5X1B

CO bound cytochrome c oxidase at 20 nsec after pump laser irradiation to release CO from O2 reduction center

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase.

Shimada, A., Kubo, M., Baba, S., Yamashita, K., Hirata, K., Ueno, G., Nomura, T., Kimura, T., Shinzawa-Itoh, K., Baba, J., Hatano, K., Eto, Y., Miyamoto, A., Murakami, H., Kumasaka, T., Owada, S., Tono, K., Yabashi, M., Yamaguchi, Y., Yanagisawa, S., Sakaguchi, M., Ogura, T., Komiya, R., Yan, J., Yamashita, E., Yamamoto, M., Ago, H., Yoshikawa, S., Tsukihara, T.

(2017) Sci Adv 3: e1603042-e1603042

  • DOI: https://doi.org/10.1126/sciadv.1603042
  • Primary Citation of Related Structures:  
    5X19, 5X1B, 5X1F

  • PubMed Abstract: 

    Bovine cytochrome c oxidase (CcO), a 420-kDa membrane protein, pumps protons using electrostatic repulsion between protons transferred through a water channel and net positive charges created by oxidation of heme a (Fe a ) for reduction of O 2 at heme a 3 (Fe a 3). For this process to function properly, timing is essential: The channel must be closed after collection of the protons to be pumped and before Fe a oxidation. If the channel were to remain open, spontaneous backflow of the collected protons would occur. For elucidation of the channel closure mechanism, the opening of the channel, which occurs upon release of CO from CcO, is investigated by newly developed time-resolved x-ray free-electron laser and infrared techniques with nanosecond time resolution. The opening process indicates that Cu B senses completion of proton collection and binds O 2 before binding to Fe a 3 to close the water channel using a conformational relay system, which includes Cu B , heme a 3 , and a transmembrane helix, to block backflow of the collected protons.

    • Organizational Affiliation: 

    Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1
A, N
514Bos taurusMutation(s): 0 
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
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UniProt GroupP00396
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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 
UniProt
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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 
UniProt
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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 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrial
E, R
109Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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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 
UniProt
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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 
UniProt
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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, mitochondrial
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 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL
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JC [auth P],
QC [auth T],
VA [auth C],
ZA [auth C]		CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
TGL
Query on TGL
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AC [auth N]
BC [auth N]
CC [auth N]
EB [auth D]
GA [auth A]
AC [auth N],
BC [auth N],
CC [auth N],
EB [auth D],
GA [auth A],
PB [auth L]
TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
HEA
Query on HEA
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AA [auth A],
BA [auth A],
SB [auth N],
TB [auth N]		HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PEK
Query on PEK
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HB [auth G]
HC [auth P]
IB [auth G]
OC [auth T]
PC [auth T]
HB [auth G],
HC [auth P],
IB [auth G],
OC [auth T],
PC [auth T],
YA [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
Query on PSC
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MC [auth R],
QA [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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AB [auth C]
HA [auth A]
IA [auth A]
IC [auth P]
JB [auth G]
AB [auth C],
HA [auth A],
IA [auth A],
IC [auth P],
JB [auth G],
UA [auth C],
YB [auth N],
ZB [auth N]
(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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RB [auth M],
TC [auth Z]		DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
CHD
Query on CHD
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FC [auth O]
KC [auth P]
LB [auth J]
LC [auth P]
PA [auth B]
FC [auth O],
KC [auth P],
LB [auth J],
LC [auth P],
PA [auth B],
SC [auth W],
WA [auth C],
XA [auth C]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
CUA
Query on CUA
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EC [auth O],
OA [auth B]		DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
ZN
Query on ZN
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FB [auth F],
NC [auth S]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU
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CA [auth A],
UB [auth N]		COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO
Query on EDO
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BB [auth C]
CB [auth C]
DB [auth C]
DC [auth N]
GB [auth F]
BB [auth C],
CB [auth C],
DB [auth C],
DC [auth N],
GB [auth F],
JA [auth A],
KA [auth A],
KB [auth G],
LA [auth A],
MA [auth A],
MB [auth K],
NA [auth A],
NB [auth K],
OB [auth K],
QB [auth L],
RA [auth B],
RC [auth T],
SA [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CMO
Query on CMO
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FA [auth A],
XB [auth N]		CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
MG
Query on MG
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DA [auth A],
VB [auth N]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA
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EA [auth A],
WB [auth N]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
UNX
Query on UNX
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GC [auth P],
TA [auth C]		UNKNOWN ATOM OR ION
X
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: 2.40 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.849α = 90
b = 209.485β = 90
c = 179.524γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
cctbx.xfeldata processing
cctbx.primedata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
X-ray Free Electron Laser Priority Strategy Program (MEXT)Japan--
JST, CRESTJapan--
JST, PRESTOJapan--
Pioneering Project "Dynamic Structural Biology" of RIKENJapan--
Photon and Quantum Basic Research Coordinated Development ProgramJapan--
JSPS KAKENHI GRANTJapan26291033
JSPS KAKENHI GRANTJapan15K18493
Machine Tool Engineering FoundationJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references