2YEV

Structure of caa3-type cytochrome oxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural Insights Into Electron Transfer in Caa3-Type Cytochrome Oxidases.

Lyons, J.A.Aragao, D.Slattery, O.Pisliakov, A.V.Soulimane, T.Caffrey, M.

(2012) Nature 487: 514

  • DOI: 10.1038/nature11182

  • PubMed Abstract: 
  • Cytochrome c oxidase is a member of the haem copper oxidase superfamily (HCO). HCOs function as the terminal enzymes in the respiratory chain of mitochondria and aerobic prokaryotes, coupling molecular oxygen reduction to transmembrane proton pumping ...

    Cytochrome c oxidase is a member of the haem copper oxidase superfamily (HCO). HCOs function as the terminal enzymes in the respiratory chain of mitochondria and aerobic prokaryotes, coupling molecular oxygen reduction to transmembrane proton pumping. Integral to the enzyme's function is the transfer of electrons from cytochrome c to the oxidase via a transient association of the two proteins. Electron entry and exit are proposed to occur from the same site on cytochrome c. Here we report the crystal structure of the caa3-type cytochrome oxidase from Thermus thermophilus, which has a covalently tethered cytochrome c domain. Crystals were grown in a bicontinuous mesophase using a synthetic short-chain monoacylglycerol as the hosting lipid. From the electron density map, at 2.36 Å resolution, a novel integral membrane subunit and a native glycoglycerophospholipid embedded in the complex were identified. Contrary to previous electron transfer mechanisms observed for soluble cytochrome c, the structure reveals the architecture of the electron transfer complex for the fused cupredoxin/cytochrome c domain, which implicates different sites on cytochrome c for electron entry and exit. Support for an alternative to the classical proton gate characteristic of this HCO class is presented.


    Organizational Affiliation

    Department of Chemical and Environmental Sciences, University of Limerick, Limerick, Ireland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE POLYPEPTIDE I+III
A, D
791Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: caaA (ctaD)
EC: 1.9.3.1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase, caa3
Find proteins for P98005 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P98005
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE SUBUNIT 2
B, E
337Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
EC: 1.9.3.1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase, caa3
Find proteins for Q5SLI2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLI2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CAA3-TYPE CYTOCHROME OXIDASE SUBUNIT IV
C, F
66Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase, caa3
Find proteins for Q5SH67 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SH67
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4AG
Query on 4AG

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A
(2R)-3-HYDROXYPROPANE-1,2-DIYL DIHEXADECANOATE
SN-1,2-DIPALMITOYL DIACYLGLYCEROL
C35 H68 O5
JEJLGIQLPYYGEE-MGBGTMOVSA-N
 Ligand Interaction
HAS
Query on HAS

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A, D
HEME-AS
C54 H64 Fe N4 O6
PDYODZVCODUKFH-QIHJKJTBDH
 Ligand Interaction
CL
Query on CL

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C, D, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
7E8
Query on 7E8

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A
(2R)-2,3-DIHYDROXYPROPYL (7Z)-TETRADEC-7-ENOATE
7.7 MAG
C17 H32 O4
LVBAGTJIDOCNIJ-XITLMJRVSA-N
 Ligand Interaction
CUA
Query on CUA

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B, E
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
 Ligand Interaction
7E9
Query on 7E9

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B
1,3-DIHYDROXYPROPAN-2-YL (Z)-TETRADEC-7-ENOATE
C17 H32 O4
SSMGVWSPWWDBRB-FPLPWBNLSA-N
 Ligand Interaction
5PL
Query on 5PL

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A, D
(1R,4S,6R)-6-({[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}METHYL)-4-HYDROXY-1-{[(15-METHYLHEXADECANOYL)OXY]METHYL}-4-OXIDO-7-OXO-3,5-DIOXA-8-AZA-4-PHOSPHAHEPTACOS-1-YL 15-METHYLHEXADECANOATE
C67 H129 N2 O15 P
LEQHPGOQHCQGAI-TYASGWLASA-N
 Ligand Interaction
MG
Query on MG

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A, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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A, D
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
HEC
Query on HEC

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B, E
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
C, F
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.171 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 127.250α = 90.00
b = 76.030β = 92.21
c = 300.267γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2012-06-27
    Type: Other
  • Version 1.2: 2012-08-01
    Type: Database references
  • Version 1.3: 2015-04-29
    Type: Data collection
  • Version 1.4: 2019-03-06
    Type: Data collection, Derived calculations, Experimental preparation, Other