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- PDB-5ttp: Cryo-EM structure of MsbA-nanodisc with ADP-vanadate -

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Basic information

Entry
Database: PDB / ID: 5ttp
TitleCryo-EM structure of MsbA-nanodisc with ADP-vanadate
ComponentsLipid A export ATP-binding/permease protein MsbA
KeywordsHYDROLASE / ABC transporter / LPS / flippase / nanodisc
Function / homologyABC transporter, conserved site / ABC transporters family signature. / Lipid A export ATP-binding/permease protein msbA family profile. / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter-like / AAA+ ATPase domain / ABC transporter type 1, transmembrane domain / ABC transporter, lipid A export, MsbA / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleoside triphosphate hydrolase ...ABC transporter, conserved site / ABC transporters family signature. / Lipid A export ATP-binding/permease protein msbA family profile. / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter-like / AAA+ ATPase domain / ABC transporter type 1, transmembrane domain / ABC transporter, lipid A export, MsbA / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleoside triphosphate hydrolase / ABC transporter type 1, transmembrane domain superfamily / ABC transporter / ABC transporter transmembrane region / lipid-transporting ATPase activity / ec:3.6.3.-: / integral component of membrane / ATP binding / plasma membrane / Lipid A export ATP-binding/permease protein MsbA
Function and homology information
Specimen sourceEscherichia coli O157:H7 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.8 Å resolution
AuthorsMi, W. / Walz, T. / Liao, M.
CitationJournal: Nature / Year: 2017
Title: Structural basis of MsbA-mediated lipopolysaccharide transport.
Authors: Wei Mi / Yanyan Li / Sung Hwan Yoon / Robert K Ernst / Thomas Walz / Maofu Liao
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 4, 2016 / Release: Sep 20, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 20, 2017Structure modelrepositoryInitial release
1.1Sep 27, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Assembly

Deposited unit
A: Lipid A export ATP-binding/permease protein MsbA
B: Lipid A export ATP-binding/permease protein MsbA


Theoretical massNumber of molelcules
Total (without water)134,6212
Polyers134,6212
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide Lipid A export ATP-binding/permease protein MsbA


Mass: 67310.445 Da / Num. of mol.: 2 / Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: msbA, Z1260, ECs0997
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P60753, EC: 3.6.3.-

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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: MsbA reconstituted in lipid nanodiscs / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Plasmid: pET-19b
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 47 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 36732 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0098942
ELECTRON MICROSCOPYf_angle_d1.39912082
ELECTRON MICROSCOPYf_dihedral_angle_d11.3337490
ELECTRON MICROSCOPYf_chiral_restr0.0661440
ELECTRON MICROSCOPYf_plane_restr0.0081532

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