5IY5: Cytochrome c oxidase subunit 1

Electron transfer complex of cytochrome c and cytochrome c oxidase at 2.0 angstrom resolution. Determined by X-ray diffraction at 2.0 Å resolution. Released 11 Jan 2017.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Bos taurus, Equus caballus
Chains: 28
Atoms: 34,765
Mol. weight: 456.57 kDa
Ligands: CU, MG, HEA, PER
Released: 11 Jan 2017

Explore 5IY5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5IY5 contains 203 α-helices and 70 β-strands across 28 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 1: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
β-strand	39	1	5
α-helix	50-53	4
β-strand	58	1	5
α-helix	61-69	9
α-helix	71-74	4
α-helix	88-101	14

Chain 2: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
β-strand	19	1	10
β-strand	31	1	10
α-helix	50-53	4
α-helix	62-67	6
α-helix	71-74	4
α-helix	88-102	15

Chain A: 30 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	336-358	23
α-helix	361-367	7
β-strand	370	1	1
α-helix	371-380	10
α-helix	381-385	5
α-helix	386-401	16
β-strand	403	1	2
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
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	61-88	28
β-strand	95-102	8	6
β-strand	105-110	6	6
β-strand	116-120	5	6
β-strand	122	1	7
α-helix	123-124	2
α-helix	125-127	3
α-helix	128-129	2
α-helix	132-133	2
β-strand	138	1	7
β-strand	142-145	4	8
β-strand	150-156	7	6
β-strand	161-165	5	9
α-helix	166-168	3
β-strand	170-174	5	9
β-strand	180-184	5	6
β-strand	190-195	6	8
α-helix	204-206	3
β-strand	208-214	7	8
α-helix	216-226	11

Chain C: 13 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	11-13	3
α-helix	16-37	22
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	11
α-helix	156-183	28
α-helix	191-223	33
α-helix	233-252	20
α-helix	253-259	7

Chain D: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
α-helix	35-43	9
α-helix	48-50	3
α-helix	53-63	11
α-helix	68-71	4
α-helix	77-102	26
α-helix	109-111	3
α-helix	113-125	13
α-helix	135-137	3
β-strand	138-139	2	12
β-strand	144-145	2	12

Chains E and R: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	8-20	13
α-helix	26-36	11
β-strand	41	1	13
α-helix	42-44	3
α-helix	45-57	13
α-helix	61-74	14
α-helix	81-96	16
α-helix	98-100	3

Chain F: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	11
α-helix	9-12	4
α-helix	15-25	11
α-helix	35-38	4
α-helix	46	1
β-strand	47-51	5	14
β-strand	55-60	6	4
α-helix	68-69	2
β-strand	70-75	6	4
β-strand	80-81	2	14
β-strand	88-93	6	14

18 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	259	Bos taurus	P00415 (AlphaFold model)
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial	D, Q	protein	144	Bos taurus	P00423 (AlphaFold model)
Cytochrome c oxidase subunit 5A, mitochondrial	E, R	protein	105	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	84	Bos taurus	P07471
Cytochrome c oxidase subunit 6B1	H, U	protein	79	Bos taurus	P00429
Cytochrome c oxidase subunit 6C	I, V	protein	73	Bos taurus	P04038
Cytochrome c oxidase subunit 7A1, mitochondrial	J, W	protein	58	Bos taurus	P07470
Cytochrome c oxidase subunit 7B, mitochondrial	K, X	protein	49	Bos taurus	P13183
Cytochrome c oxidase subunit 7C, mitochondrial	L, Y	protein	46	Bos taurus	P00430

2 more molecules are not listed.

Sequence of entity 1 (A, N), FASTA

>5IY5_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

>5IY5_2 Cytochrome c oxidase subunit 2 (chains B, O)
MAYPMQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQE
VETIWTILPAIILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLSFDS
YMIPTSELKPGELRLLEVDNRVVLPMEMTIRMLVSSEDVLHSWAVPSLGLKTDAIPGRLN
QTTLMSSRPGLYYGQCSEICGSNHSFMPIVLELVPLKYFEKWSASML

Sequence of entity 3 (C, P), FASTA

>5IY5_3 Cytochrome c oxidase subunit 3 (chains C, P)
HQTHAYHMVNPSPWPLTGALSALLMTSGLTMWFHFNSMTLLMIGLTTNMLTMYQWWRDVI
RESTFQGHHTPAVQKGLRYGMILFIISEVLFFTGFFWAFYHSSLAPTPELGGCWPPTGIH
PLNPLEVPLLNTSVLLASGVSITWAHHSLMEGDRKHMLQALFITITLGVYFTLLQASEYY
EAPFTISDGVYGSTFFVATGFHGLHVIIGSTFLIVCFFRQLKFHFTSNHHFGFEAAAWYW
HFVDVVWLFLYVSIYWWGS

