5KLV: Cytochrome b-c1 complex subunit 1, mitochondrial
Structure of bos taurus cytochrome bc1 with fenamidone inhibited. Determined by X-ray diffraction at 2.65 Å resolution. Released 12 Oct 2016.
- Method
- X-ray diffraction
- Resolution
- 2.65 Å
- Organism
- Bos taurus
- Chains
- 11
- Atoms
- 16,913
- Mol. weight
- 251.06 kDa
- Ligands
- PX4, FES, PEF, HEC
- Released
- 12 Oct 2016
Explore 5KLV in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5KLV contains 119 α-helices and 54 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: 26 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-9 | 6 | |
| α-helix | 12-13 | 2 | |
| β-strand | 15-18 | 4 | 1 |
| β-strand | 24-29 | 6 | 1 |
| β-strand | 34-41 | 8 | 1 |
| α-helix | 45-47 | 3 | |
| α-helix | 55-63 | 9 | |
| α-helix | 74-81 | 8 | |
| β-strand | 85-90 | 6 | 1 |
| β-strand | 95-102 | 8 | 1 |
| α-helix | 103-105 | 3 | |
| α-helix | 106-117 | 12 | |
| 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 | 205-215 | 11 | |
| α-helix | 231-233 | 3 | |
| β-strand | 239-245 | 7 | 2 |
| β-strand | 251-258 | 8 | 2 |
| α-helix | 266-277 | 12 | |
| β-strand | 279-281 | 3 | 2 |
| α-helix | 287-289 | 3 | |
| α-helix | 293-301 | 9 | |
| β-strand | 306-314 | 9 | 2 |
| β-strand | 317-326 | 10 | 2 |
| α-helix | 331-348 | 18 | |
| α-helix | 351-368 | 18 | |
| α-helix | 372-385 | 14 | |
| α-helix | 392-400 | 9 | |
| α-helix | 404-414 | 11 | |
| α-helix | 419-420 | 2 | |
| β-strand | 421-426 | 6 | 2 |
| α-helix | 432-433 | 2 | |
| α-helix | 434-439 | 6 | |
Chain B: 24 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 21-24 | 4 | |
| β-strand | 25-28 | 4 | 3 |
| β-strand | 34-38 | 5 | 3 |
| β-strand | 44-51 | 8 | 3 |
| α-helix | 55-57 | 3 | |
| α-helix | 65-70 | 6 | |
| β-strand | 77 | 1 | 4 |
| α-helix | 82-91 | 10 | |
| β-strand | 95-100 | 6 | 3 |
| β-strand | 105-112 | 8 | 3 |
| α-helix | 113-115 | 3 | |
| α-helix | 116-128 | 13 | |
| β-strand | 130 | 1 | 4 |
| α-helix | 134-151 | 18 | |
| α-helix | 155-167 | 13 | |
| β-strand | 168 | 1 | 5 |
| 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 | 3 |
| α-helix | 213-223 | 11 | |
| β-strand | 239 | 1 | 5 |
| β-strand | 242-247 | 6 | 6 |
| β-strand | 252-260 | 9 | 6 |
| α-helix | 267-279 | 13 | |
| β-strand | 285 | 1 | 1 |
| α-helix | 294-302 | 9 | |
| β-strand | 307-316 | 10 | 6 |
| β-strand | 319-329 | 11 | 6 |
| α-helix | 330-332 | 3 | |
| α-helix | 333-348 | 16 | |
| α-helix | 354-370 | 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 | 6 |
| α-helix | 430-432 | 3 | |
| α-helix | 436-438 | 3 | |
Chain C: 24 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-6 | 3 | |
| α-helix | 9-14 | 6 | |
| α-helix | 15-19 | 5 | |
| β-strand | 22-24 | 3 | 7 |
