5ZCQ: Cytochrome c oxidase subunit 1
Azide-bound cytochrome c oxidase structure determined using the crystals exposed to 10 mM azide solution for 2 days. Determined by X-ray diffraction at 1.65 Å resolution. Released 15 Aug 2018.
- Method
- X-ray diffraction
- Resolution
- 1.65 Å
- Organism
- Bos taurus
- Chains
- 26
- Atoms
- 33,657
- Mol. weight
- 448.5 kDa
- Ligands
- HEA, CU, MG, TGL
- Released
- 15 Aug 2018
Explore 5ZCQ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5ZCQ contains 197 α-helices and 66 β-strands across 26 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: 32 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-6 | 5 | |
| α-helix | 12-41 | 30 | |
| α-helix | 51-63 | 13 | |
| α-helix | 64-70 | 7 | |
| α-helix | 71 | 1 | |
| α-helix | 72-79 | 8 | |
| α-helix | 80-86 | 7 | |
| α-helix | 95-103 | 9 | |
| α-helix | 105-117 | 13 | |
| α-helix | 141-170 | 30 | |
| α-helix | 178-180 | 3 | |
| α-helix | 183-214 | 32 | |
| α-helix | 222-224 | 3 | |
| α-helix | 228-261 | 34 | |
| α-helix | 270-283 | 14 | |
| α-helix | 288-291 | 4 | |
| α-helix | 299-311 | 13 | |
| α-helix | 313-327 | 15 | |
| α-helix | 336-359 | 24 | |
| α-helix | 361-367 | 7 | |
| β-strand | 370 | 1 | 1 |
| α-helix | 371-377 | 7 | |
| α-helix | 378-383 | 6 | |
| α-helix | 384-401 | 18 | |
| β-strand | 403 | 1 | 2 |
| α-helix | 404-406 | 3 | |
| α-helix | 407-433 | 27 | |
| α-helix | 436 | 1 | |
| β-strand | 437 | 1 | 1 |
| α-helix | 445-447 | 3 | |
| α-helix | 448-478 | 31 | |
| β-strand | 481 | 1 | 2 |
| β-strand | 482 | 1 | 3 |
| α-helix | 488-490 | 3 | |
| α-helix | 492-494 | 3 | |
| α-helix | 500-501 | 2 | |
| α-helix | 508-509 | 2 | |
| β-strand | 510-511 | 2 | 4 |
Chain B: 10 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-12 | 4 | |
| α-helix | 15-45 | 31 | |
| α-helix | 59-86 | 28 | |
| β-strand | 95-102 | 8 | 5 |
| β-strand | 105-110 | 6 | 5 |
| β-strand | 116-120 | 5 | 5 |
| β-strand | 122 | 1 | 6 |
| α-helix | 123-124 | 2 | |
| α-helix | 125-127 | 3 | |
| α-helix | 128-129 | 2 | |
| α-helix | 132-133 | 2 | |
| β-strand | 138 | 1 | 6 |
| β-strand | 142-145 | 4 | 7 |
| β-strand | 150-156 | 7 | 5 |
| β-strand | 161-165 | 5 | 8 |
| α-helix | 166-168 | 3 | |
| β-strand | 170-174 | 5 | 8 |
| β-strand | 180-184 | 5 | 5 |
| β-strand | 190-194 | 5 | 7 |
| α-helix | 204-206 | 3 | |
| β-strand | 209-214 | 6 | 7 |
| α-helix | 216-225 | 10 | |
Chains C and P: 13 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-13 | 3 | |
| α-helix | 16-36 | 21 | |
| α-helix | 41-62 | 22 | |
| α-helix | 63-67 | 5 | |
| α-helix | 73-106 | 34 | |
| α-helix | 110-112 | 3 | |
| α-helix | 118 | 1 | |
| α-helix | 123-125 | 3 | |
| α-helix | 129-152 | 24 | |
| β-strand | 155 | 1 | 9 |
| α-helix | 156-183 | 28 | |
| α-helix | 191-223 | 33 | |
| α-helix | 233-252 | 20 | |
| α-helix | 253-259 | 7 | |
Chain D: 11 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-10 | 3 | |
| α-helix | 35-43 | 9 | |
| α-helix | 48-50 | 3 | |
| α-helix | 53-63 | 11 | |
| α-helix | 68-71 | 4 | |
| α-helix | 77-98 | 22 | |
| α-helix | 99-103 | 5 | |
| α-helix | 106-108 | 3 | |
| α-helix | 109-111 | 3 | |
| α-helix | 113-125 | 13 | |
| α-helix | 135-137 | 3 | |
| β-strand | 138-139 | 2 | 10 |
| β-strand | 144-145 | 2 | 10 |
Chain E: 7 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-20 | 13 | |
| α-helix | 26-36 | 11 | |
| β-strand | 41 | 1 | 11 |
| α-helix | 42-44 | 3 | |
| α-helix | 45-57 | 13 | |
| α-helix | 61-75 | 15 | |
| α-helix | 81-96 | 16 | |
| α-helix | 98-100 | 3 | |
Chains F and S: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5 | 1 | 9 |
| α-helix | 6-8 | 3 | |
| α-helix | 9-12 | 4 | |
| α-helix | 15-25 | 11 | |
| α-helix | 35-38 | 4 | |
| α-helix | 46 | 1 | |
| β-strand | 47-51 | 5 | 12 |
| β-strand | 55-60 | 6 | 4 |
| β-strand | 70-75 | 6 | 4 |
| β-strand | 80-81 | 2 | 12 |
| β-strand | 88-93 | 6 | 12 |
Chain G: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-19 | 7 | |
| α-helix | 20-24 | 5 | |
| α-helix | 25-37 | 13 | |
| α-helix | 45-47 | 3 | |
| β-strand | 78 | 1 | 13 |
| β-strand | 81 | 1 | 13 |
Chain H: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-16 | 3 | |
| β-strand | 24 | 1 | 5 |
| α-helix | 26-45 | 20 | |
| α-helix | 50-53 | 4 | |
| α-helix | 54-63 | 10 | |
| α-helix | 66-78 | 13 | |
15 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 c oxidase subunit 1 | A, N | protein | 514 | Bos taurus | P00396 (AlphaFold model) |
| Cytochrome c oxidase subunit 2 | B, O | protein | 227 | Bos taurus | P68530 (AlphaFold model) |
| Cytochrome c oxidase subunit 3 | C, P | protein | 261 | Bos taurus | P00415 (AlphaFold model) |
| Cytochrome c oxidase subunit 4 isoform 1, mitochondrial | D, Q | protein | 147 | Bos taurus | P00423 (AlphaFold model) |
| Cytochrome c oxidase subunit 5A, mitochondrial | E, R | protein | 109 | Bos taurus | P00426 |
| Cytochrome c oxidase subunit 5B, mitochondrial | F, S | protein | 98 | Bos taurus | P00428 |
| Cytochrome c oxidase subunit 6A2, mitochondrial | G, T | protein | 85 | Bos taurus | P07471 |
| Cytochrome c oxidase subunit 6B1 | H, U | protein | 85 | Bos taurus | P00429 |
| Cytochrome c oxidase subunit 6C | I, V | protein | 73 | Bos taurus | P04038 |
| Cytochrome c oxidase subunit 7A1, mitochondrial | J, W | protein | 59 | Bos taurus | P07470 |
| Cytochrome c oxidase subunit 7B, mitochondrial | K, X | protein | 56 | Bos taurus | P13183 |
| Cytochrome c oxidase subunit 7C, mitochondrial | L, Y | protein | 47 | Bos taurus | P00430 |
1 more molecules are not listed.
