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- PDB-5tv4: 3D cryo-EM reconstruction of nucleotide-free MsbA in lipid nanodisc -

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Basic information

Entry
Database: PDB / ID: 5tv4
Title3D cryo-EM reconstruction of nucleotide-free MsbA in lipid nanodisc
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 / 4.2 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 8, 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
1.2Nov 8, 2017Structure modelDerived calculationspdbx_struct_assembly_pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details

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Structure visualization

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,87219
Polyers134,6212
Non-polymers3,25117
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)11620
ΔGint (kcal/M)-12
Surface area (Å2)58400

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Components

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Protein/peptide , 1 types, 2 molecules AB

#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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Non-polymers , 7 types, 17 molecules

#2: Chemical ChemComp-PA1 / 2-amino-2-deoxy-alpha-D-glucopyranose


Mass: 179.171 Da / Num. of mol.: 2 / Formula: C6H13NO5
#3: Chemical ChemComp-KDO / 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID


Mass: 238.192 Da / Num. of mol.: 2 / Formula: C8H14O8 / 3-Deoxy-D-manno-oct-2-ulosonic acid
#4: Chemical ChemComp-GMH / L-GLYCERO-D-MANNO-HEPTOPYRANOSE


Mass: 210.182 Da / Num. of mol.: 3 / Formula: C7H14O7
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Formula: PO4 / Phosphate
#6: Chemical
ChemComp-FTT / 3-HYDROXY-TETRADECANOIC ACID / 3-HYDROXY-MYRISTIC ACID


Mass: 244.370 Da / Num. of mol.: 4 / Formula: C14H28O3
#7: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Formula: C14H28O2 / Myristic acid
#8: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Formula: C12H24O2 / Lauric acid

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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 nanodisc / 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-19a
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
EM software
IDNameVersionCategory
1SamViewer16.01particle selection
12RELION1.4classification
13RELION1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 67220 / Symmetry type: POINT
Least-squares processHighest resolution: 4.2 Å
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0088970
ELECTRON MICROSCOPYf_angle_d1.24512120
ELECTRON MICROSCOPYf_dihedral_angle_d10.0377510
ELECTRON MICROSCOPYf_chiral_restr0.0621442
ELECTRON MICROSCOPYf_plane_restr0.0071538

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