5X1F

CO bound cytochrome c oxidase without pump laser irradiation at 278K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1
A, N
514Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P00396 (Bos taurus)
Explore P00396 
Go to UniProtKB:  P00396
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00396
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2
B, O
227Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P68530 (Bos taurus)
Explore P68530 
Go to UniProtKB:  P68530
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68530
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3
C, P
261Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00415 (Bos taurus)
Explore P00415 
Go to UniProtKB:  P00415
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00415
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
D, Q
147Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00423 (Bos taurus)
Explore P00423 
Go to UniProtKB:  P00423
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00423
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrial
E, R
109Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00426 (Bos taurus)
Explore P00426 
Go to UniProtKB:  P00426
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00426
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B, mitochondrial
F, S
98Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00428 (Bos taurus)
Explore P00428 
Go to UniProtKB:  P00428
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00428
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2, mitochondrial
G, T
85Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P07471 (Bos taurus)
Explore P07471 
Go to UniProtKB:  P07471
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07471
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1
H, U
85Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00429 (Bos taurus)
Explore P00429 
Go to UniProtKB:  P00429
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00429
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6C
I, V
73Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P04038 (Bos taurus)
Explore P04038 
Go to UniProtKB:  P04038
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04038
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A1, mitochondrial
J, W
59Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P07470 (Bos taurus)
Explore P07470 
Go to UniProtKB:  P07470
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07470
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7B, mitochondrial
K, X
56Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P13183 (Bos taurus)
Explore P13183 
Go to UniProtKB:  P13183
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13183
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrial
L, Y
47Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00430 (Bos taurus)
Explore P00430 
Go to UniProtKB:  P00430
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00430
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8B, mitochondrial
M, Z
46Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P10175 (Bos taurus)
Explore P10175 
Go to UniProtKB:  P10175
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10175
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
IB [auth G],
LC [auth P],
UA [auth C],
UC [auth T]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
TGL
Query on TGL

Download Ideal Coordinates CCD File 
DC [auth N]
EB [auth D]
GA [auth A]
QC [auth Q]
RB [auth L]
DC [auth N],
EB [auth D],
GA [auth A],
QC [auth Q],
RB [auth L],
YC [auth Y]
TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
HEA
Query on HEA

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

Download Ideal Coordinates CCD File 
HB [auth G]
JB [auth G]
QA [auth B]
TC [auth T]
XA [auth C]
HB [auth G],
JB [auth G],
QA [auth B],
TC [auth T],
XA [auth C],
ZA [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

Download Ideal Coordinates CCD File 
IC [auth O],
PA [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

Download Ideal Coordinates CCD File 
BC [auth N]
CC [auth N]
HA [auth A]
IA [auth A]
KC [auth P]
BC [auth N],
CC [auth N],
HA [auth A],
IA [auth A],
KC [auth P],
TA [auth C],
YA [auth C],
ZC [auth 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
DMU
Query on DMU

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

Download Ideal Coordinates CCD File 
KB [auth G]
MC [auth P]
NB [auth J]
NC [auth P]
OA [auth B]
KB [auth G],
MC [auth P],
NB [auth J],
NC [auth P],
OA [auth B],
VA [auth C],
WA [auth C],
WC [auth W]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
CUA
Query on CUA

Download Ideal Coordinates CCD File 
HC [auth O],
NA [auth B]
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
FB [auth F],
RC [auth S]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU

Download Ideal Coordinates CCD File 
CA [auth A],
XB [auth N]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AB [auth C]
BB [auth C]
CB [auth C]
DB [auth C]
EC [auth N]
AB [auth C],
BB [auth C],
CB [auth C],
DB [auth C],
EC [auth N],
FC [auth N],
GB [auth F],
GC [auth N],
JA [auth A],
KA [auth A],
LA [auth A],
LB [auth G],
MA [auth A],
MB [auth I],
OB [auth K],
OC [auth P],
PB [auth K],
PC [auth P],
QB [auth K],
RA [auth B],
SB [auth L],
SC [auth S],
TB [auth L],
VC [auth T],
XC [auth X]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CMO
Query on CMO

Download Ideal Coordinates CCD File 
AC [auth N],
FA [auth A]
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
MG
Query on MG

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

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

Download Ideal Coordinates CCD File 
JC [auth P],
SA [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: 2.20 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.806α = 90
b = 208.488β = 90
c = 177.885γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
cctbx.xfeldata processing
cctbx.primedata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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
  • Version 1.2: 2018-01-24
    Changes: Data collection
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary