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- PDB-7lb8: Structure of a ferrichrome importer FhuCDB from E. coli -

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Basic information

Entry
Database: PDB / ID: 7lb8
TitleStructure of a ferrichrome importer FhuCDB from E. coli
Components
  • Iron(3+)-hydroxamate import ATP-binding protein FhuC
  • Iron(3+)-hydroxamate import system permease protein FhuB
  • Iron(3+)-hydroxamate-binding protein FhuD
KeywordsTRANSPORT PROTEIN / ABC importer / siderophore / cryo-EM
Function / homology
Function and homology information


ABC-type ferric hydroxamate transporter / ABC-type ferric hydroxamate transporter activity / iron ion import across plasma membrane / siderophore-dependent iron import into cell / plasma membrane => GO:0005886 / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / ATP binding / plasma membrane
Similarity search - Function
ABC transporter, permease protein, BtuC-like / FecCD transport family / ABC transporter, BtuC-like / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain ...ABC transporter, permease protein, BtuC-like / FecCD transport family / ABC transporter, BtuC-like / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / 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
Iron(3+)-hydroxamate import system permease protein FhuB / Iron(3+)-hydroxamate import ATP-binding protein FhuC / Iron(3+)-hydroxamate-binding protein FhuD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsHu, W. / Zheng, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126626 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)AG064572 United States
CitationJournal: Commun Biol / Year: 2021
Title: Cryo-EM reveals unique structural features of the FhuCDB Escherichia coli ferrichrome importer.
Authors: Wenxin Hu / Hongjin Zheng /
Abstract: As one of the most elegant biological processes developed in bacteria, the siderophore-mediated iron uptake demands the action of specific ATP-binding cassette (ABC) importers. Although extensive ...As one of the most elegant biological processes developed in bacteria, the siderophore-mediated iron uptake demands the action of specific ATP-binding cassette (ABC) importers. Although extensive studies have been done on various ABC importers, the molecular basis of these iron-chelated-siderophore importers are still not fully understood. Here, we report the structure of a ferrichrome importer FhuCDB from Escherichia coli at 3.4 Å resolution determined by cryo electron microscopy. The structure revealed a monomeric membrane subunit of FhuB with a substrate translocation pathway in the middle. In the pathway, there were unique arrangements of residues, especially layers of methionines. Important residues found in the structure were interrogated by mutagenesis and functional studies. Surprisingly, the importer's ATPase activity was decreased upon FhuD binding, which deviated from the current understanding about bacterial ABC importers. In summary, to the best of our knowledge, these studies not only reveal a new structural twist in the type II ABC importer subfamily, but also provide biological insights in the transport of iron-chelated siderophores.
History
DepositionJan 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation
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
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
B: Iron(3+)-hydroxamate import system permease protein FhuB
D: Iron(3+)-hydroxamate-binding protein FhuD
U: Iron(3+)-hydroxamate import ATP-binding protein FhuC
C: Iron(3+)-hydroxamate import ATP-binding protein FhuC


Theoretical massNumber of molelcules
Total (without water)162,4484
Polymers162,4484
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area10820 Å2
ΔGint-66 kcal/mol
Surface area54850 Å2

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Components

#1: Protein Iron(3+)-hydroxamate import system permease protein FhuB / Ferric hydroxamate uptake protein B / Ferrichrome transport system permease protein FhuB / ...Ferric hydroxamate uptake protein B / Ferrichrome transport system permease protein FhuB / Ferrichrome uptake protein FhuB / Iron(III)-hydroxamate import system permease protein FhuB


Mass: 71574.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fhuB, b0153, JW0149 / Production host: Escherichia coli (E. coli) / References: UniProt: P06972
#2: Protein Iron(3+)-hydroxamate-binding protein FhuD / Ferric hydroxamate uptake protein D / Ferrichrome-binding periplasmic protein / Iron(III)- ...Ferric hydroxamate uptake protein D / Ferrichrome-binding periplasmic protein / Iron(III)-hydroxamate-binding protein FhuD


Mass: 33030.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fhuD, b0152, JW0148 / Production host: Escherichia coli (E. coli) / References: UniProt: P07822
#3: Protein Iron(3+)-hydroxamate import ATP-binding protein FhuC / Ferric hydroxamate uptake protein C / Ferrichrome transport ATP-binding protein FhuC / Iron(III)- ...Ferric hydroxamate uptake protein C / Ferrichrome transport ATP-binding protein FhuC / Iron(III)-hydroxamate import ATP-binding protein FhuC


Mass: 28921.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fhuC, b0151, JW0147 / Production host: Escherichia coli (E. coli)
References: UniProt: P07821, ABC-type ferric hydroxamate transporter

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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: holocomplex of ferrichrome importer FhuCDB / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K-12
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
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
Image recordingElectron dose: 65 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18rc5_3822: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128131 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 63.73 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00210698
ELECTRON MICROSCOPYf_angle_d0.55114594
ELECTRON MICROSCOPYf_dihedral_angle_d13.5651495
ELECTRON MICROSCOPYf_chiral_restr0.0391742
ELECTRON MICROSCOPYf_plane_restr0.0041834

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