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- PDB-5ng5: multi-drug efflux; membrane transport; RND superfamily; Drug resi... -

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Basic information

Entry
Database: PDB / ID: 5ng5
Titlemulti-drug efflux; membrane transport; RND superfamily; Drug resistance
DescriptorOuter membrane protein TolC
Multidrug efflux pump accessory protein AcrZ
(Multidrug efflux pump subunit ...) x 2
KeywordsMEMBRANE PROTEIN / multi-drug efflux / membrane transport / RND superfamily / Drug resistance / membrane protein
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (6.5 Å resolution / Particle / 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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 16, 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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Assembly

Deposited unit
E: Multidrug efflux pump subunit AcrA
D: Multidrug efflux pump subunit AcrA
G: Multidrug efflux pump subunit AcrA
H: Multidrug efflux pump subunit AcrA
A: Multidrug efflux pump subunit AcrA
B: Multidrug efflux pump subunit AcrA
F: Outer membrane protein TolC
I: Outer membrane protein TolC
C: Outer membrane protein TolC
K: Multidrug efflux pump subunit AcrB
L: Multidrug efflux pump subunit AcrB
M: Multidrug efflux pump accessory protein AcrZ
N: Multidrug efflux pump accessory protein AcrZ
O: Multidrug efflux pump accessory protein AcrZ
J: Multidrug efflux pump subunit AcrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)760,71518
Polyers759,13515
Non-polymers1,5803
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)88880
ΔGint (kcal/M)-392
Surface area (Å2)244870
MethodPISA

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Components

#1: Polypeptide(L)
Multidrug efflux pump subunit AcrA / AcrAB-TolC multidrug efflux pump subunit AcrA / Acridine resistance protein A


Mass: 39800.660 Da / Num. of mol.: 6
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P0AE06

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)Outer membrane protein TolC / Multidrug efflux pump subunit TolC / Outer membrane factor TolC


Mass: 53783.355 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

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)Multidrug efflux pump subunit AcrB / AcrAB-TolC multidrug efflux pump subunit AcrB / Acridine resistance protein B


Mass: 113665.180 Da / Num. of mol.: 3
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P31224

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)Multidrug efflux pump accessory protein AcrZ / AcrAB-TolC multidrug efflux pump accessory protein AcrZ / Acridine resistance protein Z


Mass: 5995.157 Da / Num. of mol.: 3
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P0AAW9

Cellular component

Molecular function

Biological process

#5: ChemicalChemComp-5QF / 6-[2-(3,4-dimethoxyphenyl)ethylsulfanyl]-8-[4-(2-methoxyethyl)piperazin-1-yl]-3,3-dimethyl-1,4-dihydropyrano[3,4-c]pyridine-5-carbonitrile


Mass: 526.691 Da / Num. of mol.: 3 / Formula: C28H38N4O4S

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: AcrABTolC in apo state / Type: COMPLEX / Entity ID: 1, 2, 3, 4 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli
Source (recombinant)Organism: Escherichia 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 FIELD
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

EM software
IDNameVersionCategoryImage processing IDFitting ID
4CTFFIND4CTF CORRECTION1
7UCSF ChimeraMODEL FITTING1
10EMAN2.2INITIAL EULER ASSIGNMENT1
11RELION2FINAL EULER ASSIGNMENT1
14PHENIXMODEL REFINEMENT1
15CootMODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionDetails: auto box by relion / Number of particles selected: 95410
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

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