| α-helix | 29-31 | 3 | |
| α-helix | 33-52 | 20 | |
| α-helix | 59-71 | 13 | |
| α-helix | 76-103 | 28 | |
| α-helix | 106-108 | 3 | |
| α-helix | 110-131 | 22 | |
| β-strand | 136 | 1 | 8 |
| α-helix | 137-147 | 11 | |
| α-helix | 148-152 | 5 | |
| α-helix | 157-165 | 9 | |
| α-helix | 172-201 | 30 | |
| β-strand | 217-219 | 3 | 7 |
| α-helix | 220-245 | 26 | |
| α-helix | 253-256 | 4 | |
| β-strand | 258 | 1 | 8 |
| α-helix | 272-282 | 11 | |
| α-helix | 287-299 | 13 | |
| α-helix | 300-303 | 4 | |
| α-helix | 305-307 | 3 | |
| α-helix | 315-317 | 3 | |
| α-helix | 319-339 | 21 | |
| α-helix | 347-360 | 14 | |
| α-helix | 361-365 | 5 | |
| α-helix | 366-376 | 11 | |
Chain D: 15 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-8 | 3 | |
| α-helix | 19-21 | 3 | |
| α-helix | 23-32 | 10 | |
| α-helix | 33-37 | 5 | |
| β-strand | 47 | 1 | 9 |
| α-helix | 48-51 | 4 | |
| β-strand | 52 | 1 | 10 |
| β-strand | 56 | 1 | 10 |
| α-helix | 58-65 | 8 | |
| β-strand | 69-72 | 4 | 11 |
| β-strand | 81-84 | 4 | 11 |
| β-strand | 90 | 1 | 9 |
| α-helix | 91-93 | 3 | |
| α-helix | 98-104 | 7 | |
| α-helix | 110-112 | 3 | |
| α-helix | 123-131 | 9 | |
| α-helix | 136-138 | 3 | |
| α-helix | 143-144 | 2 | |
| β-strand | 148-149 | 2 | 12 |
| β-strand | 157-158 | 2 | 12 |
| α-helix | 161-162 | 2 | |
| α-helix | 179-194 | 16 | |
| α-helix | 198-231 | 34 | |
| β-strand | 234-237 | 4 | 2 |
Chain E: 8 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-9 | 3 | |
| α-helix | 26-28 | 3 | |
| α-helix | 29-62 | 34 | |
| β-strand | 74-75 | 2 | 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 | 123-126 | 4 | |
| β-strand | 132-134 | 3 | 14 |
| α-helix | 144-146 | 3 | |
| β-strand | 147-148 | 2 | 15 |
| β-strand | 156-158 | 3 | 15 |
| β-strand | 163-165 | 3 | 15 |
| β-strand | 171-173 | 3 | 15 |
| α-helix | 179-181 | 3 | |
| β-strand | 185-186 | 2 | 13 |
| β-strand | 194-195 | 2 | 13 |
Chain F: 9 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-24 | 16 | |
| α-helix | 26-29 | 4 | |
| α-helix | 33-36 | 4 | |
| α-helix | 41-48 | 8 | |
| α-helix | 52-71 | 20 | |
| α-helix | 77-79 | 3 | |
| α-helix | 81-82 | 2 | |
| α-helix | 83-85 | 3 | |
| α-helix | 91-108 | 18 | |
Chain G: 1 helix, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 11-18 | 8 | 2 |
| α-helix | 33-69 | 37 | |
Chain H: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-22 | 7 | |
| α-helix | 28-43 | 16 | |
| α-helix | 44-46 | 3 | |
| α-helix | 56-72 | 17 | |
| α-helix | 73-76 | 4 | |
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 |
|---|
| Cytochrome b-c1 complex subunit 1, mitochondrial | A | protein | 446 | Bos taurus | P31800 (AlphaFold model) |
