2GSM

Catalytic Core (Subunits I and II) of Cytochrome c oxidase from Rhodobacter sphaeroides


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Identification of conserved lipid/detergent-binding sites in a high-resolution structure of the membrane protein cytochrome c oxidase.

Qin, L.Hiser, C.Mulichak, A.Garavito, R.M.Ferguson-Miller, S.

(2006) Proc Natl Acad Sci U S A 103: 16117-16122

  • DOI: 10.1073/pnas.0606149103
  • Primary Citation of Related Structures:  
    2GSM

  • PubMed Abstract: 
  • Well ordered reproducible crystals of cytochrome c oxidase (CcO) from Rhodobacter sphaeroides yield a previously unreported structure at 2.0 A resolution that contains the two catalytic subunits and a number of alkyl chains of lipids and detergents. Comparison with crystal structures of other bacterial and mammalian CcOs reveals that the positions occupied by native membrane lipids and detergent substitutes are highly conserved, along with amino acid residues in their vicinity, suggesting a more prevalent and specific role of lipid in membrane protein structure than often envisioned ...

    Well ordered reproducible crystals of cytochrome c oxidase (CcO) from Rhodobacter sphaeroides yield a previously unreported structure at 2.0 A resolution that contains the two catalytic subunits and a number of alkyl chains of lipids and detergents. Comparison with crystal structures of other bacterial and mammalian CcOs reveals that the positions occupied by native membrane lipids and detergent substitutes are highly conserved, along with amino acid residues in their vicinity, suggesting a more prevalent and specific role of lipid in membrane protein structure than often envisioned. Well defined detergent head groups (maltose) are found associated with aromatic residues in a manner similar to phospholipid head groups, likely contributing to the success of alkyl glycoside detergents in supporting membrane protein activity and crystallizability. Other significant features of this structure include the following: finding of a previously unreported crystal contact mediated by cadmium and an engineered histidine tag; documentation of the unique His-Tyr covalent linkage close to the active site; remarkable conservation of a chain of waters in one proton pathway (D-path); and discovery of an inhibitory cadmium-binding site at the entrance to another proton path (K-path). These observations provide important insight into CcO structure and mechanism, as well as the significance of bound lipid in membrane proteins.


    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1A, C566Cereibacter sphaeroidesMutation(s): 0 
Gene Names: ctaD
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2B, D262Cereibacter sphaeroidesMutation(s): 0 
Gene Names: ctaCcoxIIctaB
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA

Download Ideal Coordinates CCD File 
GA [auth C],
HA [auth C],
L [auth A],
M [auth A]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
DMU
Query on DMU

Download Ideal Coordinates CCD File 
AA [auth C],
BA [auth C],
E [auth A],
F [auth A],
G [auth A],
AA [auth C],
BA [auth C],
E [auth A],
F [auth A],
G [auth A],
MA [auth D],
NA [auth D],
S [auth B],
T [auth B],
Z [auth C]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
 Ligand Interaction
TRD
Query on TRD

Download Ideal Coordinates CCD File 
IA [auth C],
JA [auth C],
KA [auth C],
LA [auth C],
N [auth A],
IA [auth C],
JA [auth C],
KA [auth C],
LA [auth C],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
SA [auth D],
TA [auth D],
Y [auth B]
TRIDECANE
C13 H28
IIYFAKIEWZDVMP-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download Ideal Coordinates CCD File 
QA [auth D],
RA [auth D],
W [auth B],
X [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download Ideal Coordinates CCD File 
CA [auth C],
H [auth A],
OA [auth D],
PA [auth D],
U [auth B],
CA [auth C],
H [auth A],
OA [auth D],
PA [auth D],
U [auth B],
V [auth B]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
EA [auth C],
J [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
DA [auth C],
I [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
OH
Query on OH

Download Ideal Coordinates CCD File 
FA [auth C],
K [auth A]
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.02α = 90
b = 131.639β = 90
c = 176.802γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-10
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Advisory, Refinement description