6ZMQ

Cytochrome c Heme Lyase CcmF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.273 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Architecture of the membrane-bound cytochrome c heme lyase CcmF.

Brausemann, A.Zhang, L.Ilcu, L.Einsle, O.

(2021) Nat Chem Biol 17: 800-805

  • DOI: https://doi.org/10.1038/s41589-021-00793-8
  • Primary Citation of Related Structures:  
    6ZMQ

  • PubMed Abstract: 

    The covalent attachment of one or multiple heme cofactors to cytochrome c protein chains enables cytochrome c proteins to be used in electron transfer and redox catalysis in extracytoplasmic environments. A dedicated heme maturation machinery, whose core component is a heme lyase, scans nascent peptides after Sec-dependent translocation for CX n CH-binding motifs. Here we report the three-dimensional (3D) structure of the heme lyase CcmF, a 643-amino acid integral membrane protein, from Thermus thermophilus. CcmF contains a heme b cofactor at the bottom of a large cavity that opens toward the extracellular side to receive heme groups from the heme chaperone CcmE for cytochrome maturation. A surface groove on CcmF may guide the extended apoprotein to heme attachment at or near a loop containing the functionally essential WXWD motif, which is situated above the putative cofactor binding pocket. The structure suggests heme delivery from within the membrane, redefining the role of the chaperone CcmE.


  • Organizational Affiliation

    Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome C-type biogenesis protein ccmF660Thermus thermophilus HB27Mutation(s): 0 
Gene Names: ccmFTT_C1038
Membrane Entity: Yes 
UniProt
Find proteins for Q72IU4 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72IU4 
Go to UniProtKB:  Q72IU4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72IU4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.273 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.72α = 90
b = 128.27β = 90
c = 134.98γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
AutoSolphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyCRC 1381, project ID 403222702
European Research Council (ERC)Germany310656

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-19
    Type: Initial release
  • Version 1.1: 2021-07-07
    Changes: Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references