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- PDB-6csx: Single particles Cryo-EM structure of AcrB D407A associated with ... -

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Basic information

Entry
Database: PDB / ID: 6csx
TitleSingle particles Cryo-EM structure of AcrB D407A associated with lipid bilayer at 3.0 Angstrom
ComponentsMultidrug efflux pump subunit AcrB
KeywordsTRANSPORT PROTEIN / AcrB / Native cell membrane nanoparticles / SMA / lipid bilayer
Function / homologyAcriflavin resistance protein / Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / drug:proton antiporter activity / efflux pump complex / efflux transmembrane transporter activity / drug transmembrane transport / drug transmembrane transporter activity / response to drug ...Acriflavin resistance protein / Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / drug:proton antiporter activity / efflux pump complex / efflux transmembrane transporter activity / drug transmembrane transport / drug transmembrane transporter activity / response to drug / integral component of plasma membrane / membrane / identical protein binding / plasma membrane / Multidrug efflux pump subunit AcrB
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3 Å resolution
AuthorsQiu, W. / Fu, Z. / Guo, Y.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure and activity of lipid bilayer within a membrane-protein transporter.
Authors: Weihua Qiu / Ziao Fu / Guoyan G Xu / Robert A Grassucci / Yan Zhang / Joachim Frank / Wayne A Hendrickson / Youzhong Guo
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 21, 2018 / Release: Dec 5, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 5, 2018Structure modelrepositoryInitial release
1.1Dec 19, 2018Structure modelData collection / Database referencescitation / citation_author / pdbx_database_related_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_database_related.content_type / _pdbx_database_related.db_id

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Assembly

Deposited unit
B: Multidrug efflux pump subunit AcrB
C: Multidrug efflux pump subunit AcrB
A: Multidrug efflux pump subunit AcrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,46022
Polyers344,0773
Non-polymers13,38319
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: microscopy, Single particles analysis using cryo-EM
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TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide Multidrug efflux pump subunit AcrB / AcrAB-TolC multidrug efflux pump subunit AcrB / Acridine resistance protein B


Mass: 114692.289 Da / Num. of mol.: 3 / Details: AcrB, lipid bilayer / Mutation: D407A
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12
Gene: acrB, acrE, b0462, JW0451Acriflavine resistance protein family
Production host: Escherichia coli (E. coli) / References: UniProt: P31224
#2: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 18 / Formula: C40H80NO8P / Phosphatidylethanolamine
#3: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 1 / Formula: C12H26 / Dodecane

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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: Lipid bilayer in AcrB / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.8
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD
VitrificationCryogen name: ETHANE-PROPANE

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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: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 41190 / Symmetry type: POINT

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