7EV7

Bovine heart cytochrome c oxidase in the carbon monoxide-bound fully reduced state at a 50 K

• PDB DOI: https://doi.org/10.2210/pdb7EV7/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bos taurus
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2021-05-20 Released: 2021-07-14 
• Deposition Author(s): Shimada, A., Yoshikawa, S., Tsukihara, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.178 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 

Starting Model: experimental

Literature

Structure of CO-bound fully reduced state of bovine heart cytochrome c oxidase

Shimada, A., Shinzawa-Itoh, K., Muramoto, K., Tsukihara, T., Yoshikawa, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 13-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 13-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 456.03 kDa 
• Atom Count: 34,489 
• Modelled Residue Count: 3,550 
• Deposited Residue Count: 3,614 
• Unique protein chains: 13

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	A, N	514	Bos taurus	Mutation(s): 0  EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for P00396 (Bos taurus) Explore P00396  Go to UniProtKB:  P00396

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 2	B, O	227	Bos taurus	Mutation(s): 0  EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for P68530 (Bos taurus) Explore P68530  Go to UniProtKB:  P68530

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 3	C, P	261	Bos taurus	Mutation(s): 0  EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for P00415 (Bos taurus) Explore P00415  Go to UniProtKB:  P00415

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 4 isoform 1	D, Q	147	Bos taurus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P00423 (Bos taurus) Explore P00423  Go to UniProtKB:  P00423

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 5A	E, R	109	Bos taurus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P00426 (Bos taurus) Explore P00426  Go to UniProtKB:  P00426

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 5B, mitochondrial	F, S	98	Bos taurus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P00428 (Bos taurus) Explore P00428  Go to UniProtKB:  P00428

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6A2	G, T	85	Bos taurus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P07471 (Bos taurus) Explore P07471  Go to UniProtKB:  P07471

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6B1	H, U	85	Bos taurus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P00429 (Bos taurus) Explore P00429  Go to UniProtKB:  P00429

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6C	I, V	73	Bos taurus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P04038 (Bos taurus) Explore P04038  Go to UniProtKB:  P04038

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7A1	J, W	59	Bos taurus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P07470 (Bos taurus) Explore P07470  Go to UniProtKB:  P07470

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7B	K, X	56	Bos taurus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P13183 (Bos taurus) Explore P13183  Go to UniProtKB:  P13183

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7C, mitochondrial	L, Y	47	Bos taurus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P00430 (Bos taurus) Explore P00430  Go to UniProtKB:  P00430

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 8B	M, Z	46	Bos taurus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P10175 (Bos taurus) Explore P10175  Go to UniProtKB:  P10175

Small Molecules

Ligands 16 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CDL (Subject of Investigation/LOI)	EH [auth T], TF [auth P], WB [auth C], ZC [auth G]	CARDIOLIPIN C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L
TGL	BB [auth B], IC [auth D], IE [auth N], KG [auth Q], PH [auth Y], QD [auth L]	TRISTEAROYLGLYCEROL C57 H110 O6 DCXXMTOCNZCJGO-UHFFFAOYSA-N
HEA (Subject of Investigation/LOI)	BA [auth A], CA [auth A], CE [auth N], DE [auth N]	HEME-A C49 H56 Fe N4 O6 ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PEK	OF [auth P], PF [auth P], QF [auth P], RB [auth C], SB [auth C], TB [auth C]	(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE C43 H78 N O8 P ANRKEHNWXKCXDB-BHFWLYLHSA-N
PSC	CB [auth B], FF [auth O]	(7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE C42 H81 N O8 P JLPULHDHAOZNQI-AUSZDXHESA-O
PGV	AA [auth A], BE [auth N], HA [auth A], JE [auth N], RF [auth P], SF [auth P], UB [auth C], VB [auth C]	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE C40 H77 O10 P ADYWCMPUNIVOEA-GPJPVTGXSA-N
DMU	AE [auth M], GD [auth G], HC [auth C], IG [auth P], JG [auth P], KH [auth V], TH [auth Z], UF [auth P], UH [auth Z], VD [auth M], YB [auth C]	DECYL-BETA-D-MALTOPYRANOSIDE C22 H42 O11 WOQQAWHSKSSAGF-WXFJLFHKSA-N
CHD	AD [auth G], DB [auth B], LD [auth J], LH [auth W], MF [auth P], PB [auth C], SH [auth Y], VF [auth P], WF [auth P], XB [auth C], ZB [auth C]	CHOLIC ACID C24 H40 O5 BHQCQFFYRZLCQQ-OELDTZBJSA-N
CUA	EB [auth B], GF [auth O]	DINUCLEAR COPPER ION Cu2 ALKZAGKDWUSJED-UHFFFAOYSA-N
PO4	IH [auth U], KD [auth H]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	SC [auth F], SG [auth S]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU	DA [auth A], EE [auth N]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO	AB [auth A], AC [auth C], AF [auth N], AG [auth P], AH [auth S], BC [auth C], BD [auth G], BF [auth N], BG [auth P], BH [auth S], CC [auth C], CD [auth G], CF [auth N], CG [auth P], CH [auth S], DC [auth C], DD [auth G], DF [auth N], DG [auth P], DH [auth S], EC [auth C], ED [auth G], EF [auth N], EG [auth P], FB [auth B], FC [auth C], FD [auth G], FG [auth P], FH [auth T], GB [auth B], GC [auth C], GG [auth P], GH [auth T], HB [auth B], HD [auth H], HF [auth O], HG [auth P], HH [auth U], IA [auth A], IB [auth B], ID [auth H], IF [auth O], JA [auth A], JB [auth B], JC [auth D], JD [auth H], JF [auth O], JH [auth V], KA [auth A], KB [auth B], KC [auth D], KE [auth N], KF [auth O], LA [auth A], LB [auth B], LC [auth D], LE [auth N], LF [auth O], LG [auth Q], MA [auth A], MB [auth B], MC [auth D], MD [auth J], ME [auth N], MG [auth Q], MH [auth W], NA [auth A], NB [auth B], NC [auth D], ND [auth J], NE [auth N], NG [auth R], NH [auth W], OA [auth A], OB [auth B], OC [auth D], OD [auth K], OE [auth N], OG [auth R], OH [auth W], PA [auth A], PC [auth E], PD [auth K], PE [auth N], PG [auth R], QA [auth A], QC [auth E], QE [auth N], QG [auth R], QH [auth Y], RA [auth A], RC [auth E], RD [auth L], RE [auth N], RG [auth R], RH [auth Y], SA [auth A], SD [auth L], SE [auth N], TA [auth A], TC [auth F], TD [auth L], TE [auth N], TG [auth S], UA [auth A], UC [auth F], UD [auth L], UE [auth N], UG [auth S], VA [auth A], VC [auth F], VE [auth N], VG [auth S], WA [auth A], WC [auth F], WD [auth M], WE [auth N], WG [auth S], XA [auth A], XC [auth F], XD [auth M], XE [auth N], XF [auth P], XG [auth S], YA [auth A], YC [auth F], YD [auth M], YE [auth N], YF [auth P], YG [auth S], ZA [auth A], ZD [auth M], ZE [auth N], ZF [auth P], ZG [auth S]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CMO	GA [auth A], HE [auth N]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N
MG	EA [auth A], FE [auth N]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	FA [auth A], GE [auth N], NF [auth P], QB [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME	A, N	L-PEPTIDE LINKING	C6 H11 N O3 S		MET
TPO	G, T	L-PEPTIDE LINKING	C4 H10 N O6 P		THR
SAC	I, V	L-PEPTIDE LINKING	C5 H9 N O4		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.178 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.539	α = 90
b = 203.655	β = 90
c = 177.569	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MLPHARE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-14 
Deposition Author(s): Shimada, A., Yoshikawa, S., Tsukihara, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18K06092
Japan Society for the Promotion of Science (JSPS)	Japan	15K18493
Japan Society for the Promotion of Science (JSPS)	Japan	18K14635
Japan Society for the Promotion of Science (JSPS)	Japan	26291033
Japan Science and Technology	Japan	12101577

Revision History  

• Version 1.0: 2021-07-14
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description