ISDA

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

PDB Version:

Deposition Date:

2022-06-14

Release Date:

2022-07-20

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

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:Cytochrome c oxidase subunit 1
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

Protein Blast

Polymer Type:polypeptide(L)
Description:Cytochrome c oxidase subunit 2
Chain IDs:B, O
Chain Length:227
Number of Molecules:2
Biological Source:Bos taurus

UniProt ID:P68530 Pfam ID:PF02790, PF00116 EC:7.1.1.9

Protein Blast

Polymer Type:polypeptide(L)
Description:Cytochrome c oxidase subunit 3
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

Protein Blast

Polymer Type:polypeptide(L)
Description:Cytochrome c oxidase subunit 4 isoform 1
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

Protein Blast

Polymer Type:polypeptide(L)
Description:Cytochrome c oxidase subunit 5A
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

Protein Blast

Polymer Type:polypeptide(L)
Description:Cytochrome c oxidase subunit 5B, mitochondrial
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

Protein Blast

Polymer Type:polypeptide(L)
Description:Cytochrome c oxidase subunit 6A2
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

Protein Blast

Polymer Type:polypeptide(L)
Description:Cytochrome c oxidase subunit 6B1
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

Protein Blast

Polymer Type:polypeptide(L)
Description:Cytochrome c oxidase subunit 6C
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

Protein Blast

Polymer Type:polypeptide(L)
Description:Cytochrome c oxidase subunit 7A1
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

Protein Blast

Polymer Type:polypeptide(L)
Description:Cytochrome c oxidase subunit 7B
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

Protein Blast

Polymer Type:polypeptide(L)
Description:Cytochrome c oxidase subunit 7C, mitochondrial
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

Protein Blast

Polymer Type:polypeptide(L)
Description:Cytochrome c oxidase subunit 8B
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
FME	A	MET	modified residue
SAC	I	SER	modified residue
TPO	G	THR	modified residue

Ligand Molecules

CDL

CHD

CUA

DMU

EDO

HEA

PEK

PER

PGV

PO4

PSC

TGL

Primary Citation

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.Show

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures