Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 94.86 kDa 
• Atom Count: 6695 
• Modelled Residue Count: 751 
• Deposited Residue Count: 771 
• Unique protein chains: 3

3S8G

1.8 A structure of ba3 cytochrome c oxidase mutant (A120F) from Thermus thermophilus in lipid environment

• PDB DOI: 10.2210/pdb3S8G/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Thermus thermophilus
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2011-05-27 Released: 2011-08-03 
• Deposition Author(s): Tiefenbrunn, T., Liu, W., Chen, Y., Katritch, V., Stout, C.D., Fee, J.A., Cherezov, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.196 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 

Literature

High resolution structure of the ba3 cytochrome c oxidase from Thermus thermophilus in a lipidic environment.

Tiefenbrunn, T., Liu, W., Chen, Y., Katritch, V., Stout, C.D., Fee, J.A., Cherezov, V.

(2011) PLoS One 6: e22348-e22348

• PubMed: 21814577 
• DOI: 10.1371/journal.pone.0022348
• Primary Citation of Related Structures:  
  3S8F, 3S8G


• PubMed Abstract: 
  

The fundamental chemistry underpinning aerobic life on Earth involves reduction of dioxygen to water with concomitant proton translocation. This process is catalyzed by members of the heme-copper oxidase (HCO) superfamily. Despite the availability of crystal structures for all types of HCO, the mode of action for this enzyme is not understood at the atomic level, namely how vectorial H(+) and e(-) transport are coupled. Toward addressing this problem, we report wild type and A120F mutant structures of the ba(3)-type cytochrome c oxidase from Thermus thermophilus at 1.8 Å resolution. The enzyme has been crystallized from the lipidic cubic phase, which mimics the biological membrane environment. The structures reveal 20 ordered lipid molecules that occupy binding sites on the protein surface or mediate crystal packing interfaces. The interior of the protein encloses 53 water molecules, including 3 trapped in the designated K-path of proton transfer and 8 in a cluster seen also in A-type enzymes that likely functions in egress of product water and proton translocation. The hydrophobic O(2)-uptake channel, connecting the active site to the lipid bilayer, contains a single water molecule nearest the Cu(B) atom but otherwise exhibits no residual electron density. The active site contains strong electron density for a pair of bonded atoms bridging the heme Fe(a3) and Cu(B) atoms that is best modeled as peroxide. The structure of ba(3)-oxidase reveals new information about the positioning of the enzyme within the membrane and the nature of its interactions with lipid molecules. The atomic resolution details provide insight into the mechanisms of electron transfer, oxygen diffusion into the active site, reduction of oxygen to water, and pumping of protons across the membrane. The development of a robust system for production of ba(3)-oxidase crystals diffracting to high resolution, together with an established expression system for generating mutants, opens the door for systematic structure-function studies.

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Organizational Affiliation: 

Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	A	569	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: cbaA, TTHA1135 EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for Q5SJ79 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ79  Go to UniProtKB:  Q5SJ79

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 2	B	168	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: cbaB, cbac, ctaC, TTHA1134 EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for Q5SJ80 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ80  Go to UniProtKB:  Q5SJ80

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase polypeptide 2A	C	34	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: cbaD, TTHA1133 EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P82543 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P82543  Go to UniProtKB:  P82543

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HAS	E [auth A]	HEME-AS C54 H64 Fe N4 O6 PDYODZVCODUKFH-QIHJKJTBDH
HEM	D [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
OLC	AA [auth B], BA [auth C], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], X [auth B], Y [auth B], Z [auth B]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
CUA	W [auth B]	DINUCLEAR COPPER ION Cu2 ALKZAGKDWUSJED-UHFFFAOYSA-N
CU	F [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
PER	G [auth A]	PEROXIDE ION O2 ANAIPYUSIMHBEL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.196 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.963	α = 90
b = 98.636	β = 128.07
c = 95.06	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-05-27 
• Released Date: 2011-08-03 
Deposition Author(s): Tiefenbrunn, T., Liu, W., Chen, Y., Katritch, V., Stout, C.D., Fee, J.A., Cherezov, V.

Revision History  

• Version 1.0: 2011-08-03
  Type: Initial release
  
• Version 1.1: 2012-03-21
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description