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- PDB-7zdl: IF(heme/coordinated) conformation of CydDC in AMP-PNP(CydC)/AMP-P... -

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Basic information

Entry
Database: PDB / ID: 7zdl
TitleIF(heme/coordinated) conformation of CydDC in AMP-PNP(CydC)/AMP-PNP(CydD) bound state (Dataset-8)
Components
  • ATP-binding/permease protein CydC
  • ATP-binding/permease protein CydD
KeywordsMEMBRANE PROTEIN / ABC transporter / CydDC / Heme transporter
Function / homology
Function and homology information


cysteine export across plasma membrane / ATP-binding cassette (ABC) transporter complex, integrated substrate binding / cytochrome biosynthetic process / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / glutathione transmembrane transport / heme transmembrane transport / ABC-type heme transporter activity / ATPase-coupled lipid transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / cell redox homeostasis ...cysteine export across plasma membrane / ATP-binding cassette (ABC) transporter complex, integrated substrate binding / cytochrome biosynthetic process / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / glutathione transmembrane transport / heme transmembrane transport / ABC-type heme transporter activity / ATPase-coupled lipid transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / cell redox homeostasis / ATP-binding cassette (ABC) transporter complex / transmembrane transport / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC / ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC / ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / HEME B/C / Glutathione/L-cysteine transport system ATP-binding/permease protein CydC / Glutathione/L-cysteine transport system ATP-binding/permease protein CydD
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsWu, D. / Safarian, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Chem Biol / Year: 2023
Title: Dissecting the conformational complexity and mechanism of a bacterial heme transporter.
Authors: Di Wu / Ahmad R Mehdipour / Franziska Finke / Hojjat G Goojani / Roan R Groh / Tamara N Grund / Thomas M B Reichhart / Rita Zimmermann / Sonja Welsch / Dirk Bald / Mark Shepherd / Gerhard ...Authors: Di Wu / Ahmad R Mehdipour / Franziska Finke / Hojjat G Goojani / Roan R Groh / Tamara N Grund / Thomas M B Reichhart / Rita Zimmermann / Sonja Welsch / Dirk Bald / Mark Shepherd / Gerhard Hummer / Schara Safarian /
Abstract: Iron-bound cyclic tetrapyrroles (hemes) are redox-active cofactors in bioenergetic enzymes. However, the mechanisms of heme transport and insertion into respiratory chain complexes remain unclear. ...Iron-bound cyclic tetrapyrroles (hemes) are redox-active cofactors in bioenergetic enzymes. However, the mechanisms of heme transport and insertion into respiratory chain complexes remain unclear. Here, we used cellular, biochemical, structural and computational methods to characterize the structure and function of the heterodimeric bacterial ABC transporter CydDC. We provide multi-level evidence that CydDC is a heme transporter required for functional maturation of cytochrome bd, a pharmaceutically relevant drug target. Our systematic single-particle cryogenic-electron microscopy approach combined with atomistic molecular dynamics simulations provides detailed insight into the conformational landscape of CydDC during substrate binding and occlusion. Our simulations reveal that heme binds laterally from the membrane space to the transmembrane region of CydDC, enabled by a highly asymmetrical inward-facing CydDC conformation. During the binding process, heme propionates interact with positively charged residues on the surface and later in the substrate-binding pocket of the transporter, causing the heme orientation to rotate 180°.
History
DepositionMar 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_validate_chiral
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: ATP-binding/permease protein CydC
D: ATP-binding/permease protein CydD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,7797
Polymers128,1002
Non-polymers1,6805
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area15490 Å2
ΔGint-110 kcal/mol
Surface area46070 Å2

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Components

#1: Protein ATP-binding/permease protein CydC


Mass: 62980.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: cydC, mdrA, mdrH, surB, b0886, JW0869 / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): C43 / References: UniProt: P23886
#2: Protein ATP-binding/permease protein CydD


Mass: 65118.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: cydD, htrD, b0887, JW0870 / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): C43 / References: UniProt: P29018
#3: Chemical ChemComp-HEB / HEME B/C / HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX CONTAINING FE)


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
Has ligand of interestY

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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: CydDC heterodimer / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.130 MDa / Experimental value: YES
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: K12
Buffer solutionpH: 6
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120630 / Symmetry type: POINT

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