1NTM: Mitochondrial Cytochrome bc1 Complex
Crystal Structure of Mitochondrial Cytochrome bc1 Complex at 2.4 Angstrom. Determined by X-ray diffraction at 2.4 Å resolution. Released 7 Oct 2003.
- Method
- X-ray diffraction
- Resolution
- 2.4 Å
- Organism
- Bos taurus
- Chains
- 11
- Atoms
- 17,049
- Mol. weight
- 241.22 kDa
- Ligands
- HEM, FES
- Released
- 7 Oct 2003
Explore 1NTM in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
1NTM contains 113 α-helices and 55 β-strands across 11 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 24 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-9 | 6 | |
| α-helix | 12-14 | 3 | |
| β-strand | 15-18 | 4 | 1 |
| β-strand | 24-29 | 6 | 1 |
| β-strand | 34-41 | 8 | 1 |
| α-helix | 55-63 | 9 | |
| β-strand | 67 | 1 | 2 |
| α-helix | 74-82 | 9 | |
| β-strand | 85-90 | 6 | 1 |
| β-strand | 95-102 | 8 | 1 |
| α-helix | 103-105 | 3 | |
| α-helix | 106-118 | 13 | |
| β-strand | 120 | 1 | 2 |
| α-helix | 124-141 | 18 | |
| α-helix | 145-157 | 13 | |
| α-helix | 162-164 | 3 | |
| α-helix | 171-176 | 6 | |
| α-helix | 179-189 | 11 | |
| α-helix | 192-194 | 3 | |
| β-strand | 195-201 | 7 | 1 |
| α-helix | 205-216 | 12 | |
| α-helix | 229-233 | 5 | |
| β-strand | 239-245 | 7 | 3 |
| β-strand | 251-258 | 8 | 3 |
| α-helix | 267-277 | 11 | |
| β-strand | 279-281 | 3 | 3 |
| α-helix | 293-301 | 9 | |
| β-strand | 306-314 | 9 | 3 |
| β-strand | 317-326 | 10 | 3 |
| α-helix | 328-330 | 3 | |
| α-helix | 331-348 | 18 | |
| α-helix | 351-368 | 18 | |
| α-helix | 372-385 | 14 | |
| α-helix | 392-401 | 10 | |
| α-helix | 404-414 | 11 | |
| β-strand | 421-426 | 6 | 3 |
| α-helix | 432-433 | 2 | |
| α-helix | 434-439 | 6 | |
Chain B: 22 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-21 | 4 | |
| β-strand | 25-28 | 4 | 4 |
| β-strand | 34-38 | 5 | 4 |
| β-strand | 44-51 | 8 | 4 |
| α-helix | 55-57 | 3 | |
| α-helix | 65-70 | 6 | |
| β-strand | 77 | 1 | 5 |
| β-strand | 80 | 1 | 5 |
| α-helix | 82-91 | 10 | |
| β-strand | 95-100 | 6 | 4 |
| β-strand | 105-112 | 8 | 4 |
| α-helix | 113-115 | 3 | |
| α-helix | 116-128 | 13 | |
| β-strand | 130 | 1 | 5 |
| α-helix | 134-140 | 7 | |
| α-helix | 142-151 | 10 | |
| α-helix | 155-167 | 13 | |
| β-strand | 168 | 1 | 6 |
| α-helix | 171-173 | 3 | |
| α-helix | 180-182 | 3 | |
| α-helix | 188-198 | 11 | |
| α-helix | 201-203 | 3 | |
| β-strand | 204-209 | 6 | 4 |
| α-helix | 213-223 | 11 | |
| β-strand | 239 | 1 | 6 |
| β-strand | 242-247 | 6 | 7 |
| β-strand | 252-260 | 9 | 7 |
| α-helix | 267-279 | 13 | |
| β-strand | 285 | 1 | 1 |
| α-helix | 294-302 | 9 | |
| β-strand | 307-316 | 10 | 7 |
| β-strand | 319-329 | 11 | 7 |
| α-helix | 333-348 | 16 | |
| α-helix | 355-371 | 17 | |
| α-helix | 375-389 | 15 | |
| α-helix | 395-403 | 9 | |
| α-helix | 407-419 | 13 | |
| α-helix | 421 | 1 | |
| β-strand | 422-428 | 7 | 7 |
Chain C: 24 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-7 | 4 | |
