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- PDB-7vfp: Cytochrome c-type biogenesis protein CcmABCD from E. coli in comp... -

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Basic information

Entry
Database: PDB / ID: 7vfp
TitleCytochrome c-type biogenesis protein CcmABCD from E. coli in complex with heme and single ATP
Components
  • (Heme exporter protein ...) x 3
  • Cytochrome c biogenesis ATP-binding export protein CcmA
KeywordsMEMBRANE PROTEIN / ATP-binding exporter / Heme transmembrane transporter / Cytochrome c biogenesis protein
Function / homology
Function and homology information


cytochrome c biosynthetic process / heme import across plasma membrane / ABC-type heme transporter / heme transmembrane transporter activity / ABC-type heme transporter activity / cytochrome complex assembly / ATP-binding cassette (ABC) transporter complex / heme binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Cytochrome c-type biogenesis protein CcmB / Cytochrome c-type biogenesis protein CcmC / ABC transporter, haem export, CcmA / Haem exporter protein D (CcmD) / Cytochrome c-type biogenesis protein CcmB, bacteria / : / CcmB protein / Heme exporter protein D (CcmD) / Cytochrome C biogenesis export ATP-binding protein ccmA family profile. / Cytochrome c-type biogenesis protein CcsA/CcmC ...Cytochrome c-type biogenesis protein CcmB / Cytochrome c-type biogenesis protein CcmC / ABC transporter, haem export, CcmA / Haem exporter protein D (CcmD) / Cytochrome c-type biogenesis protein CcmB, bacteria / : / CcmB protein / Heme exporter protein D (CcmD) / Cytochrome C biogenesis export ATP-binding protein ccmA family profile. / Cytochrome c-type biogenesis protein CcsA/CcmC / Cytochrome c assembly protein / Cytochrome C assembly protein / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / PROTOPORPHYRIN IX CONTAINING FE / Heme exporter protein B / Heme exporter protein C / Heme exporter protein D / Cytochrome c biogenesis ATP-binding export protein CcmA
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.03 Å
AuthorsLi, J. / Zheng, W. / Gu, M. / Zhang, K. / Zhu, J.P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Structures of the CcmABCD heme release complex at multiple states.
Authors: Jiao Li / Wan Zheng / Ming Gu / Long Han / Yanmei Luo / Koukou Yu / Mengxin Sun / Yuliang Zong / Xiuxiu Ma / Bing Liu / Ethan P Lowder / Deanna L Mendez / Robert G Kranz / Kai Zhang / Jiapeng Zhu /
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 ...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).
History
DepositionSep 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: Cytochrome c biogenesis ATP-binding export protein CcmA
B: Heme exporter protein B
C: Heme exporter protein C
D: Heme exporter protein D
E: Cytochrome c biogenesis ATP-binding export protein CcmA
F: Heme exporter protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,1819
Polymers128,0336
Non-polymers1,1483
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 2 molecules AE

#1: Protein Cytochrome c biogenesis ATP-binding export protein CcmA / Heme exporter protein A


Mass: 22551.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: ccmA / Production host: Escherichia coli (E. coli) / References: UniProt: P33931, ABC-type heme transporter

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Heme exporter protein ... , 3 types, 4 molecules BFCD

#2: Protein Heme exporter protein B / Cytochrome c-type biogenesis protein CcmB


Mass: 23632.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: ccmB / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABL8
#3: Protein Heme exporter protein C / Cytochrome c-type biogenesis protein CcmC


Mass: 27911.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: ccmC / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABM1
#4: Protein Heme exporter protein D / Cytochrome c-type biogenesis protein CcmD


Mass: 7753.103 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: ccmD / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABM5

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Non-polymers , 4 types, 5 molecules

#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Source detailsProteins used in this study were derived from Escherichia coli BL21(DE3). However, since the ...Proteins used in this study were derived from Escherichia coli BL21(DE3). However, since the sequence references were not available in UNIPROT at the time of data processing, all references were derived from Escherichia coli K12.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The cytochrome c maturation complex CcmABCD / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.13 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 1.4388 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58617 / Symmetry type: POINT

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