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- EMDB-23251: Structure of a ferrichrome importer FhuCDB from E. coli -

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Basic information

Entry
Database: EMDB / ID: EMD-23251
TitleStructure of a ferrichrome importer FhuCDB from E. coli
Map dataferrichrome importer FhuCDB
Sample
  • Complex: holocomplex of ferrichrome importer FhuCDB
    • Protein or peptide: Iron(3+)-hydroxamate import system permease protein FhuB
    • Protein or peptide: Iron(3+)-hydroxamate-binding protein FhuD
    • Protein or peptide: Iron(3+)-hydroxamate import ATP-binding protein FhuC
KeywordsABC importer / siderophore / cryo-EM / TRANSPORT PROTEIN
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) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsHu W / Zheng H
Funding support United States, 2 items
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, 2021-
Header (metadata) releaseNov 24, 2021-
Map releaseNov 24, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
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  • Surface view with fitted model
  • Atomic models: PDB-7lb8
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23251.png

Downloads & links

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Map

FileDownload / File: emd_23251.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationferrichrome importer FhuCDB
Voxel sizeX=Y=Z: 0.799 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.089492805 - 0.12915275
Average (Standard dev.)0.0000029508801 (±0.0031230284)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 255.68001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.7990.7990.799
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z255.680255.680255.680
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ260260260
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0890.1290.000

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Supplemental data

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Sample components

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Entire : holocomplex of ferrichrome importer FhuCDB

EntireName: holocomplex of ferrichrome importer FhuCDB
Components
  • Complex: holocomplex of ferrichrome importer FhuCDB
    • Protein or peptide: Iron(3+)-hydroxamate import system permease protein FhuB
    • Protein or peptide: Iron(3+)-hydroxamate-binding protein FhuD
    • Protein or peptide: Iron(3+)-hydroxamate import ATP-binding protein FhuC

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Supramolecule #1: holocomplex of ferrichrome importer FhuCDB

SupramoleculeName: holocomplex of ferrichrome importer FhuCDB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K-12

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Macromolecule #1: Iron(3+)-hydroxamate import system permease protein FhuB

MacromoleculeName: Iron(3+)-hydroxamate import system permease protein FhuB
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 71.574867 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSKRIALFPA LLLALLVIVA TALTWMNFSQ ALPRSQWAQA AWSPNINVIE QMIFHYSLLP RLAISLLVGA GLGLVGVLFQ QVLRNPLAE PTTLGVATGA QLGITVTTLW AIPGAMASQF AALAGACVVG LIVFGVAWGK RLSPVTLILA GLVVSLYCGA I NQLLVIFH ...String:
MSKRIALFPA LLLALLVIVA TALTWMNFSQ ALPRSQWAQA AWSPNINVIE QMIFHYSLLP RLAISLLVGA GLGLVGVLFQ QVLRNPLAE PTTLGVATGA QLGITVTTLW AIPGAMASQF AALAGACVVG LIVFGVAWGK RLSPVTLILA GLVVSLYCGA I NQLLVIFH HDQLQSMFLW STGTLTQTDW GGVERLWPQL LGGVMLTLLL LRPLTLMGLD DGVARNLGLA LSLARLAALS LA IVISALL VNAVGIIGFI GLFAPLLAKM LGARRLLPRL MLASLIGALI LWLSDQIILW LTRVWMEVST GSVTALIGAP LLL WLLPRL RSISAPDMKV NDRVATERQH VLAFALAGGV LLLMAVVVAL SFGRDAHGWT WASGALLDDL MPWRWPRIMA ALFA GVMLA VAGCIIQRLT GNPMASPEVL GISSGAAFGV VLMLFLVPGN AFGWLLPAGS LGAAVTLLII MIAAGRGGFS PHRML LAGM ALSTAFTMLL MMLQASGDPR MAQVLTWISG STYNATDAQV WRTGIVMVIL LAITPLCRRW LTILPLGGDT ARAVGM ALT PTRIALLLLA ACLTATATMT IGPLSFVGLM APHIARMMGF RRTMPHIVIS ALVGGLLLVF ADWCGRMVLF PFQIPAG LL STFIGAPYFI YLLRKQSRHH HHHHHH

UniProtKB: Iron(3+)-hydroxamate import system permease protein FhuB

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Macromolecule #2: Iron(3+)-hydroxamate-binding protein FhuD

MacromoleculeName: Iron(3+)-hydroxamate-binding protein FhuD / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 33.030258 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSGLPLISRR RLLTAMALSP LLWQMNTAHA AAIDPNRIVA LEWLPVELLL ALGIVPYGVA DTINYRLWVS EPPLPDSVID VGLRTEPNL ELLTTMRPSF MVWSAGYGPS PEMLARIAPG RGFNFSDGKQ PLAMARKSLT EMADLLNLQS AAETHLAQYE D FIRSMKPR ...String:
MSGLPLISRR RLLTAMALSP LLWQMNTAHA AAIDPNRIVA LEWLPVELLL ALGIVPYGVA DTINYRLWVS EPPLPDSVID VGLRTEPNL ELLTTMRPSF MVWSAGYGPS PEMLARIAPG RGFNFSDGKQ PLAMARKSLT EMADLLNLQS AAETHLAQYE D FIRSMKPR FVKRGARPLL LTTLIDPRHM LVFGPNSLFQ EILDEYGIPN AWQGETNFWG STAVSIDRLA AYKDVDVLCF DH DNSKDMD ALMATPLWQA MPFVRAGRFQ RVPAVWFYGA TLSAMHFVRV LDNAIGGKA

UniProtKB: Iron(3+)-hydroxamate-binding protein FhuD

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Macromolecule #3: Iron(3+)-hydroxamate import ATP-binding protein FhuC

MacromoleculeName: Iron(3+)-hydroxamate import ATP-binding protein FhuC / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: ABC-type ferric hydroxamate transporter
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 28.921424 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQEYTNHSDT TFALRNISFR VPGRTLLHPL SLTFPAGKVT GLIGHNGSGK STLLKMLGRH QPPSEGEILL DAQPLESWSS KAFARKVAY LPQQLPPAEG MTVRELVAIG RYPWHGALGR FGAADREKVE EAISLVGLKP LAHRLVDSLS GGERQRAWIA M LVAQDSRC ...String:
MQEYTNHSDT TFALRNISFR VPGRTLLHPL SLTFPAGKVT GLIGHNGSGK STLLKMLGRH QPPSEGEILL DAQPLESWSS KAFARKVAY LPQQLPPAEG MTVRELVAIG RYPWHGALGR FGAADREKVE EAISLVGLKP LAHRLVDSLS GGERQRAWIA M LVAQDSRC LLLDEPTSAL DIAHQVDVLS LVHRLSQERG LTVIAVLHDI NMAARYCDYL VALRGGEMIA QGTPAEIMRG ET LEMIYGI PMGILPHPAG AAPVSFVY

UniProtKB: Iron(3+)-hydroxamate import ATP-binding protein FhuC

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 128131
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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