3ASO

Bovine heart cytochrome C oxidase in the fully oxidized state measured at 0.9 angstrom wavelength


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.169 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Distinguishing between Cl- and O2(2-) as the bridging element between Fe3+ and Cu2+ in resting-oxidized cytochrome c oxidase

Suga, M.Yano, N.Muramoto, K.Shinzawa-Itoh, K.Maeda, T.Yamashita, E.Tsukihara, T.Yoshikawa, S.

(2011) Acta Crystallogr D Biol Crystallogr 67: 742-744

  • DOI: 10.1107/S0907444911022803
  • Primary Citation of Related Structures:  
    3ASN, 3ASO

  • PubMed Abstract: 
  • Fully oxidized cytochrome c oxidase (CcO) under enzymatic turnover is capable of pumping protons, while fully oxidized CcO as isolated is not able to do so upon one-electron reduction. The functional difference is expected to be a consequence of structural differences: [Fe(3+)-OH(-)] under enzymatic turnover versus [Fe(3+)-O(2)(2-)-Cu(2+)] for the as-isolated CcO ...

    Fully oxidized cytochrome c oxidase (CcO) under enzymatic turnover is capable of pumping protons, while fully oxidized CcO as isolated is not able to do so upon one-electron reduction. The functional difference is expected to be a consequence of structural differences: [Fe(3+)-OH(-)] under enzymatic turnover versus [Fe(3+)-O(2)(2-)-Cu(2+)] for the as-isolated CcO. However, the electron density for O(2)(2-) is equally assignable to Cl(-). An anomalous dispersion analysis was performed in order to conclusively demonstrate the absence of Cl(-) between the Fe(3+) and Cu(2+). Thus, the peroxide moiety receives electron equivalents from cytochrome c without affecting the oxidation states of the metal sites. The metal-site reduction is coupled to the proton pump.


    Organizational Affiliation

    Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1A, N514Bos taurusMutation(s): 0 
Gene Names: MT-CO1COICOXIMTCO1
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P00396 (Bos taurus)
Explore P00396 
Go to UniProtKB:  P00396
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2B, O227Bos taurusMutation(s): 0 
Gene Names: MT-CO2COIICOX2COXIIMTCO2
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P68530 (Bos taurus)
Explore P68530 
Go to UniProtKB:  P68530
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3C, P261Bos taurusMutation(s): 0 
Gene Names: MT-CO3COIIICOXIIIMTCO3
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P00415 (Bos taurus)
Explore P00415 
Go to UniProtKB:  P00415
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1D, Q147Bos taurusMutation(s): 0 
Gene Names: COX4I1COX4
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P00423 (Bos taurus)
Explore P00423 
Go to UniProtKB:  P00423
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5AE, R109Bos taurusMutation(s): 0 
Gene Names: COX5A
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P00426 (Bos taurus)
Explore P00426 
Go to UniProtKB:  P00426
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5BF, S98Bos taurusMutation(s): 0 
Gene Names: COX5B
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P00428 (Bos taurus)
Explore P00428 
Go to UniProtKB:  P00428
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2G, T85Bos taurusMutation(s): 0 
Gene Names: COX6A2COX6A
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P07471 (Bos taurus)
Explore P07471 
Go to UniProtKB:  P07471
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1H, U85Bos taurusMutation(s): 0 
Gene Names: COX6B1COX6B
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P00429 (Bos taurus)
Explore P00429 
Go to UniProtKB:  P00429
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6CI, V73Bos taurusMutation(s): 0 
Gene Names: COX6C
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P04038 (Bos taurus)
Explore P04038 
Go to UniProtKB:  P04038
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A1J, W59Bos taurusMutation(s): 0 
Gene Names: COX7A1COX7ACOX7AH
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P07470 (Bos taurus)
Explore P07470 
Go to UniProtKB:  P07470
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7BK, X56Bos taurusMutation(s): 0 
Gene Names: COX7B
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P13183 (Bos taurus)
Explore P13183 
Go to UniProtKB:  P13183
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7CL, Y47Bos taurusMutation(s): 0 
Gene Names: COX7CCOX7CP1
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P00430 (Bos taurus)
Explore P00430 
Go to UniProtKB:  P00430
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8BM, Z46Bos taurusMutation(s): 0 
Gene Names: COX8BCOX8H
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P10175 (Bos taurus)
Explore P10175 
Go to UniProtKB:  P10175
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 14 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
QA [auth C], QB [auth P], VA [auth G], XB [auth T]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
TGL
Query on TGL

Download Ideal Coordinates CCD File 
FA [auth A], GB [auth N], HB [auth N], SA [auth D], SB [auth Q], ZA [auth L]TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
 Ligand Interaction
HEA
Query on HEA

Download Ideal Coordinates CCD File 
AA [auth A], BA [auth A], BB [auth N], CB [auth N]HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
PEK
Query on PEK

Download Ideal Coordinates CCD File 
NA [auth C], UA [auth G], UB [auth T], VB [auth T], WB [auth T], XA [auth G](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
 Ligand Interaction
PSC
Query on PSC

Download Ideal Coordinates CCD File 
JA [auth B], LB [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
 Ligand Interaction
PGV
Query on PGV

Download Ideal Coordinates CCD File 
GA [auth A], HA [auth A], IB [auth N], JB [auth N], OA [auth C], OB [auth P], PA [auth C], PB [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
 Ligand Interaction
DMU
Query on DMU

Download Ideal Coordinates CCD File 
AB [auth M], ZB [auth Z]DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
 Ligand Interaction
CHD
Query on CHD

Download Ideal Coordinates CCD File 
KA [auth B], MA [auth C], NB [auth P], RA [auth C], RB [auth P], WA [auth G], YA [auth J], YB [auth W]CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
 Ligand Interaction
CUA
Query on CUA

Download Ideal Coordinates CCD File 
IA [auth B], KB [auth O]DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
TA [auth F], TB [auth S]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download Ideal Coordinates CCD File 
CA [auth A], DB [auth N]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
DA [auth A], EB [auth N]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
EA [auth A], FB [auth N]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download Ideal Coordinates CCD File 
LA [auth C], MB [auth P]UNKNOWN ATOM OR ION
X
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
A, NL-PEPTIDE LINKINGC6 H11 N O3 SMET
TPO
Query on TPO
G, TL-PEPTIDE LINKINGC4 H10 N O6 PTHR
SAC
Query on SAC
I, VL-PEPTIDE LINKINGC5 H9 N O4SER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.874α = 90
b = 204.106β = 90
c = 177.874γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-03
    Type: Initial release
  • Version 1.1: 2012-04-18
    Changes: Database references