8GVM

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: 0.188 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 5Z84


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.Sinzawa-Itoh, K.Yamashita, E.Mutamoto, K.Tsukihara, T.Yoshikawa, S.

(2018) J Biol Chem 293: 14868-14879

  • DOI: https://doi.org/10.1074/jbc.RA118.003123
  • Primary Citation of Related Structures:  
    5Z84, 5Z85, 5Z86, 5ZCO, 5ZCP, 5ZCQ, 8GVM

  • 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 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1
A, N
514Bos taurusMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2
B, O
227Bos taurusMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3
C, P
261Bos taurusMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
D, Q
147Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A
E, R
109Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B, mitochondrial
F, S
98Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2, mitochondrial
G, T
85Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1
H, U
85Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6C
I, V
73Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A1
J, W
59Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7B, mitochondrial
K, X
56Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrial
L, Y
47Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8B, mitochondrial
M, Z
46Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Small Molecules
Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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DB [auth C],
TE [auth T],
VC [auth N],
WD [auth P]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
TGL
Query on TGL

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ED [auth N]
FE [auth Q]
RC [auth L]
SB [auth D]
TA [auth B]
ED [auth N],
FE [auth Q],
RC [auth L],
SB [auth D],
TA [auth B],
YE [auth Y]
TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
HEA
Query on HEA

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AA [auth A],
BA [auth A],
WC [auth N],
XC [auth N]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PEK
Query on PEK

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EE [auth P]
FB [auth C]
IC [auth G]
KC [auth G]
RB [auth C]
EE [auth P],
FB [auth C],
IC [auth G],
KC [auth G],
RB [auth C],
SE [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
Query on PSC

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PD [auth O],
WA [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
Query on PGV

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CB [auth C]
DD [auth N]
GB [auth C]
HA [auth A]
IA [auth A]
CB [auth C],
DD [auth N],
GB [auth C],
HA [auth A],
IA [auth A],
LC [auth G],
ND [auth N],
VD [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
Query on DMU

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AB [auth C]
AE [auth P]
HB [auth C]
IB [auth C]
SC [auth L]
AB [auth C],
AE [auth P],
HB [auth C],
IB [auth C],
SC [auth L],
UC [auth M],
YD [auth P],
ZD [auth P],
ZE [auth Z]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
CHD
Query on CHD

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EB [auth C]
JC [auth G]
QC [auth J]
TD [auth P]
UA [auth B]
EB [auth C],
JC [auth G],
QC [auth J],
TD [auth P],
UA [auth B],
XD [auth P],
XE [auth W],
ZA [auth C]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
CUA
Query on CUA

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OD [auth O],
VA [auth B]
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
ZN
Query on ZN

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CC [auth F],
PE [auth S]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU

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CA [auth A],
YC [auth N]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO
Query on EDO

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AC [auth E]
BC [auth E]
BE [auth P]
CE [auth P]
DC [auth F]
AC [auth E],
BC [auth E],
BE [auth P],
CE [auth P],
DC [auth F],
DE [auth P],
EC [auth F],
FC [auth F],
FD [auth N],
GC [auth F],
GD [auth N],
GE [auth Q],
HC [auth F],
HD [auth N],
HE [auth Q],
ID [auth N],
IE [auth R],
JA [auth A],
JB [auth C],
JD [auth N],
JE [auth R],
KA [auth A],
KB [auth C],
KD [auth N],
KE [auth R],
LA [auth A],
LB [auth C],
LD [auth N],
LE [auth R],
MA [auth A],
MB [auth C],
MC [auth G],
MD [auth N],
ME [auth R],
NA [auth A],
NB [auth C],
NC [auth G],
NE [auth R],
OA [auth A],
OB [auth C],
OC [auth H],
OE [auth S],
PA [auth A],
PB [auth C],
PC [auth H],
QA [auth A],
QB [auth C],
QD [auth O],
QE [auth S],
RA [auth A],
RD [auth O],
RE [auth S],
SA [auth A],
SD [auth O],
TB [auth D],
TC [auth L],
UB [auth D],
UE [auth T],
VB [auth D],
VE [auth U],
WB [auth D],
WE [auth V],
XA [auth B],
XB [auth E],
YA [auth B],
YB [auth E],
ZB [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
AZI
Query on AZI

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BD [auth N],
CD [auth N],
FA [auth A],
GA [auth A]
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
MG
Query on MG

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DA [auth A],
ZC [auth N]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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AD [auth N],
BB [auth C],
EA [auth A],
UD [auth P]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A, N
L-PEPTIDE LINKINGC6 H11 N O3 SMET
TPO
Query on TPO
G, T
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
SAC
Query on SAC
I, V
L-PEPTIDE LINKINGC5 H9 N O4SER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.164 
  • 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
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
DMphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan18K06092
Japan Society for the Promotion of Science (JSPS)Japan18K14635

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description