5B3S

Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at 1.68 angstrom resolution (50 K)

• PDB DOI: https://doi.org/10.2210/pdb5B3S/pdb

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


• Deposited: 2016-03-11 Released: 2017-03-22 
• Deposition Author(s): Shimada, A., Shinzawa-Ito, K., Yoshikawa, S., Tsukihara, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.177 
• R-Value Work: 0.153 
• R-Value Observed: 0.154 

Literature

Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at 1.68 angstrom resolution (50 K)

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

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: 451.59 kDa 
• Atom Count: 34,917 
• Modelled Residue Count: 3,550 
• Deposited Residue Count: 3,550 
• 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	259	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, mitochondrial	D, Q	144	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, mitochondrial	E, R	105	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	94	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, mitochondrial	G, T	84	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	79	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, mitochondrial	J, W	58	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, mitochondrial	K, X	49	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	46	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, mitochondrial	M, Z	43	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	LB [auth C], LC [auth G], XF [auth T], YE [auth P]	CARDIOLIPIN C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L
TGL	DD [auth L], JF [auth Q], LG [auth Y], TD [auth N], WA [auth B], ZA [auth B]	TRISTEAROYLGLYCEROL C57 H110 O6 DCXXMTOCNZCJGO-UHFFFAOYSA-N
HEA	AA [auth A], BA [auth A], MD [auth N], ND [auth N]	HEME-A C49 H56 Fe N4 O6 ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PEK	HB [auth C], IB [auth C], UE [auth P], VE [auth P], WE [auth P], WF [auth T]	(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	NE [auth O], YA [auth B]	(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	GA [auth A], HA [auth A], JB [auth C], KB [auth C], OC [auth G], SD [auth N], UD [auth N], XE [auth P]	(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	AD [auth K], BD [auth K], BF [auth P], CD [auth K], ED [auth L], FG [auth X], GD [auth M], GG [auth X], HG [auth X], IF [auth P], IG [auth X], JG [auth X], LD [auth M], MB [auth C], MC [auth G], NB [auth C], NG [auth Z], OE [auth O], XC [auth K], YC [auth K], YF [auth T], ZC [auth K], ZE [auth P]	DECYL-BETA-D-MALTOPYRANOSIDE C22 H42 O11 WOQQAWHSKSSAGF-WXFJLFHKSA-N
CHD	AF [auth P], EG [auth W], GB [auth C], KG [auth Y], NC [auth G], TC [auth J], TE [auth P], UC [auth J], VF [auth T]	CHOLIC ACID C24 H40 O5 BHQCQFFYRZLCQQ-OELDTZBJSA-N
CUA	ME [auth O], XA [auth B]	DINUCLEAR COPPER ION Cu2 ALKZAGKDWUSJED-UHFFFAOYSA-N
PO4	CG [auth U], RC [auth H]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	FC [auth F], PF [auth S]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU	CA [auth A], OD [auth N]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO	AB [auth B], AC [auth D], AE [auth N], AG [auth T], BB [auth B], BC [auth D], BE [auth N], BG [auth U], CB [auth B], CC [auth E], CE [auth N], CF [auth P], DB [auth B], DC [auth E], DE [auth N], DF [auth P], DG [auth V], EB [auth B], EC [auth E], EE [auth N], EF [auth P], FB [auth B], FD [auth L], FE [auth N], FF [auth P], GC [auth F], GE [auth N], GF [auth P], HC [auth F], HD [auth M], HE [auth N], HF [auth P], IA [auth A], IC [auth F], ID [auth M], IE [auth N], JA [auth A], JC [auth F], JD [auth M], JE [auth N], KA [auth A], KC [auth F], KD [auth M], KE [auth N], KF [auth Q], LA [auth A], LE [auth N], LF [auth Q], MA [auth A], MF [auth Q], MG [auth Y], NA [auth A], NF [auth R], OA [auth A], OB [auth C], OF [auth R], PA [auth A], PB [auth C], PC [auth G], PE [auth O], QA [auth A], QB [auth C], QC [auth G], QE [auth O], QF [auth S], RA [auth A], RB [auth C], RE [auth O], RF [auth S], SA [auth A], SB [auth C], SC [auth I], SE [auth O], SF [auth S], TA [auth A], TB [auth C], TF [auth S], UA [auth A], UB [auth C], UF [auth S], VA [auth A], VB [auth C], VC [auth J], VD [auth N], WB [auth C], WC [auth J], WD [auth N], XB [auth D], XD [auth N], YB [auth D], YD [auth N], ZB [auth D], ZD [auth N], ZF [auth T]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CMO	FA [auth A], RD [auth N]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N
MG	DA [auth A], PD [auth N]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	EA [auth A], QD [auth N]	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: 1.68 Å
• R-Value Free: 0.177 
• R-Value Work: 0.153 
• R-Value Observed: 0.154 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.491	α = 90
b = 203.303	β = 90
c = 177.484	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
DENZO	data reduction
REFMAC	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-03-22 
Deposition Author(s): Shimada, A., Shinzawa-Ito, K., Yoshikawa, S., Tsukihara, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18K06092

Revision History  

• Version 1.0: 2017-03-22
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection
• Version 2.0: 2022-03-02
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Refinement description