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- PDB-9pv0: NorA in outward-open conformation bound to inhibitor IMP2380 -

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Basic information

Entry
Database: PDB / ID: 9pv0
TitleNorA in outward-open conformation bound to inhibitor IMP2380
ComponentsQuinolone resistance protein NorA, Soluble cytochrome b562 chimera
KeywordsTRANSPORT PROTEIN/INHIBITOR / efflux pump / membrane protein / TRANSPORT PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


transmembrane transporter activity / electron transport chain / electron transfer activity / periplasmic space / iron ion binding / heme binding / plasma membrane
Similarity search - Function
: / Tetracycline resistance protein TetA/multidrug resistance protein MdtG / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
: / Soluble cytochrome b562 / Quinolone resistance protein NorA
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.52 Å
AuthorsSuwatthee, T. / Gray, J.L. / Ledger, E.V.K. / Wang, D. / Edwards, A. / Tate, E.W. / Traaseth, N.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI165782 United States
CitationJournal: To Be Published
Title: Small molecule inhibitors of the NorA multidrug efflux pump potentiate antibiotic activity by binding the outward-open conformation
Authors: Gray, J.L. / Ledger, E.V.K. / Suwatthee, T. / Lanyon-Hogg, T. / Burden, T.J. / Arvaniti, K. / Sefton, A. / Papagora, L.E. / Clarke, T.B. / Riley, J. / Pinto, E.G. / Cunningham, F. / Gilbert, ...Authors: Gray, J.L. / Ledger, E.V.K. / Suwatthee, T. / Lanyon-Hogg, T. / Burden, T.J. / Arvaniti, K. / Sefton, A. / Papagora, L.E. / Clarke, T.B. / Riley, J. / Pinto, E.G. / Cunningham, F. / Gilbert, I.H. / Gray, D. / Wang, D. / Read, K.D. / Traaseth, N.J. / Edwards, A. / Tate, E.W.
History
DepositionJul 31, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Z: Quinolone resistance protein NorA, Soluble cytochrome b562 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5932
Polymers54,1831
Non-polymers4101
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Quinolone resistance protein NorA, Soluble cytochrome b562 chimera / Cytochrome b-562


Mass: 54183.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria), (gene. exp.) Escherichia coli (E. coli)
Gene: norA, SACOL0754, cybC / Plasmid: pET29 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q5HHX4, UniProt: P0ABE7
#2: Chemical ChemComp-A1CLB / (3E)-3-(1,3-benzothiazol-2-yl)-4-[3-(4-chlorophenyl)-1-methyl-1H-pyrazol-4-yl]but-3-enoic acid


Mass: 409.889 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H16ClN3O2S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: NorA-BRIL in complex with IMP2380, BAG2 (Fab), and anti-kappa VHH domain
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.12272 MDa / Experimental value: NO
Source (natural)Organism: Staphylococcus aureus (bacteria) / Cellular location: membrane
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: C43 (DE3) / Plasmid: pET29
Buffer solutionpH: 7.5 / Details: NorA-BRIL reconstituted in PMAL-C8 amphipol
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMsodium phosphateNa2HPO41
2100 mMsodium chlorideNaCl1
SpecimenConc.: 5.24 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 K

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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: DIFFRACTION / Nominal defocus max: 2500 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm / Alignment procedure: OTHER
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.8 sec. / Electron dose: 47.12 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 13288
EM imaging opticsEnergyfilter slit width: 15 eV
Image scansWidth: 11520 / Height: 8184

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
9PHENIX1.21.2_5419:model refinement
13Coot3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 8279459
3D reconstructionResolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 634207 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 112.1 / Protocol: AB INITIO MODEL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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