Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 20-mer - A2B2C2D2E2F2G2H2I2J1K1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 20-mer - A4B2C2D2E2F2G2H2I1J1 

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

Macromolecule Content

• Total Structure Weight: 488.12 kDa 
• Atom Count: 33549 
• Residue Count: 3998 
• Unique protein chains: 10

1PPJ

Bovine cytochrome bc1 complex with stigmatellin and antimycin

• DOI: 10.2210/pdb1PPJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2003-06-16 Released: 2004-07-20 
• Deposition Author(s): Huang, L.S., Cobessi, D., Tung, E.Y., Berry, E.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.260 
• R-Value Work: 0.224 
• R-Value Observed: 0.224 

Literature

Binding of the Respiratory Chain Inhibitor Antimycin to the Mitochondrial bc(1) Complex: A New Crystal Structure Reveals an Altered Intramolecular Hydrogen-bonding Pattern.

Huang, L.S., Cobessi, D., Tung, E.Y., Berry, E.A.

(2005) J Mol Biol 351: 573-597

• PubMed: 16024040 
• DOI: 10.1016/j.jmb.2005.05.053
• Primary Citation of Related Structures:  
  2A06, 1PPJ, 1PP9


• PubMed Abstract: 
  

Antimycin A (antimycin), one of the first known and most potent inhibitors of the mitochondrial respiratory chain, binds to the quinone reduction site of the cytochrome bc1 complex. Structure-activity relationship studies have shown that the N-formylamino-salicyl-amide group is responsible for most of the binding specificity, and suggested that a low pKa for the phenolic OH group and an intramolecular H-bond between that OH and the carbonyl O of the salicylamide linkage are important. Two previous X-ray structures of antimycin bound to vertebrate bc1 complex gave conflicting results. A new structure reported here of the bovine mitochondrial bc1 complex at 2.28 A resolution with antimycin bound, allows us for the first time to reliably describe the binding of antimycin and shows that the intramolecular hydrogen bond described in solution and in the small-molecule structure is replaced by one involving the NH rather than carbonyl O of the amide linkage, with rotation of the amide group relative to the aromatic ring. The phenolic OH and formylamino N form H-bonds with conserved Asp228 of cytochrome b, and the formylamino O H-bonds via a water molecule to Lys227. A strong density, the right size and shape for a diatomic molecule is found between the other side of the dilactone ring and the alphaA helix.

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Organizational Affiliation: 

Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquinol-cytochrome C reductase complex core protein I, mitochondrial	A, N	446	Bos taurus	Mutation(s): 0  Gene Names: UQCRC1 EC: 1.10.2.2
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, O	439	Bos taurus	Mutation(s): 0  Gene Names: UQCRC2 EC: 1.10.2.2
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, P	379	Bos taurus	Mutation(s): 0  Gene Names: MT-CYB, COB, CYTB, MTCYB EC: 1.10.2.2
Find proteins for P00157 (Bos taurus) Explore P00157  Go to UniProtKB:  P00157

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c1, heme protein, mitochondrial	D, Q	241	Bos taurus	Mutation(s): 0  Gene Names: CYC1 EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (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, R	196	Bos taurus	Mutation(s): 0  Gene Names: UQCRFS1 EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (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, S	110	Bos taurus	Mutation(s): 0  Gene Names: UQCRB EC: 1.10.2.2
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, T	81	Bos taurus	Mutation(s): 0  Gene Names: UQCRQ EC: 1.10.2.2
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, U	78	Bos taurus	Mutation(s): 0  Gene Names: UQCRH EC: 1.10.2.2
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 iron-sulfur subunit, mitochondrial	I, V	78	Bos taurus	Mutation(s): 0  Gene Names: UQCRFS1 EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (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, W	62	Bos taurus	Mutation(s): 0  Gene Names: UQCR10 EC: 1.10.2.2
Find proteins for P00130 (Bos taurus) Explore P00130  Go to UniProtKB:  P00130

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CDL	D, G, P, T	CARDIOLIPIN C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PEE	C, D, P, Q	1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine C41 H83 N O8 P LVNGJLRDBYCPGB-LDLOPFEMSA-O
HEC	D, Q	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM	C, P	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
ANY	C, P	2-METHYL-BUTYRIC ACID 3-(3-FORMYLAMINO-2-HYDROXY-BENZOYLAMINO)-8-HEPTYL-2,6-DIMETHYL-4,9-DIOXO-[1,5]DIOXONAN-7-YL ESTER C29 H42 N2 O9 BSSBWOQOFMLGAF-GMRPKDQWSA-N
SMA	C, P	STIGMATELLIN A C30 H42 O7 UZHDGDDPOPDJGM-WPPYOTIYSA-N
JZR	A, C, D, F, P, R, S	hexyl beta-D-glucopyranoside C12 H24 O6 JVAZJLFFSJARQM-RMPHRYRLSA-N
FES	E, R	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
PO4	A, C, F, P, S	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	B, C, O, P, R	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
AZI	A, C, G, O, P	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.260 
• R-Value Work: 0.224 
• R-Value Observed: 0.224 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.53	α = 90
b = 168.748	β = 90
c = 231.533	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-06-16 
• Released Date: 2004-07-20 
Deposition Author(s): Huang, L.S., Cobessi, D., Tung, E.Y., Berry, E.A.

Revision History 

• Version 1.0: 2004-07-20
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2014-10-29
  Changes: Other
• Version 2.0: 2017-12-20
  Changes: Advisory, Atomic model, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations