Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 196.73 kDa 
• Atom Count: 13601 
• Residue Count: 1578 
• Unique protein chains: 2

3FYI

Catalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides in the reduced state bound with cyanide

• DOI: 10.2210/pdb3FYI/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rhodobacter sphaeroides
• Expression System: Rhodobacter sphaeroides
• Mutation(s): No 


• Deposited: 2009-01-22 Released: 2009-06-16 
• Deposition Author(s): Qin, L., Mills, D.A., Proshlyakov, D.A., Hiser, C., Ferguson-Miller, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.219 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Literature

Redox dependent conformational changes in cytochrome c oxidase suggest a gating mechanism for proton uptake.

Qin, L., Liu, J., Mills, D., Proshlyakov, D.A., Hiser, C., Ferguson-Miller, S.

(2009) Biochemistry 48: 5121-5130

• PubMed: 19397279 
• DOI: 10.1021/bi9001387
• Primary Citation of Related Structures:  
  3FYE, 3FYI


• PubMed Abstract: 
  

A role for conformational change in the coupling mechanism of cytochrome c oxidase is the subject of controversy. Relatively small conformational changes have been reported in comparisons of reduced and oxidized crystal structures of bovine oxidase but none in bacterial oxidases. Comparing the X-ray crystal structures of the reduced (at 2.15 A resolution) and oxidized forms of cytochrome c oxidase from Rhodobacter sphaeroides, we observe a displacement of heme a(3) involving both the porphyrin ring and the hydroxyl farnesyl tail, accompanied by protein movements in nearby regions, including the mid part of helix VIII of subunit I which harbors key residues of the K proton uptake path, K362 and T359. The conformational changes in the reduced form are reversible upon reoxidation. They result in an opening of the top of the K pathway and more ordered waters being resolved in that region, suggesting an access path for protons into the active site. In all high-resolution structures of oxidized R. sphaeroides cytochrome c oxidase, a water molecule is observed in the hydrophobic region above the top of the D path, strategically positioned to facilitate the connection of residue E286 of subunit I to the active site or to the proton pumping exit path. In the reduced and reduced plus cyanide structures, this water molecule disappears, implying disruption of proton conduction from the D path under conditions when the K path is open, thus providing a mechanism for alternating access to the active site.

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Organizational Affiliation: 

Biochemistry and Molecular Biology Department, Michigan State University, East Lansing, Michigan 48824, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	A, C	566	Rhodobacter sphaeroides	Mutation(s): 0  Gene Names: ctaD EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Find proteins for P33517 (Rhodobacter sphaeroides) Explore P33517  Go to UniProtKB:  P33517

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 2	B, D	262	Rhodobacter sphaeroides	Mutation(s): 0  Gene Names: ctaC, coxII, ctaB EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Find proteins for Q03736 (Rhodobacter sphaeroides) Explore Q03736  Go to UniProtKB:  Q03736

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEA	A, C	HEME-A C49 H56 Fe N4 O6 ZGGYGTCPXNDTRV-PRYGPKJJSA-L
DMU	A, B, C, D	DECYL-BETA-D-MALTOPYRANOSIDE C22 H42 O11 WOQQAWHSKSSAGF-WXFJLFHKSA-N
TRD	A, C, D	TRIDECANE C13 H28 IIYFAKIEWZDVMP-UHFFFAOYSA-N
HTO	B	HEPTANE-1,2,3-TRIOL C7 H16 O3 HXYCHJFUBNTKQR-RNFRBKRXSA-N
CD	B, D	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
CU1	A, B, C, D	COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N
CA	A, C	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CYN	A, C	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N
MG	A, C	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.219 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.344	α = 90
b = 131.877	β = 90
c = 176.16	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MD2	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASES	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-01-22 
• Released Date: 2009-06-16 
Deposition Author(s): Qin, L., Mills, D.A., Proshlyakov, D.A., Hiser, C., Ferguson-Miller, S.

Revision History 

• Version 1.0: 2009-06-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Advisory, Refinement description