Sequence of entity 1 (A, N), FASTA
>5ZCQ_1 Cytochrome c oxidase subunit 1 (chains A, N)
MFINRWLFSTNHKDIGTLYLLFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVVVTA
HAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLLASSMVEA
GAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAMSQYQ
TPLFVWSVMITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGH
PEVYILILPGFGMISHIVTYYSGKKEPFGYMGMVWAMMSIGFLGFIVWAHHMFTVGMDVD
TRAYFTSATMIIAIPTGVKVFSWLATLHGGNIKWSPAMMWALGFIFLFTVGGLTGIVLAN
SSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFVHWFPLFSGYTLNDTWAKIHFAIMFVG
VNMTFFPQHFLGLSGMPRRYSDYPDAYTMWNTISSMGSFISLTAVMLMVFIIWEAFASKR
EVLTVDLTTTNLEWLNGCPPPYHTFEEPTYVNLK
Sequence of entity 2 (B, O), FASTA
>5ZCQ_2 Cytochrome c oxidase subunit 2 (chains B, O)
MAYPMQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQE
VETIWTILPAIILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLSFDS
YMIPTSELKPGELRLLEVDNRVVLPMEMTIRMLVSSEDVLHSWAVPSLGLKTDAIPGRLN
QTTLMSSRPGLYYGQCSEICGSNHSFMPIVLELVPLKYFEKWSASML
Sequence of entity 3 (C, P), FASTA
>5ZCQ_3 Cytochrome c oxidase subunit 3 (chains C, P)
MTHQTHAYHMVNPSPWPLTGALSALLMTSGLTMWFHFNSMTLLMIGLTTNMLTMYQWWRD
VIRESTFQGHHTPAVQKGLRYGMILFIISEVLFFTGFFWAFYHSSLAPTPELGGCWPPTG
IHPLNPLEVPLLNTSVLLASGVSITWAHHSLMEGDRKHMLQALFITITLGVYFTLLQASE
YYEAPFTISDGVYGSTFFVATGFHGLHVIIGSTFLIVCFFRQLKFHFTSNHHFGFEAAAW
YWHFVDVVWLFLYVSIYWWGS
Sequence of entity 4 (D, Q), FASTA
>5ZCQ_4 Cytochrome c oxidase subunit 4 isoform 1, mitochondrial (chains D, Q)
AHGSVVKSEDYALPSYVDRRDYPLPDVAHVKNLSASQKALKEKEKASWSSLSIDEKVELY
RLKFKESFAEMNRSTNEWKTVVGAAMFFIGFTALLLIWEKHYVYGPIPHTFEEEWVAKQT
KRMLDMKVAPIQGFSAKWDYDKNEWKK
Sequence of entity 5 (E, R), FASTA
>5ZCQ_5 Cytochrome c oxidase subunit 5A, mitochondrial (chains E, R)
SHGSHETDEEFDARWVTYFNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLND
FASAVRILEVVKDKAGPHKEIYPYVIQELRPTLNELGISTPEELGLDKV
Sequence of entity 6 (F, S), FASTA
>5ZCQ_6 Cytochrome c oxidase subunit 5B, mitochondrial (chains F, S)
ASGGGVPTDEEQATGLEREVMLAARKGQDPYNILAPKATSGTKEDPNLVPSITNKRIVGC
ICEEDNSTVIWFWLHKGEAQRCPSCGTHYKLVPHQLAH
Sequence of entity 7 (G, T), FASTA
>5ZCQ_7 Cytochrome c oxidase subunit 6A2, mitochondrial (chains G, T)
ASAAKGDHGGTGARTWRFLTFGLALPSVALCTLNSWLHSGHRERPAFIPYHHLRIRTKPF
SWGDGNHTFFHNPRVNPLPTGYEKP
Sequence of entity 8 (H, U), FASTA
>5ZCQ_8 Cytochrome c oxidase subunit 6B1 (chains H, U)
AEDIQAKIKNYQTAPFDSRFPNQNQTRNCWQNYLDFHRCEKAMTAKGGDVSVCEWYRRVY
KSLCPISWVSTWDDRRAEGTFPGKI
Sequence of entity 9 (I, V), FASTA
>5ZCQ_9 Cytochrome c oxidase subunit 6C (chains I, V)
STALAKPQMRGLLARRLRFHIVGAFMVSLGFATFYKFAVAEKRKKAYADFYRNYDSMKDF
EEMRKAGIFQSAK
Sequence of entity 10 (J, W), FASTA
>5ZCQ_10 Cytochrome c oxidase subunit 7A1, mitochondrial (chains J, W)
FENRVAEKQKLFQEDNGLPVHLKGGATDNILYRVTMTLCLGGTLYSLYCLGWASFPHKK
