7F04

Cytochrome c-type biogenesis protein CcmABCD from E. coli in complex with Heme and ATP.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures of the CcmABCD heme release complex at multiple states.

Li, J.Zheng, W.Gu, M.Han, L.Luo, Y.Yu, K.Sun, M.Zong, Y.Ma, X.Liu, B.Lowder, E.P.Mendez, D.L.Kranz, R.G.Zhang, K.Zhu, J.

(2022) Nat Commun 13: 6422-6422

  • DOI: https://doi.org/10.1038/s41467-022-34136-5
  • Primary Citation of Related Structures:  
    7F02, 7F03, 7F04, 7VFJ, 7VFP

  • PubMed Abstract: 

    Cytochromes c use heme as a cofactor to carry electrons in respiration and photosynthesis. The cytochrome c maturation system I, consisting of eight membrane proteins (CcmABCDEFGH), results in the attachment of heme to cysteine residues of cytochrome c proteins. Since all c-type cytochromes are periplasmic, heme is first transported to a periplasmic heme chaperone, CcmE. A large membrane complex, CcmABCD has been proposed to carry out this transport and linkage to CcmE, yet the structural basis and mechanisms underlying the process are unknown. We describe high resolution cryo-EM structures of CcmABCD in an unbound form, in complex with inhibitor AMP-PNP, and in complex with ATP and heme. We locate the ATP-binding site in CcmA and the heme-binding site in CcmC. Based on our structures combined with functional studies, we propose a hypothetic model of heme trafficking, heme transfer to CcmE, and ATP-dependent release of holoCcmE from CcmABCD. CcmABCD represents an ABC transporter complex using the energy of ATP hydrolysis for the transfer of heme from one binding partner (CcmC) to another (CcmE).


  • Organizational Affiliation

    School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c biogenesis ATP-binding export protein CcmA
A, E
207Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: ccmA
EC: 7.6.2.5
Membrane Entity: Yes 
UniProt
Find proteins for P33931 (Escherichia coli (strain K12))
Explore P33931 
Go to UniProtKB:  P33931
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33931
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Heme exporter protein B
B, F
220Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: ccmB
Membrane Entity: Yes 
UniProt
Find proteins for P0ABL8 (Escherichia coli (strain K12))
Explore P0ABL8 
Go to UniProtKB:  P0ABL8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABL8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Heme exporter protein C245Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: ccmC
Membrane Entity: Yes 
UniProt
Find proteins for P0ABM1 (Escherichia coli (strain K12))
Explore P0ABM1 
Go to UniProtKB:  P0ABM1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABM1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Heme exporter protein D69Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: ccmD
Membrane Entity: Yes 
UniProt
Find proteins for P0ABM5 (Escherichia coli (strain K12))
Explore P0ABM5 
Go to UniProtKB:  P0ABM5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABM5
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3PE (Subject of Investigation/LOI)
Query on 3PE

Download Ideal Coordinates CCD File 
J [auth D]1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
I [auth C]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
ATP
Query on ATP

Download Ideal Coordinates CCD File 
H [auth A],
L [auth E]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
K [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2024-06-12
    Changes: Data collection