7Y44

Re-refinement of damage free X-ray structure of bovine cytochrome c oxidase at 1.9 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CDLClick on this verticalbar to view detailsBest fitted TGLClick on this verticalbar to view detailsBest fitted HEAClick on this verticalbar to view detailsBest fitted PEKClick on this verticalbar to view detailsBest fitted PSCClick on this verticalbar to view detailsBest fitted PGVClick on this verticalbar to view detailsBest fitted DMUClick on this verticalbar to view detailsBest fitted CHDClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL.

Hirata, K.Shinzawa-Itoh, K.Yano, N.Takemura, S.Kato, K.Hatanaka, M.Muramoto, K.Kawahara, T.Tsukihara, T.Yamashita, E.Tono, K.Ueno, G.Hikima, T.Murakami, H.Inubushi, Y.Yabashi, M.Ishikawa, T.Yamamoto, M.Ogura, T.Sugimoto, H.Shen, J.R.Yoshikawa, S.Ago, H.

(2014) Nat Methods 11: 734-736

  • DOI: https://doi.org/10.1038/nmeth.2962
  • Primary Citation of Related Structures:  
    3WG7, 7Y44

  • PubMed Abstract: 

    We report a method of femtosecond crystallography for solving radiation damage-free crystal structures of large proteins at sub-angstrom spatial resolution, using a large single crystal and the femtosecond pulses of an X-ray free-electron laser (XFEL). We demonstrated the performance of the method by determining a 1.9-Å radiation damage-free structure of bovine cytochrome c oxidase, a large (420-kDa), highly radiation-sensitive membrane protein.


  • Organizational Affiliation

    1] RIKEN SPring-8 Center, Sayo, Japan. [2] Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology (CREST), Kawaguchi, Japan. [3].


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 
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
Find proteins for P68530 (Bos taurus)
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UniProt GroupP68530
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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
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
E, R
109Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP00426
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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
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 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6C
I, V
73Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A1
J, W
59Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P07470 (Bos taurus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7B
K, X
56Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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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 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8B
M, Z
46Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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KE [auth T],
ND [auth P],
PB [auth G],
ZA [auth C]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
TGL
Query on TGL

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CC [auth L]
DD [auth O]
IB [auth D]
QA [auth B]
VE [auth Y]
TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
HEA
Query on HEA

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

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CB [auth C]
EB [auth C]
LD [auth P]
QB [auth G]
QD [auth P]
(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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QC [auth N],
SA [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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DB [auth C]
GA [auth A]
HA [auth A]
ID [auth P]
JD [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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AC [auth K]
AE [auth Q]
BC [auth K]
DC [auth L]
HB [auth C]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
CHD
Query on CHD

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AB [auth C]
BB [auth C]
EC [auth L]
JE [auth T]
NE [auth W]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
CUA
Query on CUA

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ED [auth O],
RA [auth B]
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
PO4
Query on PO4

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ME [auth U],
UB [auth H]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
Query on ZN

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

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

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AD [auth N]
BD [auth N]
BE [auth R]
CD [auth N]
DE [auth S]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
PER
Query on PER

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FA [auth A],
OC [auth N]
PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N
MG
Query on MG

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

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EA [auth A],
KD [auth P],
NC [auth N],
WA [auth C]
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: 1.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.6α = 90
b = 204.51β = 90
c = 178.29γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CDLClick on this verticalbar to view detailsBest fitted TGLClick on this verticalbar to view detailsBest fitted HEAClick on this verticalbar to view detailsBest fitted PEKClick on this verticalbar to view detailsBest fitted PSCClick on this verticalbar to view detailsBest fitted PGVClick on this verticalbar to view detailsBest fitted DMUClick on this verticalbar to view detailsBest fitted CHDClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-20
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-05-01
    Changes: Database references