Sequence of entity 11 (K, X), FASTA
>5ZCQ_11 Cytochrome c oxidase subunit 7B, mitochondrial (chains K, X)
IHQKRAPDFHDKYGNAVLASGATFCVAVWVYMATQIGIEWNPSPVGRVTPKEWREQ
Sequence of entity 12 (L, Y), FASTA
>5ZCQ_12 Cytochrome c oxidase subunit 7C, mitochondrial (chains L, Y)
SHYEEGPGKNIPFSVENKWRLLAMMTLFFGSGFAAPFFIVRHQLLKK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| HEA | Heme-a | C49 H56 Fe N4 O6 | 4 |
| CU | Copper (II) ion | Cu | 2 |
| MG | Magnesium ion | Mg | 2 |
| TGL | Tristearoylglycerol | C57 H110 O6 | 6 |
| PGV | (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoylo… | C40 H77 O10 P | 8 |
| CHD | Cholic acid | C24 H40 O5 | 8 |
| CUA | Dinuclear copper ion | Cu2 | 2 |
| PSC | (7R,17E,20E)-4-hydroxy-n,n,n-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-tri… | C42 H81 N O8 P | 2 |
| DMU | Decyl-beta-D-maltopyranoside | C22 H42 O11 | 9 |
| CDL | Cardiolipin | C81 H156 O17 P2 | 4 |
| PEK | (1S)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(stearoyloxy)methyl]ethyl… | C43 H78 N O8 P | 6 |
| ZN | Zinc ion | Zn | 2 |
| AZI | Azide ion | N3 | 4 |
Water and common crystallization additives (NA, EDO, UNX) are not listed.
Primary citation
X-ray structural analyses of azide-bound cytochromecoxidases reveal that the H-pathway is critically important for the proton-pumping activity. Shimada, A., Hatano, K., Tadehara, H. et al. J Biol Chem (2018) 293:14868-14879. DOI 10.1074/jbc.RA118.003123 · PubMed
Other PDB entries of the same protein (UniProt P00396 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7COH 1.3 Å, Dimeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Oxidized State
- 7W3E 1.45 Å, Bovine cytochrome c oxidese in CN-bound fully reduced state at 50 K
- 5B1A 1.5 Å, Bovine heart cytochrome c oxidase in the fully oxidized state at 1.5 angstrom resolution
- 7YPY 1.5 Å, Bovine heart cytochrome c oxidase in fully oxidized state at 1.5 angstrom resolution
- 5B1B 1.6 Å, Bovine heart cytochrome c oxidase in the fully reduced state at 1.6 angstrom resolution
- 7VUW 1.6 Å, Bovine heart cytochrome c oxidase in the cyanide-bound fully oxidized state at 50 K
- 9M56 1.6 Å, Bovine Heart Cytochrome c Oxidase in the Fully Reduced State
- 5ZCP 1.65 Å, azide-bound cytochrome c oxidase structure determined using the crystals exposed to 20…
- 7VVR 1.65 Å, Bovine cytochrome c oxidese in CN-bound mixed valence state at 50 K
- 5B3S 1.68 Å, Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at…
- 7EV7 1.7 Å, Bovine heart cytochrome c oxidase in the carbon monoxide-bound fully reduced state at a…
- 8H8R 1.7 Å, Bovine Heart Cytochrome c Oxidase in the Calcium-bound Fully Oxidized State
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