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- PDB-8zal: EmrAB-TolC MFS-type tripartite multidrug efflux pump EA -

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Basic information

Entry
Database: PDB / ID: 8zal
TitleEmrAB-TolC MFS-type tripartite multidrug efflux pump EA
Components
  • Multidrug export protein EmrA
  • Multidrug export protein EmrB
  • Outer membrane protein TolC
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


MacAB-TolC complex / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane / response to steroid hormone / bile acid and bile salt transport ...MacAB-TolC complex / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane / response to steroid hormone / bile acid and bile salt transport / porin activity / monoatomic ion channel activity / efflux transmembrane transporter activity / transmembrane transporter activity / xenobiotic transmembrane transporter activity / cell outer membrane / response to toxic substance / transmembrane transport / outer membrane-bounded periplasmic space / monoatomic ion transmembrane transport / response to xenobiotic stimulus / response to antibiotic / identical protein binding / membrane / plasma membrane
Similarity search - Function
Drug resistance transporter EmrB-like / Efflux pump membrane protein / : / Type I secretion outer membrane protein, TolC / : / Cation efflux system protein CusB, domain 1 / : / RND efflux pump, membrane fusion protein, barrel-sandwich domain / : / Outer membrane efflux protein ...Drug resistance transporter EmrB-like / Efflux pump membrane protein / : / Type I secretion outer membrane protein, TolC / : / Cation efflux system protein CusB, domain 1 / : / RND efflux pump, membrane fusion protein, barrel-sandwich domain / : / Outer membrane efflux protein / Outer membrane efflux protein / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Outer membrane protein TolC / Multidrug export protein EmrB / Multidrug export protein EmrA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsDu, D. / Zhong, Z. / Tuerxunjiang, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971133 China
CitationJournal: To Be Published
Title: EmrAB-TolC MFS-type tripartite multidrug efflux pump EA
Authors: Du, D. / Zhong, Z. / Tuerxunjiang, M.
History
DepositionApr 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multidrug export protein EmrA
B: Multidrug export protein EmrA
C: Multidrug export protein EmrA
D: Multidrug export protein EmrA
E: Multidrug export protein EmrA
F: Multidrug export protein EmrA
G: Outer membrane protein TolC
H: Outer membrane protein TolC
I: Outer membrane protein TolC
J: Multidrug export protein EmrB


Theoretical massNumber of molelcules
Total (without water)420,57010
Polymers420,57010
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Multidrug export protein EmrA


Mass: 37594.523 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: emrA / Production host: Escherichia coli B (bacteria) / References: UniProt: P27303
#2: Protein Outer membrane protein TolC / Multidrug efflux pump subunit TolC / Outer membrane factor TolC


Mass: 47003.840 Da / Num. of mol.: 3 / Mutation: V169L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: tolC / Production host: Escherichia coli B (bacteria) / References: UniProt: P02930
#3: Protein Multidrug export protein EmrB


Mass: 53991.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: emrB / Production host: Escherichia coli B (bacteria) / References: UniProt: P0AEJ0
Has protein modificationN

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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: EmrAB-TolC / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli B (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in.
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/HE
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19180 / Symmetry type: POINT
RefinementHighest resolution: 3.11 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00329983
ELECTRON MICROSCOPYf_angle_d0.43640800
ELECTRON MICROSCOPYf_dihedral_angle_d11.45211045
ELECTRON MICROSCOPYf_chiral_restr0.0384829
ELECTRON MICROSCOPYf_plane_restr0.0045352

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