Sequence of entity 4 (D, Q), FASTA

>5IY5_4 Cytochrome c oxidase subunit 4 isoform 1, mitochondrial (chains D, Q)
SVVKSEDYALPSYVDRRDYPLPDVAHVKNLSASQKALKEKEKASWSSLSIDEKVELYRLK
FKESFAEMNRSTNEWKTVVGAAMFFIGFTALLLIWEKHYVYGPIPHTFEEEWVAKQTKRM
LDMKVAPIQGFSAKWDYDKNEWKK

Sequence of entity 5 (E, R), FASTA

>5IY5_5 Cytochrome c oxidase subunit 5A, mitochondrial (chains E, R)
HETDEEFDARWVTYFNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASA
VRILEVVKDKAGPHKEIYPYVIQELRPTLNELGISTPEELGLDKV

Sequence of entity 6 (F, S), FASTA

>5IY5_6 Cytochrome c oxidase subunit 5B, mitochondrial (chains F, S)
ASGGGVPTDEEQATGLEREVMLAARKGQDPYNILAPKATSGTKEDPNLVPSITNKRIVGC
ICEEDNSTVIWFWLHKGEAQRCPSCGTHYKLVPHQLAH

Sequence of entity 7 (G, T), FASTA

>5IY5_7 Cytochrome c oxidase subunit 6A2, mitochondrial (chains G, T)
ASAAKGDHGGTGARTWRFLTFGLALPSVALCTLNSWLHSGHRERPAFIPYHHLRIRTKPF
SWGDGNHTFFHNPRVNPLPTGYEK

Sequence of entity 8 (H, U), FASTA

>5IY5_8 Cytochrome c oxidase subunit 6B1 (chains H, U)
KIKNYQTAPFDSRFPNQNQTRNCWQNYLDFHRCEKAMTAKGGDVSVCEWYRRVYKSLCPI
SWVSTWDDRRAEGTFPGKI

Sequence of entity 9 (I, V), FASTA

>5IY5_9 Cytochrome c oxidase subunit 6C (chains I, V)
STALAKPQMRGLLARRLRFHIVGAFMVSLGFATFYKFAVAEKRKKAYADFYRNYDSMKDF
EEMRKAGIFQSAK

Sequence of entity 10 (J, W), FASTA

>5IY5_10 Cytochrome c oxidase subunit 7A1, mitochondrial (chains J, W)
FENRVAEKQKLFQEDNGLPVHLKGGATDNILYRVTMTLCLGGTLYSLYCLGWASFPHK

Sequence of entity 11 (K, X), FASTA

>5IY5_11 Cytochrome c oxidase subunit 7B, mitochondrial (chains K, X)
APDFHDKYGNAVLASGATFCVAVWVYMATQIGIEWNPSPVGRVTPKEWR

Sequence of entity 12 (L, Y), FASTA

>5IY5_12 Cytochrome c oxidase subunit 7C, mitochondrial (chains L, Y)
HYEEGPGKNIPFSVENKWRLLAMMTLFFGSGFAAPFFIVRHQLLKK

Ligands and cofactors

ID	Name	Formula	Copies
CU	Copper (II) ion	Cu	2
MG	Magnesium ion	Mg	2
HEA	Heme-a	C49 H56 Fe N4 O6	4
PER	Peroxide ion	O2	2
PGV	(1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoylo…	C40 H77 O10 P	7
TGL	Tristearoylglycerol	C57 H110 O6	5
CUA	Dinuclear copper ion	Cu2	2
CHD	Cholic acid	C24 H40 O5	8
PEK	(1S)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(stearoyloxy)methyl]ethyl…	C43 H78 N O8 P	2
CDL	Cardiolipin	C81 H156 O17 P2	4
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
ZN	Zinc ion	Zn	2
DMU	Decyl-beta-D-maltopyranoside	C22 H42 O11	2
HEC	Heme C	C34 H36 Fe N4 O4	2

Water and common crystallization additives (NA, EDO, UNL) are not listed.

Primary citation

Complex structure of cytochrome c-cytochrome c oxidase reveals a novel protein-protein interaction mode. Shimada, S., Shinzawa-Itoh, K., Baba, J. et al. EMBO J (2017) 36:291-300. DOI 10.15252/embj.201695021 · 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…
5ZCQ 1.65 Å, Azide-bound cytochrome c oxidase structure determined using the crystals exposed to 10…
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…

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