5Z84

The structure of azide-bound cytochrome c oxidase determined using the crystals exposed to 20 mM azide solution for 4 days


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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

(2018) J Biol Chem 293: 14868-14879

  • DOI: 10.1074/jbc.RA118.003123
  • Primary Citation of Related Structures:  
    5Z84, 5Z86, 5Z85, 5ZCO, 5ZCQ, 5ZCP

  • PubMed Abstract: 
  • Cytochrome c oxidase (CcO) is the terminal oxidase of cellular respiration, reducing O 2 to water and pumping protons. X-ray structural features have suggested that CcO pumps protons via a mechanism involving electrostatic repuls ...

    Cytochrome c oxidase (CcO) is the terminal oxidase of cellular respiration, reducing O 2 to water and pumping protons. X-ray structural features have suggested that CcO pumps protons via a mechanism involving electrostatic repulsions between pumping protons in the hydrogen-bond network of a proton-conducting pathway (the H-pathway) and net positive charges created upon oxidation of an iron site, heme a (Fe a 2+ ), for reduction of O 2 at another iron site, heme a 3 (Fe a 3 2+ ). The protons for pumping are transferred to the hydrogen-bond network from the N-side via the water channel of the H-pathway. Back-leakage of protons to the N-side is thought to be blocked by closure of the water channel. To experimentally test this, we examined X-ray structures of the azide-bound, oxidized bovine CcO and found that an azide derivative (N 3 - -Fe a 3 3+ , Cu B 2+ -N 3 - ) induces a translational movement of the heme a 3 plane. This was accompanied by opening of the water channel, revealing that Fe a 3 and the H-pathway are tightly coupled. The channel opening in the oxidized state is likely to induce back-leakage of pumping protons, which lowers the proton level in the hydrogen-bond network during enzymatic turnover. The proton level decrease weakens the electron affinity of Fe a , if Fe a electrostatically interacts with protons in the hydrogen-bond network. The previously reported azide-induced redox-potential decrease in Fe a supports existence of the electrostatic interaction. In summary, our results indicate that the H-pathway is critical for CcO's proton-pumping function.


    Organizational Affiliation

    From the Picobiology Institute and yoshi@sci.u-hyogo.ac.jp.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1AN514Bos taurusMutation(s): 0 
Gene Names: MT-CO1COICOXIMTCO1
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome c oxidase with bound azide (4-day soak, 20 mM azide)
Find proteins for P00396 (Bos taurus)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2BO227Bos taurusMutation(s): 0 
Gene Names: MT-CO2COIICOX2COXIIMTCO2
EC: 7.1.1.9
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome c oxidase with bound azide (4-day soak, 20 mM azide)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3CP261Bos taurusMutation(s): 0 
Gene Names: MT-CO3COIIICOXIIIMTCO3
EC: 7.1.1.9
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome c oxidase with bound azide (4-day soak, 20 mM azide)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1, mitochondrialDQ147Bos taurusMutation(s): 0 
Gene Names: COX4I1COX4
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome c oxidase with bound azide (4-day soak, 20 mM azide)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrialER109Bos taurusMutation(s): 0 
Gene Names: COX5A
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome c oxidase with bound azide (4-day soak, 20 mM azide)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B, mitochondrialFS98Bos taurusMutation(s): 0 
Gene Names: COX5B
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome c oxidase with bound azide (4-day soak, 20 mM azide)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2, mitochondrialGT85Bos taurusMutation(s): 0 
Gene Names: COX6A2COX6A
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome c oxidase with bound azide (4-day soak, 20 mM azide)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1HU85Bos taurusMutation(s): 0 
Gene Names: COX6B1COX6B
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome c oxidase with bound azide (4-day soak, 20 mM azide)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6CIV73Bos taurusMutation(s): 0 
Gene Names: COX6C
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome c oxidase with bound azide (4-day soak, 20 mM azide)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A1, mitochondrialJW59Bos taurusMutation(s): 0 
Gene Names: COX7A1COX7ACOX7AH
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome c oxidase with bound azide (4-day soak, 20 mM azide)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
cytochrome c oxidase subunit 11, Cytochrome c oxidase subunit 7B, mitochondrialKX56Bos taurusMutation(s): 0 
Gene Names: COX7B
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome c oxidase with bound azide (4-day soak, 20 mM azide)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrialLY47Bos taurusMutation(s): 0 
Gene Names: COX7CCOX7CP1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome c oxidase with bound azide (4-day soak, 20 mM azide)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8B, mitochondrialMZ46Bos taurusMutation(s): 0 
Gene Names: COX8BCOX8H
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome c oxidase with bound azide (4-day soak, 20 mM azide)
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  • Reference Sequence
Small Molecules
Ligands 16 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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C, N, P, T
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
TGL
Query on TGL

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A, D, L, N, Q, Y
TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
 Ligand Interaction
HEA
Query on HEA

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A, N
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
PEK
Query on PEK

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C, G, P, 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
 Ligand Interaction
PSC
Query on PSC

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B, 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

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A, C, G, N, P, Z
(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

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C, L, M, P, Z
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
 Ligand Interaction
CHD
Query on CHD

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B, C, G, J, P, W
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
 Ligand Interaction
CUA
Query on CUA

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B, O
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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F, S
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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A, N
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A, B, C, D, E, F, G, H, J, L, N, O, P, Q, R, S, T, U, V
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
AZI
Query on AZI

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A, N
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, N
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A, N
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

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C, 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: 1.85 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.405α = 90
b = 206.272β = 90
c = 177.609γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPS KAKENHIJapan15K18493
JSPS KAKENHIJapan22370060
JSPS KAKENHIJapan26291033
JST CRESTJapan--

Revision History 

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2018-09-05
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-03
    Changes: Data collection, Database references