5X1F

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1126/sciadv.1603042
  • Primary Citation of Related Structures:  5X19, 5X1B

  • 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 O2 at heme ...

    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 O2 at heme a3 (Fe a3). 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 CuB senses completion of proton collection and binds O2 before binding to Fe a3 to close the water channel using a conformational relay system, which includes CuB, heme a3, 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 1
A, N
514Bos taurusGene Names: MT-CO1 (COI, COXI, MTCO1)
EC: 1.9.3.1
Find proteins for P00396 (Bos taurus)
Go to Gene View: MT-CO1
Go to UniProtKB:  P00396
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 2
B, O
227Bos taurusGene Names: MT-CO2 (COII, COXII, MTCO2)
Find proteins for P68530 (Bos taurus)
Go to Gene View: MT-CO2
Go to UniProtKB:  P68530
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 3
C, P
261Bos taurusGene Names: MT-CO3 (COIII, COXIII, MTCO3)
Find proteins for P00415 (Bos taurus)
Go to Gene View: MT-CO3
Go to UniProtKB:  P00415
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
D, Q
147Bos taurusGene Names: COX4I1 (COX4)
Find proteins for P00423 (Bos taurus)
Go to Gene View: COX4I1
Go to UniProtKB:  P00423
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 5A, mitochondrial
E, R
109Bos taurusGene Names: COX5A
Find proteins for P00426 (Bos taurus)
Go to Gene View: COX5A
Go to UniProtKB:  P00426
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 5B, mitochondrial
F, S
98Bos taurusGene Names: COX5B
Find proteins for P00428 (Bos taurus)
Go to Gene View: COX5B
Go to UniProtKB:  P00428
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 6A2, mitochondrial
G, T
85Bos taurusGene Names: COX6A2 (COX6A)
Find proteins for P07471 (Bos taurus)
Go to Gene View: COX6A2
Go to UniProtKB:  P07471
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 6B1
H, U
85Bos taurusGene Names: COX6B1 (COX6B)
Find proteins for P00429 (Bos taurus)
Go to Gene View: COX6B1
Go to UniProtKB:  P00429
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 6C
I, V
73Bos taurusGene Names: COX6C
Find proteins for P04038 (Bos taurus)
Go to Gene View: COX6C
Go to UniProtKB:  P04038
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 7A1, mitochondrial
J, W
59Bos taurusGene Names: COX7A1 (COX7A, COX7AH)
Find proteins for P07470 (Bos taurus)
Go to Gene View: COX7A1
Go to UniProtKB:  P07470
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 7B, mitochondrial
K, X
56Bos taurusGene Names: COX7B
Find proteins for P13183 (Bos taurus)
Go to Gene View: COX7B
Go to UniProtKB:  P13183
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 7C, mitochondrial
L, Y
47Bos taurusGene Names: COX7C (COX7CP1)
Find proteins for P00430 (Bos taurus)
Go to Gene View: COX7C
Go to UniProtKB:  P00430
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 8B, mitochondrial
M, Z
46Bos taurusGene Names: COX8B (COX8H)
Find proteins for P10175 (Bos taurus)
Go to UniProtKB:  P10175
Small Molecules
Ligands 16 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA

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

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

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

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B, C, G, T
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE
PHOSPHATIDYLETHANOLAMINE, 2-ARACHIDONOYL-1-STEAROYL-SN-GLYCEROL-3-PHOSPHOETHANOLAMINE
C43 H78 N O8 P
ANRKEHNWXKCXDB-BHFWLYLHSA-N
 Ligand Interaction
CDL
Query on CDL

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C, G, P, T
CARDIOLIPIN
DIPHOSPHATIDYL GLYCEROL; BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
DMU
Query on DMU

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M, Z
DECYL-BETA-D-MALTOPYRANOSIDE
DECYLMALTOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
 Ligand Interaction
UNX
Query on UNX

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C, P
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
CUA
Query on CUA

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

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A, B, C, F, G, I, K, L, N, P, S, T, X
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-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
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
PHOSPHATIDYLCHOLINE, 2-LINOLEOYL-1-PALMITOYL-SN-GYCEROL-3-PHOSPHOCHOLINE
C42 H81 N O8 P
JLPULHDHAOZNQI-AUSZDXHESA-O
 Ligand Interaction
MG
Query on MG

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

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

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

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A, C, N, P, Z
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
PHOSPHATIDYLGLYCEROL, 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
 Ligand Interaction
CMO
Query on CMO

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A, N
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
A, B, N, O
L-PEPTIDE LINKINGC6 H11 N O3 SMET
SAC
Query on SAC
I, V
L-PEPTIDE LINKINGC5 H9 N O4SER
TPO
Query on TPO
G, T
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 184.806α = 90.00
b = 208.488β = 90.00
c = 177.885γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
cctbx.xfeldata processing
cctbx.primedata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant 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 

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Data collection