5NDC | pdb_00005ndc

Structure of ba3-type cytochrome c oxidase from Thermus thermophilus by serial femtosecond crystallography

• PDB DOI: https://doi.org/10.2210/pdb5NDC/pdb

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


• Deposited: 2017-03-08 Released: 2017-08-23 
• Deposition Author(s): Andersson, R., Safari, C., Dods, R., Nango, E., Tanaka, R., Nakane, T., Tono, K., Joti, Y., Bath, P., Dunevall, E., Bosman, E., Nureki, O., Iwata, S., Neutze, R., Branden, G.
• Funding Organization(s): The Swedish Foundation of Strategic Research, The Knut and Alice Wallenberg Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.197 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.162 (Depositor) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Serial femtosecond crystallography structure of cytochrome c oxidase at room temperature.

Andersson, R., Safari, C., Dods, R., Nango, E., Tanaka, R., Yamashita, A., Nakane, T., Tono, K., Joti, Y., Bath, P., Dunevall, E., Bosman, R., Nureki, O., Iwata, S., Neutze, R., Branden, G.

(2017) Sci Rep 7: 4518-4518

• PubMed: 28674417 
• DOI: https://doi.org/10.1038/s41598-017-04817-z
• Primary Citation Related Structures: 
  5NDC


• PubMed Abstract: 
  

  Cytochrome c oxidase catalyses the reduction of molecular oxygen to water while the energy released in this process is used to pump protons across a biological membrane. Although an extremely well-studied biological system, the molecular mechanism of proton pumping by cytochrome c oxidase is still not understood. Here we report a method to produce large quantities of highly diffracting microcrystals of ba ₃ -type cytochrome c oxidase from Thermus thermophilus suitable for serial femtosecond crystallography. The room-temperature structure of cytochrome c oxidase is solved to 2.3 Å resolution from data collected at an X-ray Free Electron Laser. We find overall agreement with earlier X-ray structures solved from diffraction data collected at cryogenic temperature. Previous structures solved from synchrotron radiation data, however, have shown conflicting results regarding the identity of the active-site ligand. Our room-temperature structure, which is free from the effects of radiation damage, reveals that a single-oxygen species in the form of a water molecule or hydroxide ion is bound in the active site. Structural differences between the ba ₃ -type and aa ₃ -type cytochrome c oxidases around the proton-loading site are also described.

---

Organizational Affiliation: 
• Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530, Gothenburg, Sweden.
RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan.
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan.
Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530, Gothenburg, Sweden. [e-mail].

Biological Assembly 1  

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: 92.97 kDa 
• Atom Count: 6,386 
• Modeled Residue Count: 752 
• Deposited Residue Count: 771 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	A	569	Thermus thermophilus	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	Mutation(s): 0  Gene Names: cbaB, 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 IIA	C	34	Thermus thermophilus	Mutation(s): 0  Gene Names: HGMM_F04D06C07, TTMY_0198 EC: 7.1.1.9 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HAS	F [auth A]	HEME-AS C54 H64 Fe N4 O6 PDYODZVCODUKFH-ZOMLSHGTSA-L
HEM	E [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
OLC	G [auth A], 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], S [auth B], T [auth C], U [auth C], V [auth C]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
CUA	R [auth B]	DINUCLEAR COPPER ION Cu2 ALKZAGKDWUSJED-UHFFFAOYSA-N
CU	D [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.197 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.162 (Depositor) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.85	α = 90
b = 100.32	β = 126.76
c = 96.62	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-08-23 
Deposition Author(s): Andersson, R., Safari, C., Dods, R., Nango, E., Tanaka, R., Nakane, T., Tono, K., Joti, Y., Bath, P., Dunevall, E., Bosman, E., Nureki, O., Iwata, S., Neutze, R., Branden, G.

---

Funding Organization	Location	Grant Number
The Swedish Foundation of Strategic Research	Sweden	SRL10-0036
The Swedish Foundation of Strategic Research	Sweden	2015-00560, 349-2011-6485
The Knut and Alice Wallenberg Foundation	Sweden	KAW 2012.0284

Revision History  

• Version 1.0: 2017-08-23
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Data collection
• Version 1.2: 2018-11-14
  Changes: Data collection
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description