3FYI

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

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 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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

  • DOI: 10.1021/bi9001387
  • Structures With Same Primary Citation

  • 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 b ...

    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.

    Organizational Affiliation: 

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 1
A, C
566Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: ctaD
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Find proteins for P33517 (Rhodobacter sphaeroides)
Go to UniProtKB:  P33517

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 2
B, D
262Rhodobacter sphaeroidesMutation(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)
Go to UniProtKB:  Q03736
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA
Download CCD File 
A, C
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L		 Ligand Interaction
DMU
Query on DMU
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A, B, C, D
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N		 Ligand Interaction
TRD
Query on TRD
Download CCD File 
A, C, D
TRIDECANE
C13 H28
IIYFAKIEWZDVMP-UHFFFAOYSA-N		 Ligand Interaction
HTO
Query on HTO
Download CCD File 
B
HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N		 Ligand Interaction
CD
Query on CD
Download CCD File 
B, D
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N		 Ligand Interaction
CU1
Query on CU1
Download CCD File 
A, B, C, D
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
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A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
CYN
Query on CYN
Download CCD File 
A, C
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
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 = 124.344α = 90
b = 131.877β = 90
c = 176.16γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MD2data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

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