| α-helix | 11-18 | 8 | |
| β-strand | 22-24 | 3 | 8 |
| α-helix | 29-31 | 3 | |
| α-helix | 33-52 | 20 | |
| α-helix | 59-71 | 13 | |
| α-helix | 76-104 | 29 | |
| α-helix | 106-108 | 3 | |
| α-helix | 110-132 | 23 | |
| β-strand | 136 | 1 | 9 |
| α-helix | 137-148 | 12 | |
| α-helix | 149-152 | 4 | |
| α-helix | 157-165 | 9 | |
| α-helix | 173-201 | 29 | |
| α-helix | 214-216 | 3 | |
| β-strand | 217-219 | 3 | 8 |
| α-helix | 220-245 | 26 | |
| α-helix | 253-256 | 4 | |
| β-strand | 258 | 1 | 9 |
| α-helix | 272-274 | 3 | |
| α-helix | 275-282 | 8 | |
| α-helix | 287-298 | 12 | |
| α-helix | 299-302 | 4 | |
| α-helix | 304-307 | 4 | |
| α-helix | 319-339 | 21 | |
| α-helix | 345-360 | 16 | |
| α-helix | 361-365 | 5 | |
| α-helix | 366-377 | 12 | |
Chain D: 11 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 20-22 | 3 | |
| α-helix | 24-35 | 12 | |
| α-helix | 37-39 | 3 | |
| β-strand | 47 | 1 | 10 |
| α-helix | 50-54 | 5 | |
| α-helix | 58-65 | 8 | |
| α-helix | 72-74 | 3 | |
| β-strand | 90 | 1 | 10 |
| α-helix | 99-104 | 6 | |
| α-helix | 116-119 | 4 | |
| α-helix | 124-132 | 9 | |
| β-strand | 149 | 1 | 11 |
| β-strand | 157 | 1 | 11 |
| α-helix | 179-194 | 16 | |
| α-helix | 198-232 | 35 | |
| β-strand | 234-237 | 4 | 3 |
Chain E: 10 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-4 | 3 | |
| α-helix | 7-9 | 3 | |
| β-strand | 14 | 1 | 12 |
| α-helix | 16-18 | 3 | |
| α-helix | 26-60 | 35 | |
| β-strand | 74-77 | 4 | 13 |
| α-helix | 78-80 | 3 | |
| β-strand | 86-91 | 6 | 14 |
| β-strand | 94-100 | 7 | 14 |
| α-helix | 103-110 | 8 | |
| α-helix | 114-116 | 3 | |
| α-helix | 123-125 | 3 | |
| β-strand | 132-136 | 5 | 14 |
| α-helix | 146 | 1 | |
| β-strand | 147-148 | 2 | 15 |
| β-strand | 154-158 | 5 | 15 |
| β-strand | 163-166 | 4 | 15 |
| β-strand | 171-173 | 3 | 15 |
| α-helix | 179-181 | 3 | |
| β-strand | 185-187 | 3 | 13 |
| β-strand | 192-195 | 4 | 13 |
Chain F: 8 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-24 | 17 | |
| α-helix | 26-29 | 4 | |
| α-helix | 33-36 | 4 | |
| α-helix | 41-49 | 9 | |
| α-helix | 52-71 | 20 | |
| α-helix | 77-79 | 3 | |
| α-helix | 81-82 | 2 | |
| α-helix | 91-107 | 17 | |
Chain G: 1 helix, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 11-18 | 8 | 3 |
| β-strand | 23 | 1 | 12 |
| α-helix | 33-69 | 37 | |
Chain H: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-26 | 11 | |
| α-helix | 28-45 | 18 | |
| α-helix | 56-72 | 17 | |
3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ubiquinol-cytochrome C reductase complex core protein I, mitochondrial | A | protein | 446 | Bos taurus | P31800 (AlphaFold model) |
| Ubiquinol-cytochrome C reductase complex core protein 2, mitochondrial | B | protein | 439 | Bos taurus | P23004 (AlphaFold model) |
| Cytochrome b | C | protein | 379 | Bos taurus | P00157 (AlphaFold model) |
| cytochrome c1 | D | protein | 241 | Bos taurus | P00125 (AlphaFold model) |
| UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, mitochondrial | E | protein | 196 | Bos taurus | P13272 |
| Ubiquinol-cytochrome C reductase complex 14 kDa protein | F | protein | 110 | Bos taurus | P00129 |
| Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C | G | protein | 81 | Bos taurus | P13271 |
| Ubiquinol-cytochrome C reductase complex 11 kDa protein | H | protein | 78 | Bos taurus | P00126 |
| Ubiquinol-cytochrome C reductase 8 kDa protein | I | protein | 57 | Bos taurus | P13272 |
| Ubiquinol-cytochrome C reductase complex 7.2 kDa protein | J | protein | 62 | Bos taurus | P00130 |
| Ubiquinol-cytochrome C reductase complex 6.4 kDa protein | K | protein | 56 | Bos taurus | P07552 |
Sequence of entity 1 (A), FASTA
>1NTM_1 Ubiquinol-cytochrome C reductase complex core protein I, mitochondrial (chains A)
TATYAQALQSVPETQVSQLDNGLRVASEQSSQPTCTVGVWIDAGSRYESEKNNGAGYFVE
HLAFKGTKNRPGNALEKEVESMGAHLNAYSTREHTAYYIKALSKDLPKAVELLADIVQNC
SLEDSQIEKERDVILQELQENDTSMRDVVFNYLHATAFQGTPLAQSVEGPSENVRKLSRA
DLTEYLSRHYKAPRMVLAAAGGLEHRQLLDLAQKHFSGLSGTYDEDAVPTLSPCRFTGSQ
ICHREDGLPLAHVAIAVEGPGWAHPDNVALQVANAIIGHYDCTYGGGAHLSSPLASIAAT
NKLCQSFQTFNICYADTGLLGAHFVCDHMSIDDMMFVLQGQWMRLCTSATESEVLRGKNL
LRNALVSHLDGTTPVCEDIGRSLLTYGRRIPLAEWESRIAEVDARVVREVCSKYFYDQCP
AVAGFGPIEQLPDYNRIRSGMFWLRF
Sequence of entity 2 (B), FASTA
>1NTM_2 Ubiquinol-cytochrome C reductase complex core protein 2, mitochondrial (chains B)
SLKVAPKVKATEAPAGVPPHPQDLEFTRLPNGLVIASLENYAPASRIGLFIKAGSRYENS
NNLGTSHLLRLASSLTTKGASSFKITRGIEAVGGKLSVTSTRENMAYTVECLRDDVDILM
EFLLNVTTAPEFRRWEVAALQPQLRIDKAVALQNPQAHVIENLHAAAYRNALANSLYCPD
YRIGKVTPVELHDYVQNHFTSARMALIGLGVSHPVLKQVAEQFLNIRGGLGLSGAKAKYH
GGEIREQNGDSLVHAALVAESAAIGSAEANAFSVLQHVLGAGPHVKRGSNATSSLYQAVA
KGVHQPFDVSAFNASYSDSGLFGFYTISQAASAGDVIKAAYNQVKTIAQGNLSNPDVQAA
KNKLKAGYLMSVESSEGFLDEVGSQALAAGSYTPPSTVLQQIDAVADADVINAAKKFVSG
RKSMAASGNLGHTPFIDEL
Sequence of entity 3 (C), FASTA
>1NTM_3 Cytochrome b (chains C)
MTNIRKSHPLMKIVNNAFIDLPAPSNISSWWNFGSLLGICLILQILTGLFLAMHYTSDTT
TAFSSVTHICRDVNYGWIIRYMHANGASMFFICLYMHVGRGLYYGSYTFLETWNIGVILL
LTVMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTNLVEWIWGGFSVDKATLTRFFA
FHFILPFIIMAIAMVHLLFLHETGSNNPTGISSDVDKIPFHPYYTIKDILGALLLILALM
LLVLFAPDLLGDPDNYTPANPLNTPPHIKPEWYFLFAYAILRSIPNKLGGVLALAFSILI
LALIPLLHTSKQRSMMFRPLSQCLFWALVADLLTLTWIGGQPVEHPYITIGQLASVLYFL
LILVLMPTAGTIENKLLKW
Sequence of entity 4 (D), FASTA
>1NTM_4 cytochrome c1 (chains D)
SDLELHPPSYPWSHRGLLSSLDHTSIRRGFQVYKQVCSSCHSMDYVAYRHLVGVCYTEDE
AKALAEEVEVQDGPNEDGEMFMRPGKLSDYFPKPYPNPEAARAANNGALPPDLSYIVRAR
HGGEDYVFSLLTGYCEPPTGVSLREGLYFNPYFPGQAIGMAPPIYNEVLEFDDGTPATMS
QVAKDVCTFLRWAAEPEHDHRKRMGLKMLLMMGLLLPLVYAMKRHKWSVLKSRKLAYRPP
K
Sequence of entity 5 (E), FASTA
>1NTM_5 UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, mitochondrial (chains E)
SHTDIKVPDFSDYRRPEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVS
SMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDP
QHDLERVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNL
EVPSYEFTSDDMVIVG
Sequence of entity 6 (F), FASTA
>1NTM_6 Ubiquinol-cytochrome C reductase complex 14 kDa protein (chains F)
AGRPAVSASSRWLEGIRKWYYNAAGFNKLGLMRDDTIHENDDVKEAIRRLPENLYDDRVF
RIKRALDLSMRQQILPKEQWTKYEEDKSYLEPYLKEVIRERKEREEWAKK
Sequence of entity 7 (G), FASTA
>1NTM_7 Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C (chains G)
GRQFGHLTRVRHVITYSLSPFEQRAFPHYFSKGIPNVLRRTRACILRVAPPFVAFYLVYT
WGTQEFEKSKRKNPAAYENDR
Sequence of entity 8 (H), FASTA
>1NTM_8 Ubiquinol-cytochrome C reductase complex 11 kDa protein (chains H)
GDPKEEEEEEEELVDPLTTVREQCEQLEKCVKARERLELCDERVSSRSQTEEDCTEELLD
FLHARDHCVAHKLFNSLK
Sequence of entity 9 (I), FASTA
>1NTM_9 Ubiquinol-cytochrome C reductase 8 kDa protein (chains I)
MLSVAARSGPFAPVLSATSRGVAGALRPLVQAAVPATSESPVLDLKRSVLCRESLRG
Sequence of entity 10 (J), FASTA
>1NTM_10 Ubiquinol-cytochrome C reductase complex 7.2 kDa protein (chains J)
VAPTLTARLYSLLFRRTSTFALTIVVGALFFERAFDQGADAIYEHINEGKLWKHIKHKYE
NK
Sequence of entity 11 (K), FASTA
>1NTM_11 Ubiquinol-cytochrome C reductase complex 6.4 kDa protein (chains K)
MLTRFLGPRYRQLARNWVPTAQLWGAVGAVGLVWATDWRLILDWVPYINGKFKKDD
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| HEM | Protoporphyrin IX containing FE | C34 H32 Fe N4 O4 | 3 |
| FES | FE2/S2 (inorganic) cluster | Fe2 S2 | 1 |
Primary citation
Structural basis for the quinone reduction in the bc(1) complex: a comparative analysis of crystal structures of mitochondrial cytochrome bc(1) with bound substrate and inhibitors at the Q(i) site. Gao, X., Wen, X., Esser, L. et al. Biochemistry (2003) 42:9067-9080. DOI 10.1021/bi0341814 · PubMed
Other PDB entries of the same protein (UniProt P31800 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1PP9 2.1 Å, Bovine cytochrome bc1 complex with stigmatellin bound
- 1PPJ 2.1 Å, Bovine cytochrome bc1 complex with stigmatellin and antimycin
- 2A06 2.1 Å, Bovine cytochrome bc1 complex with stigmatellin bound
- 9W2X 2.2 Å, Cryo-EM structure of complex III on the bovine heart submitochondrial particles, III-1
- 2FYU 2.26 Å, Crystal structure of bovine heart mitochondrial bc1 with jg144 inhibitor
- 1L0L 2.35 Å, structure of bovine mitochondrial cytochrome bc1 complex with a bound fungicide famoxadone
- 9W2Y 2.4 Å, Cryo-EM structure of complex III on the bovine heart submitochondrial particles, III-2
- 1L0N 2.6 Å, native structure of bovine mitochondrial cytochrome bc1 complex
- 1NTK 2.6 Å, Crystal Structure of Mitochondrial Cytochrome bc1 in Complex with Antimycin A1
- 1NTZ 2.6 Å, Crystal Structure of Mitochondrial Cytochrome bc1 Complex Bound with Ubiquinone
- 1SQX 2.6 Å, Crystal Structure Analysis of Bovine Bc1 with Stigmatellin A
- 5KLV 2.65 Å, Structure of bos taurus cytochrome bc1 with fenamidone inhibited
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