7Y44 image
Deposition Date 2022-06-14
Release Date 2022-07-20
Last Version Date 2025-09-17
Entry Detail
PDB ID:
7Y44
Keywords:
OXIDOREDUCTASE
Title:
Re-refinement of damage free X-ray structure of bovine cytochrome c oxidase at 1.9 angstrom resolution
Biological Source:
Source Organism:
Bos taurus (Taxon ID: 9913)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.90 Å
R-Value Free:
0.22
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 21 21 21
7Y44 validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 1
Gene (Uniprot):MT-CO1
Chain IDs:A, N
Chain Length:514
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P00396 Pfam ID:PF00115 EC:7.1.1.9
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 2
Gene (Uniprot):MT-CO2
Chain IDs:B, O
Chain Length:227
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P68530 Pfam ID:PF02790, PF00116
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 3
Gene (Uniprot):MT-CO3
Chain IDs:C, P
Chain Length:261
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P00415 Pfam ID:PF00510 EC:7.1.1.9
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 4 isoform 1
Gene (Uniprot):COX4I1
Chain IDs:D, Q
Chain Length:147
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P00423 Pfam ID:PF02936 EC:7.1.1.9
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 5A
Gene (Uniprot):COX5A
Chain IDs:E, R
Chain Length:109
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P00426 Pfam ID:PF02284 EC:7.1.1.9
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 5B, mitochondrial
Gene (Uniprot):COX5B
Chain IDs:F, S
Chain Length:98
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P00428 Pfam ID:PF01215 EC:7.1.1.9
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 6A2
Gene (Uniprot):COX6A2
Chain IDs:G, T
Chain Length:85
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P07471 Pfam ID:PF02046 EC:7.1.1.9
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 6B1
Gene (Uniprot):COX6B1
Chain IDs:H, U
Chain Length:85
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P00429 Pfam ID:PF02297 EC:7.1.1.9
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 6C
Gene (Uniprot):COX6C
Chain IDs:I, V
Chain Length:73
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P04038 Pfam ID:PF02937 EC:7.1.1.9
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 7A1
Gene (Uniprot):COX7A1
Chain IDs:J, W
Chain Length:59
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P07470 Pfam ID:PF02238 EC:7.1.1.9
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 7B
Gene (Uniprot):COX7B
Chain IDs:K, X
Chain Length:56
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P13183 Pfam ID:PF05392 EC:7.1.1.9
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 7C, mitochondrial
Gene (Uniprot):COX7C
Chain IDs:L, Y
Chain Length:47
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P00430 Pfam ID:PF02935 EC:7.1.1.9
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 8B
Gene (Uniprot):COX8B
Chain IDs:M, Z
Chain Length:46
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P10175 Pfam ID:PF02285 EC:7.1.1.9
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
FME A MET modified residue
SAC I SER modified residue
TPO G THR modified residue
Ligand Molecules
CDL
CHD
CU
CUA
DMU
EDO
HEA
MG
NA
PEK
PER
PGV
PO4
PSC
TGL
ZN
Primary Citation
Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL.
Nat.Methods 11 734 736 (2014)
PMID: 24813624 DOI: 10.1038/nmeth.2962

Abstact

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.

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Disease

Primary Citation of related structures
7Y44