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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Ligand Structure Quality Assessment 


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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UniProt GroupP00423
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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
Find proteins for P13183 (Bos taurus)
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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
Find proteins for P10175 (Bos taurus)
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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]
CC [auth L],
DD [auth O],
IB [auth D],
QA [auth B],
VE [auth Y],
YD [auth Q]
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]
CB [auth C],
EB [auth C],
LD [auth P],
QB [auth G],
QD [auth P],
XA [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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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]
DB [auth C],
GA [auth A],
HA [auth A],
ID [auth P],
JD [auth P],
MD [auth P],
PC [auth N],
YA [auth C]
(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]
AC [auth K],
AE [auth Q],
BC [auth K],
DC [auth L],
HB [auth C],
HC [auth M],
HD [auth O],
JB [auth D],
LE [auth T],
PA [auth A],
QE [auth X],
RE [auth X],
SB [auth G],
SE [auth X],
TE [auth X],
VA [auth B],
VD [auth P],
WB [auth K],
XB [auth K],
XD [auth P],
YB [auth K],
YE [auth Z],
ZB [auth K]
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]
AB [auth C],
BB [auth C],
EC [auth L],
JE [auth T],
NE [auth W],
OD [auth P],
PD [auth P],
RB [auth G],
UE [auth X],
VB [auth J],
WE [auth Y]
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]
AD [auth N],
BD [auth N],
BE [auth R],
CD [auth N],
DE [auth S],
EE [auth S],
FB [auth C],
FC [auth L],
FD [auth O],
FE [auth S],
GB [auth C],
GC [auth L],
GD [auth O],
GE [auth S],
HE [auth S],
IA [auth A],
IC [auth M],
IE [auth S],
JA [auth A],
KA [auth A],
LA [auth A],
LB [auth F],
MA [auth A],
MB [auth F],
NA [auth A],
NB [auth F],
OA [auth A],
OB [auth F],
OE [auth W],
PE [auth W],
RC [auth N],
RD [auth P],
SC [auth N],
SD [auth P],
TA [auth B],
TB [auth G],
TC [auth N],
TD [auth P],
UA [auth B],
UC [auth N],
UD [auth P],
VC [auth N],
WC [auth N],
WD [auth P],
XC [auth N],
XE [auth Y],
YC [auth N],
ZC [auth N],
ZD [auth Q]
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 


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