| Cytochrome b-c1 complex subunit 2, mitochondrial | B | protein | 439 | Bos taurus | P23004 (AlphaFold model) |
| Cytochrome b | C | protein | 379 | Bos taurus | P00157 (AlphaFold model) |
| Cytochrome c1, heme protein, mitochondrial | D | protein | 241 | Bos taurus | P00125 (AlphaFold model) |
| Cytochrome b-c1 complex subunit Rieske, mitochondrial | E | protein | 196 | Bos taurus | P13272 |
| Cytochrome b-c1 complex subunit 7 | F | protein | 110 | Bos taurus | P00129 |
| Cytochrome b-c1 complex subunit 8 | G | protein | 80 | Bos taurus | P13271 |
| Cytochrome b-c1 complex subunit 6, mitochondrial | H | protein | 78 | Bos taurus | P00126 |
| Cytochrome b-c1 complex subunit Rieske, mitochondrial | I | protein | 78 | Bos taurus | P13272 |
| Cytochrome b-c1 complex subunit 9 | J | protein | 63 | Bos taurus | P00130 |
| Cytochrome b-c1 complex subunit 10 | K | protein | 55 | Bos taurus | P07552 |
Sequence of entity 1 (A), FASTA
>5KLV_1 Cytochrome b-c1 complex subunit 1, mitochondrial (chains A)
TATYAQALQSVPETQVSQLDNGLRVASEQSSQPTCTVGVWIDAGSRYESEKNNGAGYFVE
HLAFKGTKNRPGNALEKEVESMGAHLNAYSTREHTAYYIKALSKDLPKAVELLADIVQNC
SLEDSQIEKERDVILQELQENDTSMRDVVFNYLHATAFQGTPLAQSVEGPSENVRKLSRA
DLTEYLSRHYKAPRMVLAAAGGLEHRQLLDLAQKHFSGLSGTYDEDAVPTLSPCRFTGSQ
ICHREDGLPLAHVAIAVEGPGWAHPDNVALQVANAIIGHYDCTYGGGAHLSSPLASIAAT
NKLCQSFQTFNICYADTGLLGAHFVCDHMSIDDMMFVLQGQWMRLCTSATESEVLRGKNL
LRNALVSHLDGTTPVCEDIGRSLLTYGRRIPLAEWESRIAEVDARVVREVCSKYFYDQCP
AVAGFGPIEQLPDYNRIRSGMFWLRF
Sequence of entity 2 (B), FASTA
>5KLV_2 Cytochrome b-c1 complex subunit 2, mitochondrial (chains B)
SLKVAPKVKATEAPAGVPPHPQDLEFTRLPNGLVIASLENYAPASRIGLFIKAGSRYENS
NNLGTSHLLRLASSLTTKGASSFKITRGIEAVGGKLSVTSTRENMAYTVECLRDDVDILM
EFLLNVTTAPEFRRWEVAALQPQLRIDKAVALQNPQAHVIENLHAAAYRNALANSLYCPD
YRIGKVTPVELHDYVQNHFTSARMALIGLGVSHPVLKQVAEQFLNIRGGLGLSGAKAKYH
GGEIREQNGDSLVHAALVAESAAIGSAEANAFSVLQHVLGAGPHVKRGSNATSSLYQAVA
KGVHQPFDVSAFNASYSDSGLFGFYTISQAASAGDVIKAAYNQVKTIAQGNLSNPDVQAA
KNKLKAGYLMSVESSEGFLDEVGSQALAAGSYTPPSTVLQQIDAVADADVINAAKKFVSG
RKSMAASGNLGHTPFIDEL
Sequence of entity 3 (C), FASTA
>5KLV_3 Cytochrome b (chains C)
MTNIRKSHPLMKIVNNAFIDLPAPSNISSWWNFGSLLGICLILQILTGLFLAMHYTSDTT
TAFSSVTHICRDVNYGWIIRYMHANGASMFFICLYMHVGRGLYYGSYTFLETWNIGVILL
LTVMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTNLVEWIWGGFSVDKATLTRFFA
FHFILPFIIMAIAMVHLLFLHETGSNNPTGISSDVDKIPFHPYYTIKDILGALLLILALM
LLVLFAPDLLGDPDNYTPANPLNTPPHIKPEWYFLFAYAILRSIPNKLGGVLALAFSILI
LALIPLLHTSKQRSMMFRPLSQCLFWALVADLLTLTWIGGQPVEHPYITIGQLASVLYFL
LILVLMPTAGTIENKLLKW
Sequence of entity 4 (D), FASTA
>5KLV_4 Cytochrome c1, heme protein, mitochondrial (chains D)
SDLELHPPSYPWSHRGLLSSLDHTSIRRGFQVYKQVCSSCHSMDYVAYRHLVGVCYTEDE
AKALAEEVEVQDGPNEDGEMFMRPGKLSDYFPKPYPNPEAARAANNGALPPDLSYIVRAR
HGGEDYVFSLLTGYCEPPTGVSLREGLYFNPYFPGQAIGMAPPIYNEVLEFDDGTPATMS
