PDBsum entry: 1qcr

Oxidoreductase

PDB-id: 1qcr

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Contents

Description

Header details

Header records

References

Protein chains

446 a.a.* *

423 a.a.* *

378 a.a.* *

75 a.a.* *

196 a.a.* *

103 a.a.* *

70 a.a.* *

60 a.a.* *

28 a.a.* *

59 a.a.* *

45 a.a.* *

Ligands

HEM

* C-alpha coords only

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

1qcr

Name:

Oxidoreductase

Title:

Crystal structure of bovine mitochondrial cytochrome bc1 complex, alpha carbon atoms only

Structure:

Ubiquinol cytochromE C oxidoreductase. Chain: a. Synonym: cytochrome bc1, qcr. Ubiquinol cytochromE C oxidoreductase. Chain: b. Synonym: cytochrome bc1, qcr. Ubiquinol cytochromE C oxidoreductase. Chain: c. Synonym: cytochrome bc1, qcr.

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Organ: heart. Tissue: muscle. Organelle: mitochondrion. Cellular_location: mitochondrial inner membrane. Cellular_location: mitochondrial inner membrane

UniProt:

Chain A: P31800 (QCR1_BOVIN)

Seq:
Struc:
	Seq:	480 a.a.
	Struc:	446 a.a.*

Chain B: P23004 (QCR2_BOVIN)

Seq:
Struc:
	Seq:	453 a.a.
	Struc:	423 a.a.

Chain C: P00157 (CYB_BOVIN)

Seq:
Struc:
	Seq:	379 a.a.
	Struc:	378 a.a.

Chain D: P00125 (CY1_BOVIN)

Seq:
Struc:
	Seq:	325 a.a.
	Struc:	75 a.a.

Chain E: P13272 (UCRI_BOVIN)

Seq:
Struc:
	Seq:	274 a.a.
	Struc:	196 a.a.

Chain F: P00129 (QCR7_BOVIN)

Seq:	111 a.a.
Struc:	103 a.a.*

Chain G: P13271 (QCR8_BOVIN)

Seq:	82 a.a.
Struc:	70 a.a.

Chain H: P00126 (QCR6_BOVIN)

Seq:	91 a.a.
Struc:	60 a.a.

Chain I: P13272 (UCRI_BOVIN)

Seq:
Struc:
	Seq:	274 a.a.
	Struc:	28 a.a.

Chain J: P00130 (QCR9_BOVIN)

Seq:	64 a.a.
Struc:	59 a.a.*

Chain K: P07552 (QCR10_BOVIN)

Seq:

56 a.a.

Struc:

45 a.a.*

Key:

PfamA domain

Secondary structure

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme class:

Chains E, I: E.C.1.10.2.2   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

QH₂ + 2 ferricytochrome c = Q + 2 ferrocytochrome c + 2 H⁺ (see diagram below)

Resolution:

2.70Å

R-factor:

0.300

R-free:

0.375

Authors:

D.Xia,C.A.Yu,H.Kim,J.Z.Xia,A.Kachurin,L.Zhang,L.Yu, J.Deisenhofer

Key ref:

D.Xia et al. (1997). Crystal structure of the cytochrome bc1 complex from bovine heart mitochondria.. Science, 277, 60-66. [PubMed id: 9204897] [DOI: 10.1126/science.277.5322.60]

Date:

17-May-97

Release date:

14-Oct-98

Quick_links

Key reference

DOI no: 10.1126/science.277.5322.60

Science 277:60-66 (1997)

PubMed id: 9204897

Crystal structure of the cytochrome bc1 complex from bovine heart mitochondria.

D.Xia, C.A.Yu, H.Kim, J.Z.Xia, A.M.Kachurin, L.Zhang, L.Yu, J.Deisenhofer.

ABSTRACT

On the basis of x-ray diffraction data to a resolution of 2.9 angstroms, atomic models of most protein components of the bovine cytochrome bc1 complex were built, including core 1, core 2, cytochrome b, subunit 6, subunit 7, a carboxyl-terminal fragment of cytochrome c1, and an amino-terminal fragment of the iron-sulfur protein. The positions of the four iron centers within the bc1 complex and the binding sites of the two specific respiratory inhibitors antimycin A and myxothiazol were identified. The membrane-spanning region of each bc1 complex monomer consists of 13 transmembrane helices, eight of which belong to cytochrome b. Closely interacting monomers are arranged as symmetric dimers and form cavities through which the inhibitor binding pockets can be accessed. The proteins core 1 and core 2 are structurally similar to each other and consist of two domains of roughly equal size and identical folding topology.

Selected figure(s)

Figure 2.
Fig. 2. Anomalous scattering difference-Fourier map contoured at 5.1 (red) and difference densities between inhibitor-bound and^ native crystals contoured at 4.5 (antimycin A) and 4.0 (myxothiazol). (A) View parallel to the membrane plane, with the intermembrane^ space at the top and the matrix space at the bottom. Peaks were^ assigned to hemes b[H], b[L], and c[1] and to the Rieske iron-sulfur cluster, respectively, as shown. Distances between some iron pairs are indicated (see Table 2). The twofold symmetry axis of the^ bc[1] dimer (purple line) runs in the plane of the diagram. (B) View perpendicular to the membrane plane.

Figure 3.
Fig. 3. Inhibitor binding sites in the cytochrome bc[1] complex. (A) Stereo diagram of the antimycin A binding pocket. The helices a, A, D, and E of cytochrome b form the pocket as shown. The DE^ loop is the bottom, and the b[H] heme (yellow ball-and-stick model) is the back wall of the pocket. The difference density between inhibitor-bound and native crystals is contoured at 4.5 (blue) and at -4.5 (brown). An antimycin molecule is fitted to the positive^ density. (B) Stereo diagram of the myxothiazol binding pocket, formed by helices C, F, cd1, and ef of cytochrome b, as indicated. The b[L] heme (yellow ball-and-stick model) and the Rieske^ iron-sulfur center (green and yellow dots) are about equally distant from the pocket. The difference density is contoured at 4.0 (blue).

The above figures are reprinted by permission from the AAAs: Science (1997, 277, 60-66) copyright 1997.

Figures were selected by the author.