Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 22-mer - A2B2C2D2E2F2G2H2I2J2K2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 22-mer - A4B2C2D2E2F2G2H2I2J2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 241.75 kDa 
• Atom Count: 17118 
• Modelled Residue Count: 2114 
• Deposited Residue Count: 2145 
• Unique protein chains: 11

1NTK

Crystal Structure of Mitochondrial Cytochrome bc1 in Complex with Antimycin A1

• PDB DOI: 10.2210/pdb1NTK/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bos taurus
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2003-01-30 Released: 2003-10-07 
• Deposition Author(s): Gao, X., Wen, X., Esser, L., Quinn, B., Yu, L., Yu, C.-A., Xia, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.270 
• R-Value Work: 0.233 
• R-Value Observed: 0.234 

Literature

Structural basis for the quinone reduction in the bc(1) complex: a comparative analysis of crystal structures of mitochondrial cytochrome bc(1) with bound substrate and inhibitors at the Q(i) site

Gao, X., Wen, X., Esser, L., Quinn, B., Yu, L., Yu, C.-A., Xia, D.

(2003) Biochemistry 42: 9067-9080

• PubMed: 12885240 
• DOI: 10.1021/bi0341814
• Primary Citation of Related Structures:  
  1NTK, 1NTM, 1NTZ, 1NU1


• PubMed Abstract: 
  

Cytochrome bc(1) is an integral membrane protein complex essential to cellular respiration and photosynthesis. The Q cycle reaction mechanism of bc(1) postulates a separated quinone reduction (Q(i)) and quinol oxidation (Q(o)) site. In a complete catalytic cycle, a quinone molecule at the Q(i) site receives two electrons from the b(H) heme and two protons from the negative side of the membrane; this process is specifically inhibited by antimycin A and NQNO. The structures of bovine mitochondrial bc(1) in the presence or absence of bound substrate ubiquinone and with either the bound antimycin A(1) or NQNO were determined and refined. A ubiquinone with its first two isoprenoid repeats and an antimycin A(1) were identified in the Q(i) pocket of the substrate and inhibitor bound structures, respectively; the NQNO, on the other hand, was identified in both Q(i) and Q(o) pockets in the inhibitor complex. The two inhibitors occupied different portions of the Q(i) pocket and competed with substrate for binding. In the Q(o) pocket, the NQNO behaves similarly to stigmatellin, inducing an iron-sulfur protein conformational arrest. Extensive binding interactions and conformational adjustments of residues lining the Q(i) pocket provide a structural basis for the high affinity binding of antimycin A and for phenotypes of inhibitor resistance. A two-water-mediated ubiquinone protonation mechanism is proposed involving three Q(i) site residues His(201), Lys(227), and Asp(228).

---

Organizational Affiliation: 

Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquinol-cytochrome C reductase complex core protein I, mitochondrial	A	446	Bos taurus	Mutation(s): 0  Gene Names: UQCRC1 EC: 1.10.2.2 Membrane Entity: Yes
UniProt
Find proteins for P31800 (Bos taurus) Explore P31800  Go to UniProtKB:  P31800

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquinol-cytochrome C reductase complex core protein 2, mitochondrial	B	439	Bos taurus	Mutation(s): 0  Gene Names: UQCRC2 EC: 1.10.2.2 Membrane Entity: Yes
UniProt
Find proteins for P23004 (Bos taurus) Explore P23004  Go to UniProtKB:  P23004

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b	C	379	Bos taurus	Mutation(s): 0  Gene Names: MT-CYB, COB, CYTB, MTCYB Membrane Entity: Yes
UniProt
Find proteins for P00157 (Bos taurus) Explore P00157  Go to UniProtKB:  P00157

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
cytochrome c1	D	241	Bos taurus	Mutation(s): 0  Gene Names: CYC1 EC: 7.1.1.8 Membrane Entity: Yes
UniProt
Find proteins for P00125 (Bos taurus) Explore P00125  Go to UniProtKB:  P00125

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, MITOCHONDRIAL	E	196	Bos taurus	Mutation(s): 0  Gene Names: UQCRFS1 EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P13272 (Bos taurus) Explore P13272  Go to UniProtKB:  P13272

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquinol-cytochrome C reductase complex 14 kDa protein	F	110	Bos taurus	Mutation(s): 0  Gene Names: UQCRB EC: 1.10.2.2 Membrane Entity: Yes
UniProt
Find proteins for P00129 (Bos taurus) Explore P00129  Go to UniProtKB:  P00129

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C	G	81	Bos taurus	Mutation(s): 0  Gene Names: UQCRQ EC: 1.10.2.2 Membrane Entity: Yes
UniProt
Find proteins for P13271 (Bos taurus) Explore P13271  Go to UniProtKB:  P13271

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquinol-cytochrome C reductase complex 11 kDa protein	H	78	Bos taurus	Mutation(s): 0  Gene Names: UQCRH EC: 1.10.2.2 Membrane Entity: Yes
UniProt
Find proteins for P00126 (Bos taurus) Explore P00126  Go to UniProtKB:  P00126

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquinol-cytochrome C reductase 8 kDa protein	I	57	Bos taurus	Mutation(s): 0  Gene Names: UQCRFS1 EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P13272 (Bos taurus) Explore P13272  Go to UniProtKB:  P13272

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquinol-cytochrome C reductase complex 7.2 kDa protein	J	62	Bos taurus	Mutation(s): 0  Gene Names: UQCR10 EC: 1.10.2.2 Membrane Entity: Yes
UniProt
Find proteins for P00130 (Bos taurus) Explore P00130  Go to UniProtKB:  P00130

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquinol-cytochrome C reductase complex 6.4 kDa protein	K	56	Bos taurus	Mutation(s): 0  Gene Names: UQCR11, UQCR EC: 1.10.2.2 Membrane Entity: Yes
UniProt
Find proteins for P07552 (Bos taurus) Explore P07552  Go to UniProtKB:  P07552

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	L [auth C], M [auth C], O [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
AY1	N [auth C]	[(2R,3S,6S,7R,8R)-3-[(3-formamido-2-oxidanyl-phenyl)carbonylamino]-8-hexyl-2,6-dimethyl-4,9-bis(oxidanylidene)-1,5-dioxonan-7-yl] 2-methylpropanoate C27 H38 N2 O9 KHLDVDGEVBRYTL-JABWOZRQSA-N
FES	P [auth E]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AY1	PDBBind:  1NTK	Kd: 0.03 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.270 
• R-Value Work: 0.233 
• R-Value Observed: 0.234 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.785	α = 90
b = 153.785	β = 90
c = 592.498	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-01-30 
• Released Date: 2003-10-07 
Deposition Author(s): Gao, X., Wen, X., Esser, L., Quinn, B., Yu, L., Yu, C.-A., Xia, D.

Revision History  

• Version 1.0: 2003-10-07
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2016-03-16
  Changes: Non-polymer description