Selenomethionine-labelled soluble domain of Rieske iron-sulfur protein from chlorobaculum tepidum

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

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This is version 2.0 of the entry. See complete history


Soluble domains of cytochrome c-556 and Rieske iron-sulfur protein from Chlorobaculum tepidum: Crystal structures and interaction analysis.

Kishimoto, H.Azai, C.Yamamoto, T.Mutoh, R.Nakaniwa, T.Tanaka, H.Miyanoiri, Y.Kurisu, G.Oh-Oka, H.

(2023) Curr Res Struct Biol 5: 100101-100101

  • DOI: https://doi.org/10.1016/j.crstbi.2023.100101
  • Primary Citation of Related Structures:  
    8HN2, 8HN3

  • PubMed Abstract: 

    In photosynthetic green sulfur bacteria, the electron transfer reaction from menaquinol:cytochrome c oxidoreductase to the P840 reaction center (RC) complex occurs directly without any involvement of soluble electron carrier protein(s). X-ray crystallography has determined the three-dimensional structures of the soluble domains of the CT0073 gene product and Rieske iron-sulfur protein (ISP). The former is a mono-heme cytochrome c with an α-absorption peak at 556 nm. The overall fold of the soluble domain of cytochrome c -556 (designated as cyt c -556 sol ) consists of four α-helices and is very similar to that of water-soluble cyt c -554 that independently functions as an electron donor to the P840 RC complex. However, the latter's remarkably long and flexible loop between the α3 and α4 helices seems to make it impossible to be a substitute for the former. The structure of the soluble domain of the Rieske ISP (Rieske sol protein) shows a typical β-sheets-dominated fold with a small cluster-binding and a large subdomain. The architecture of the Rieske sol protein is bilobal and belongs to those of b 6 f -type Rieske ISPs. Nuclear magnetic resonance (NMR) measurements revealed weak non-polar but specific interaction sites on Rieske sol protein when mixed with cyt c -556 sol . Therefore, menaquinol:cytochrome c oxidoreductase in green sulfur bacteria features a Rieske/cyt b complex tightly associated with membrane-anchored cyt c -556.

  • Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex iron-sulfur subunit
A, B
110Chlorobaculum tepidumMutation(s): 0 
Gene Names: petCCT0302
Find proteins for Q9F722 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS))
Explore Q9F722 
Go to UniProtKB:  Q9F722
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9F722
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.64α = 90
b = 58.695β = 112.04
c = 49.68γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan19H04724
Japan Society for the Promotion of Science (JSPS)Japan15K21122
Japan Society for the Promotion of Science (JSPS)JapanT18K061530
Japan Science and TechnologyJapanJPMJCR20E1

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-05
    Type: Initial release
  • Version 2.0: 2023-11-15
    Type: Coordinate replacement
    Reason: Atoms with unrealistic or zero occupancies
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary