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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
DescriptorOuter membrane protein TolC
Multidrug efflux pump subunit AcrA
Multidrug efflux pump subunit AcrB
KeywordsMEMBRANE PROTEIN / multi-drug efflux / membrane transport / RND superfamily / Drug resistance
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (6.5 A resolution / Single particle)
Authorswang, Z. / fan, G. / Hryc, C.F. / Blaza, J.N. / Serysheva, I.I. / Schmid, M.F. / Chiu, W. / Luisi, B.F. / Du, D.
CitationElife, 2017, 6

Elife, 2017, 6 StrPapers
An allosteric transport mechanism for the AcrAB-TolC multidrug efflux pump.
Zhao Wang / Guizhen Fan / Corey F Hryc / James N Blaza / Irina I Serysheva / Michael F Schmid / Wah Chiu / Ben F Luisi / Dijun Du

DateDeposition: Mar 15, 2017 / Release: Apr 19, 2017

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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 (A2)52030
ΔGint (kcal/M)-193
Surface area (A2)290930
MethodPISA

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Components

#1: Polypeptide(L)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 / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P02930
#2: Polypeptide(L)
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 / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P0AE07
#3: Polypeptide(L)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 / bacteria / / References: UniProt: P31224

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE

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Sample preparation

Assembly of specimen
ID
1
2
3
ComponentName: AcrABTolC in apo state / Type: COMPLEX
Specimen supportGrid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %
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 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD

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Processing

SoftwareName: PHENIX / Version: dev_2415: / Classification: refinement
ComputingStructure refinement: PHENIX (dev_2415: phenix.real_space_refine)
3D reconstructionResolution: 6.5 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 13544 / Number of class averages: 1
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: 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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