3A9F

Crystal structure of the C-terminal domain of cytochrome cz from Chlorobium tepidum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 

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Literature

Crystal structure of the electron carrier domain of the reaction center cytochrome c(z) subunit from green photosynthetic bacterium Chlorobium tepidum

Hirano, Y.Higuchi, M.Azai, C.Oh-Oka, H.Miki, K.Wang, Z.-Y.

(2010) J Mol Biol 397: 1175-1187

  • DOI: https://doi.org/10.1016/j.jmb.2010.02.011
  • Primary Citation of Related Structures:  
    3A9F

  • PubMed Abstract: 

    In green sulfur photosynthetic bacteria, the cytochrome c(z) (cyt c(z)) subunit in the reaction center complex mediates electron transfer mainly from menaquinol/cytochrome c oxidoreductase to the special pair (P840) of the reaction center. The cyt c(z) subunit consists of an N-terminal transmembrane domain and a C-terminal soluble domain that binds a single heme group. The periplasmic soluble domain has been proposed to be highly mobile and to fluctuate between oxidoreductase and P840 during photosynthetic electron transfer. We have determined the crystal structure of the oxidized form of the C-terminal functional domain of the cyt c(z) subunit (C-cyt c(z)) from thermophilic green sulfur bacterium Chlorobium tepidum at 1.3-A resolution. The overall fold of C-cyt c(z) consists of four alpha-helices and is similar to that of class I cytochrome c proteins despite the low similarity in their amino acid sequences. The N-terminal structure of C-cyt c(z) supports the swinging mechanism previously proposed in relation with electron transfer, and the surface properties provide useful information on possible interaction sites with its electron transfer partners. Several characteristic features are observed for the heme environment: These include orientation of the axial ligands with respect to the heme plane, surface-exposed area of the heme, positions of water molecules, and hydrogen-bond network involving heme propionate groups. These structural features are essential for elucidating the mechanism for regulating the redox state of cyt c(z).


  • Organizational Affiliation

    Faculty of Science, Ibaraki University, 2-1-1 Bunkyo, Mito 310-8512, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c
A, B
92Chlorobaculum tepidumMutation(s): 0 
Gene Names: pscC
UniProt
Find proteins for O07091 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS))
Explore O07091 
Go to UniProtKB:  O07091
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO07091
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
P33
Query on P33

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F [auth A]3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
PG4
Query on PG4

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I [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

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G [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4
Query on SO4

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E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
NA
Query on NA

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D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.619α = 90
b = 74.619β = 90
c = 111.211γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
OASISmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
OASISphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-01-22
    Changes: Database references
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations, Structure summary