3FYE

Catalytic core subunits (I and II) of cytochrome c oxidase from Rhodobacter sphaeroides in the reduced state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome C oxidase subunit 1
A, C
566Cereibacter sphaeroidesMutation(s): 0 
Gene Names: ctaD
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P33517 (Cereibacter sphaeroides)
Explore P33517 
Go to UniProtKB:  P33517
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33517
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome C oxidase subunit 2
B, D
262Cereibacter sphaeroidesMutation(s): 0 
Gene Names: ctaCcoxIIctaB
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for Q03736 (Cereibacter sphaeroides)
Explore Q03736 
Go to UniProtKB:  Q03736
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03736
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA

Download Ideal Coordinates CCD File 
BA [auth C],
CA [auth C],
E [auth A],
F [auth A]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
DMU
Query on DMU

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AA [auth B]
IA [auth C]
JA [auth C]
K [auth A]
L [auth A]
AA [auth B],
IA [auth C],
JA [auth C],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
RA [auth D],
UA [auth D],
Y [auth B]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
TRD
Query on TRD

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HA [auth C]
KA [auth C]
LA [auth C]
MA [auth C]
O [auth A]
HA [auth C],
KA [auth C],
LA [auth C],
MA [auth C],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
SA [auth D],
TA [auth D],
Z [auth B]
TRIDECANE
C13 H28
IIYFAKIEWZDVMP-UHFFFAOYSA-N
HTO
Query on HTO

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T [auth B]HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
CD
Query on CD

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PA [auth D],
QA [auth D],
W [auth B],
X [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
CU1
Query on CU1

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DA [auth C]
G [auth A]
NA [auth D]
OA [auth D]
U [auth B]
DA [auth C],
G [auth A],
NA [auth D],
OA [auth D],
U [auth B],
V [auth B]
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
CA
Query on CA

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FA [auth C],
I [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

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EA [auth C],
H [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNX
Query on UNX

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GA [auth C],
J [auth A]
UNKNOWN ATOM OR ION
X
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.613α = 90
b = 131.472β = 90
c = 176.192γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-09-06
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description