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- PDB-5v5s: multi-drug efflux; membrane transport; RND superfamily; Drug resi... -

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Basic information

Entry
Database: PDB / ID: 5v5s
Titlemulti-drug efflux; membrane transport; RND superfamily; Drug resistance
Components
  • Multidrug efflux pump subunit AcrA
  • Multidrug efflux pump subunit AcrB
  • Outer membrane protein TolC
KeywordsMEMBRANE PROTEIN / multi-drug efflux / membrane transport / RND superfamily / Drug resistance
Function / homologyMultidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Outer membrane efflux protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / Barrel-sandwich domain of CusB or HlyD membrane-fusion / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Type I secretion outer membrane protein, TolC / RND efflux pump, membrane fusion protein / Acriflavin resistance protein / Hydrophobe/amphiphile efflux-1 HAE1 / HlyD membrane-fusion protein of T1SS ...Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Outer membrane efflux protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / Barrel-sandwich domain of CusB or HlyD membrane-fusion / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Type I secretion outer membrane protein, TolC / RND efflux pump, membrane fusion protein / Acriflavin resistance protein / Hydrophobe/amphiphile efflux-1 HAE1 / HlyD membrane-fusion protein of T1SS / AcrB/AcrD/AcrF family / Outer membrane efflux protein / enterobactin transport / drug:proton antiporter activity / efflux pump complex / efflux transmembrane transporter activity / drug transmembrane transport / drug transmembrane transporter activity / intrinsic component of plasma membrane / porin activity / ion transmembrane transport / transporter activity / bile acid and bile salt transport / cell outer membrane / response to organic cyclic compound / transmembrane transport / outer membrane-bounded periplasmic space / protein N-terminus binding / ion channel activity / response to drug / response to antibiotic / integral component of plasma membrane / membrane / integral component of membrane / identical protein binding / plasma membrane / Outer membrane protein TolC / Multidrug efflux pump subunit AcrA / Multidrug efflux pump subunit AcrA / Multidrug efflux pump subunit AcrB
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 6.5 Å resolution
Authorswang, Z. / fan, G. / Hryc, C.F. / Blaza, J.N. / Serysheva, I.I. / Schmid, M.F. / Chiu, W. / Luisi, B.F. / Du, D.
CitationJournal: Elife / Year: 2017
Title: An allosteric transport mechanism for the AcrAB-TolC multidrug efflux pump.
Authors: Zhao Wang / Guizhen Fan / Corey F Hryc / James N Blaza / Irina I Serysheva / Michael F Schmid / Wah Chiu / Ben F Luisi / Dijun Du
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 15, 2017 / Release: Apr 19, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 19, 2017Structure modelrepositoryInitial release
1.1Aug 2, 2017Structure modelData collection / Refinement descriptionem_3d_fitting / em_software_em_3d_fitting.target_criteria / _em_software.name

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Structure visualization

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  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-8636
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Outer membrane protein TolC
B: Outer membrane protein TolC
C: Outer membrane protein TolC
D: Multidrug efflux pump subunit AcrA
E: Multidrug efflux pump subunit AcrA
F: Multidrug efflux pump subunit AcrA
G: Multidrug efflux pump subunit AcrA
H: Multidrug efflux pump subunit AcrA
I: Multidrug efflux pump subunit AcrA
J: Multidrug efflux pump subunit AcrB
K: Multidrug efflux pump subunit AcrB
L: Multidrug efflux pump subunit AcrB


Theoretical massNumber of molelcules
Total (without water)740,58612
Polyers740,58612
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)52030
ΔGint (kcal/M)-193
Surface area (Å2)290930
MethodPISA

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Components

#1: Protein/peptide Outer membrane protein TolC / Multidrug efflux pump subunit TolC / Outer membrane factor TolC


Mass: 48673.801 Da / Num. of mol.: 3 / Source: (gene. exp.) Escherichia coli (E. coli)
Gene: tolC, colE1-i, mtcB, mukA, refI, toc, weeA, b3035, JW5503
Production host: Escherichia coli (E. coli) / References: UniProt: P02930
#2: Protein/peptide
Multidrug efflux pump subunit AcrA / AcrAB-TolC multidrug efflux pump subunit AcrA / Acriflavine resistance protein A


Mass: 42253.551 Da / Num. of mol.: 6 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: acrA, Z0578, ECs0516 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AE07, UniProt: P0AE06*PLUS
#3: Protein/peptide Multidrug efflux pump subunit AcrB / AcrAB-TolC multidrug efflux pump subunit AcrB / Acridine resistance protein B


Mass: 113681.242 Da / Num. of mol.: 3 / Source: (gene. exp.) Escherichia coli / Gene: acrB, acrE, b0462, JW0451 / Production host: Escherichia coli (E. coli) / References: UniProt: P31224

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: AcrABTolC in apo state / Type: COMPLEX / Entity ID: 1, 2, 3 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 2 mg/ml / Details: AcrABTolC complex in apo state / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 20 kelvins
Details: a 3ul aliquot at a concentration of 2 mg per ml was applied onto glow-discharged holey carbon grid (Quantifoil Au R1.21.3, 300 mesh)

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 45

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Processing

SoftwareName: PHENIX / Version: dev_2415: / Classification: refinement
EM software
IDNameVersionCategory
1RELION2particle selection
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
10EMAN2.2initial Euler assignment
11RELION2final Euler assignment
14PHENIXmodel refinement
15Cootmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionDetails: auto box by relion / Number of particles selected: 95410
SymmetryPoint symmetry: C3
3D reconstructionResolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 13544 / Algorithm: BACK PROJECTION / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingDetails: Crystal structures were rigid-body fit into the density map and model optimization was then carried out with Phenix real-space refine. Due to the weaker resolution, stronger stereochemical and secondary structure restraints were used to ensure that alpha-helices and beta-sheets did not deviate far from their expected geometry. Manual adjustments were kept to a minimum to reduce human bias in the modeling procedure, with Coot only being used to fix obvious errors such as C-beta deviations. A final check of MolProbity and cross correlation was done to ensure model quality.
Ref protocol: FLEXIBLE FIT / Ref space: REAL / Target criteria: Cross-correlation coefficient
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01849461
ELECTRON MICROSCOPYf_angle_d1.25267203
ELECTRON MICROSCOPYf_dihedral_angle_d9.16930015
ELECTRON MICROSCOPYf_chiral_restr0.0647959
ELECTRON MICROSCOPYf_plane_restr0.0078754

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