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- EMDB-31396: Cytochrome c-type biogenesis protein CcmABCD from E. coli in comp... -

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Basic information

Entry
Database: EMDB / ID: EMD-31396
TitleCytochrome c-type biogenesis protein CcmABCD from E. coli in complex with Heme and ATP.
Map data
Sample
  • Complex: Cytochrome c-type biogenesis protein CcmABCD
    • Protein or peptide: Cytochrome c biogenesis ATP-binding export protein CcmA
    • Protein or peptide: Heme exporter protein B
    • Protein or peptide: Heme exporter protein C
    • Protein or peptide: Heme exporter protein D
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: water
Function / homology
Function and homology information


cytochrome c biosynthetic process / heme import across plasma membrane / ABC-type heme transporter / ABC-type heme transporter activity / heme transmembrane 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 assembly protein ...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
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(DE3) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsLi J / Zheng W / Gu M / Zhang K / Zhu JP
Funding support1 items
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
DepositionJun 3, 2021-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateNov 9, 2022-
Current statusNov 9, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31396.png

Downloads & links

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Map

FileDownload / File: emd_31396.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.832 Å
Density
Contour LevelBy AUTHOR: 0.212
Minimum - Maximum-1.0752972 - 1.701379
Average (Standard dev.)0.001502109 (±0.041804776)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cytochrome c-type biogenesis protein CcmABCD

EntireName: Cytochrome c-type biogenesis protein CcmABCD
Components
  • Complex: Cytochrome c-type biogenesis protein CcmABCD
    • Protein or peptide: Cytochrome c biogenesis ATP-binding export protein CcmA
    • Protein or peptide: Heme exporter protein B
    • Protein or peptide: Heme exporter protein C
    • Protein or peptide: Heme exporter protein D
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: water

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Supramolecule #1: Cytochrome c-type biogenesis protein CcmABCD

SupramoleculeName: Cytochrome c-type biogenesis protein CcmABCD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 130 KDa

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Macromolecule #1: Cytochrome c biogenesis ATP-binding export protein CcmA

MacromoleculeName: Cytochrome c biogenesis ATP-binding export protein CcmA
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ABC-type heme transporter
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 23.080213 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGMLEARELL CERDERTLFS GLSFTLNAGE WVQITGSNGA GKTTLLRLLT GLSRPDAGEV LWQGQPLHQV RDSYHQNLLW IGHQPGIKT RLTALENLHF YHRDGDTAQC LEALAQAGLA GFEDIPVNQL SAGQQRRVAL ARLWLTRATL WILDEPFTAI D VNGVDRLT ...String:
MGMLEARELL CERDERTLFS GLSFTLNAGE WVQITGSNGA GKTTLLRLLT GLSRPDAGEV LWQGQPLHQV RDSYHQNLLW IGHQPGIKT RLTALENLHF YHRDGDTAQC LEALAQAGLA GFEDIPVNQL SAGQQRRVAL ARLWLTRATL WILDEPFTAI D VNGVDRLT QRMAQHTEQG GIVILTTHQP LNVAESKIRR ISLTQTRAA

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Macromolecule #2: Heme exporter protein B

MacromoleculeName: Heme exporter protein B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 23.632676 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MMFWRIFRLE LRVAFRHSAE IANPLWFFLI VITLFPLSIG PEPQLLARIA PGIIWVAALL SSLLALERLF RDDLQDGSLE QLMLLPLPL PAVVLAKVMA HWMVTGLPLL ILSPLVAMLL GMDVYGWQVM ALTLLLGTPT LGFLGAPGVA LTVGLKRGGV L LSILVLPL ...String:
MMFWRIFRLE LRVAFRHSAE IANPLWFFLI VITLFPLSIG PEPQLLARIA PGIIWVAALL SSLLALERLF RDDLQDGSLE QLMLLPLPL PAVVLAKVMA HWMVTGLPLL ILSPLVAMLL GMDVYGWQVM ALTLLLGTPT LGFLGAPGVA LTVGLKRGGV L LSILVLPL TIPLLIFATA AMDAASMHLP VDGYLAILGA LLAGTATLSP FATAAALRIS IQ

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Macromolecule #3: Heme exporter protein C

MacromoleculeName: Heme exporter protein C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 27.911264 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MWKTLHQLAI PPRLYQICGW FIPWLAIASV VVLTVGWIWG FGFAPADYQQ GNSYRIIYLH VPAAIWSMGI YASMAVAAFI GLVWQMKMA NLAVAAMAPI GAVFTFIALV TGSAWGKPMW GTWWVWDARL TSELVLLFLY VGVIALWHAF DDRRLAGRAA G ILVLIGVV ...String:
MWKTLHQLAI PPRLYQICGW FIPWLAIASV VVLTVGWIWG FGFAPADYQQ GNSYRIIYLH VPAAIWSMGI YASMAVAAFI GLVWQMKMA NLAVAAMAPI GAVFTFIALV TGSAWGKPMW GTWWVWDARL TSELVLLFLY VGVIALWHAF DDRRLAGRAA G ILVLIGVV NLPIIHYSVE WWNTLHQGST RMQQSIDPAM RSPLRWSIFG FLLLSATLTL MRMRNLILLM EKRRPWVSEL IL KRGRK

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Macromolecule #4: Heme exporter protein D

MacromoleculeName: Heme exporter protein D / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 7.753103 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTPAFASWNE FFAMGGYAFF VWLAVVMTVI PLVVLVVHSV MQHRAILRGV AQQRAREARL RAAQQQEAA

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Macromolecule #7: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 7 / Number of copies: 1 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

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Macromolecule #8: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 8 / Number of copies: 1 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM / Phosphatidylethanolamine

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.4388 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 270825

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