QVAKDVCTFLRWAAEPEHDHRKRMGLKMLLMMGLLLPLVYAMKRHKWSVLKSRKLAYRPP
K
Sequence of entity 5 (E), FASTA
>5KLV_5 Cytochrome b-c1 complex subunit Rieske, mitochondrial (chains E)
SHTDIKVPDFSDYRRPEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVS
SMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDP
QHDLERVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNL
EVPSYEFTSDDMVIVG
Sequence of entity 6 (F), FASTA
>5KLV_6 Cytochrome b-c1 complex subunit 7 (chains F)
AGRPAVSASSRWLEGIRKWYYNAAGFNKLGLMRDDTIHENDDVKEAIRRLPENLYNDRVF
RIKRALDLSMRQQILPKEQWTKYEEDKSYLEPYLKEVIRERKEREEWAKK
Sequence of entity 7 (G), FASTA
>5KLV_7 Cytochrome b-c1 complex subunit 8 (chains G)
GRQFGHLTRVRHVITYSLSPFEQRAFPHYFSKGIPNVLRRTRACILRVAPPFVAFYLVYT
WGTQEFEKSKRKNPAAYEND
Sequence of entity 8 (H), FASTA
>5KLV_8 Cytochrome b-c1 complex subunit 6, mitochondrial (chains H)
GDPKEEEEEEEELVDPLTTVREQCEQLEKCVKARERLELCDERVSSRSQTEEDCTEELLD
FLHARDHCVAHKLFNSLK
Sequence of entity 9 (I), FASTA
>5KLV_9 Cytochrome b-c1 complex subunit Rieske, mitochondrial (chains I)
MLSVAARSGPFAPVLSATSRGVAGALRPLVQAAVPATSESPVLDLKRSVLCRESLRGQAA
GRPLVASVSLNVPASVRY
Sequence of entity 10 (J), FASTA
>5KLV_10 Cytochrome b-c1 complex subunit 9 (chains J)
VAPTLTARLYSLLFRRTSTFALTIVVGALFFERAFDQGADAIYEHINEGKLWKHIKHKYE
NKE
Sequence of entity 11 (K), FASTA
>5KLV_11 Cytochrome b-c1 complex subunit 10 (chains K)
LTRFLGPRYRQLARNWVPTASLWGAVGAVGLVWATDWRLILDWVPYINGKFKKDD
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| PX4 | 1,2-dimyristoyl-sn-glycero-3-phosphocholine | C36 H73 N O8 P | 1 |
| FES | FE2/S2 (inorganic) cluster | Fe2 S2 | 1 |
| PEF | Di-palmitoyl-3-sn-phosphatidylethanolamine | C37 H74 N O8 P | 1 |
| HEC | Heme C | C34 H36 Fe N4 O4 | 1 |
| 8PE | (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl… | C37 H74 N O8 P | 1 |
| FNM | (5S)-5-methyl-2-(methylsulfanyl)-5-phenyl-3-(phenylamino)-3,5-dihydro-4H-imidaz… | C17 H17 N3 O S | 1 |
| HEM | Protoporphyrin IX containing FE | C34 H32 Fe N4 O4 | 2 |
| CDL | Cardiolipin | C81 H156 O17 P2 | 3 |
| 6PE | 1,2-dihexanoyl-sn-glycero-3-phosphoethanolamine | C17 H33 N O8 P | 2 |
Water and common crystallization additives (CL, GOL) are not listed.
Primary citation
Hydrogen Bonding to the Substrate Is Not Required for Rieske Iron-Sulfur Protein Docking to the Quinol Oxidation Site of Complex III. Esser, L., Zhou, F., Zhou, Y. et al. J Biol Chem (2016) 291:25019-25031. DOI 10.1074/jbc.M116.744391 · 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
- 1NTM 2.4 Å, Crystal Structure of Mitochondrial Cytochrome bc1 Complex at 2.4 Angstrom
- 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
Browse structure collections
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