTASE, MEMBRANE SUBUNIT M, | polymer | 391 | 33293.9 | 1 | ESCHERICHIA COLI | SUBUNIT OF NADH\: UBIQUINONE OXIDOREDUCTASE I | |
| 36 | UA (o) | NADH-QUINONE OXIDOREDUCTASE SUBUNIT N | polymer | 378 | 32187.6 | 1 | ESCHERICHIA COLI | NADH DEHYDROGENASE I SUBUNIT N, NDH-1 SUBUNIT N | |
| 37 | VA (p) | NADH-QUINONE OXIDOREDUCTASE SUBUNIT K | polymer | 281 | 23932.4 | 1 | ESCHERICHIA COLI | NADH DEHYDROGENASE I SUBUNIT K, NDH-1 SUBUNIT K | |
| 38 | CB, DB, EB, KB, MB... (3, 6, 8, 1) | IRON/SULFUR CLUSTER | non-polymer | 351.6 | 7 | Chemie (SF4) | |||
| 39 | XA (1) | FLAVIN MONONUCLEOTIDE | non-polymer | 456.3 | 1 | Chemie (FMN) | |||
| 40 | YA (1) | 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE | non-polymer | 665.4 | 1 | Chemie (NAI) | |||
| 41 | BB, GB, HB, IB, JB... (2, 3, 4, 5, 1...) | MAGNESIUM ION | non-polymer | 24.3 | 7 | Chemie (MG) | |||
| 42 | AB, FB, KC, TB (2, 3, e, E) | FE2/S2 (INORGANIC) CLUSTER | non-polymer | 175.8 | 4 | Chemie (FES) | |||
| 43 | LB (7) | CALCIUM ION | non-polymer | 40.1 | 1 | Chemie (CA) | |||
| 44 | DC, EC, FC, OB, PB (Y, c, C) | PROTOPORPHYRIN IX CONTAINING FE | non-polymer | 616.5 | 5 | Chemie (HEM) | |||
| 45 | GC, QB (c, C) | STIGMATELLIN A | non-polymer | 514.6 | 2 | Chemie (SMA) | |||
| 46 | HC, RB (c, C) | UBIQUINONE-1 | non-polymer | 250.3 | 2 | Chemie (UQ1) | |||
| 47 | IC, SB (d, D) | HEME C | non-polymer | 618.5 | 2 | Chemie (HEC) | |||
| 48 | JC, LC, UB, VB (d, g, G) | CARDIOLIPIN | non-polymer | 1464.0 | 4 | Chemie (CDL) | |||
| 49 | WB, XB (L) | HEME-A | non-polymer | 852.8 | 2 | Chemie (HEA) | |||
| 50 | AC, BC, YB (M, L) | COPPER (II) ION | non-polymer | 63.5 | 3 | Chemie (CU) | |||
| 51 | CC (Q) | ZINC ION | non-polymer | 65.4 | 1 | Chemie (ZN) | |||
| 52 | AD, BD, CD, DD, ED... (d, e, f, g, h...) | water | water | 18.0 | 1598 | Chemie (HOH) |
Sequence modifications
F, f: 1 - 110 (UniProt: P00129)
| PDB | External Database | Details |
|---|---|---|
| Asp 56 | Asn 57 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 48 |
| Total formula weight | 1107060.4 | |
| Non-Polymers* | Number of molecules | 42 |
| Total formula weight | 18164.0 | |
| All* | Total formula weight | 1125224.3 |
