6ZMQ | pdb_00006zmq

Cytochrome c Heme Lyase CcmF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 
    0.308 (Depositor), 0.310 (DCC) 
  • R-Value Work: 
    0.271 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 
    0.273 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view details

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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PTY
Query on PTY

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
LMT
Query on LMT

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free:  0.308 (Depositor), 0.310 (DCC) 
  • R-Value Work:  0.271 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 0.273 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view details

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