+Open data
-Basic information
Entry | Database: PDB / ID: 7lb8 | |||||||||
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Title | Structure of a ferrichrome importer FhuCDB from E. coli | |||||||||
Components |
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Keywords | TRANSPORT 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 | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Hu, W. / Zheng, H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7lb8.cif.gz | 241.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lb8.ent.gz | 190.6 KB | Display | PDB format |
PDBx/mmJSON format | 7lb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lb8_validation.pdf.gz | 946.8 KB | Display | wwPDB validaton report |
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Full document | 7lb8_full_validation.pdf.gz | 964.4 KB | Display | |
Data in XML | 7lb8_validation.xml.gz | 47.2 KB | Display | |
Data in CIF | 7lb8_validation.cif.gz | 71.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/7lb8 ftp://data.pdbj.org/pub/pdb/validation_reports/lb/7lb8 | HTTPS FTP |
-Related structure data
Related structure data | 23251MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 |
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#2: Protein | 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 | 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 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: holocomplex of ferrichrome importer FhuCDB / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: K-12 |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 65 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18rc5_3822: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128131 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.73 Å2 | ||||||||||||||||||||||||
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