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- EMDB-8469: 3D cryo-EM reconstruction of nucleotide-free MsbA in lipid nanodisc -

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Basic information

Entry
Database: EMDB / ID: 8469
Title3D cryo-EM reconstruction of nucleotide-free MsbA in lipid nanodisc
SampleMsbA reconstituted in lipid nanodisc
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map data3D cryo-EM reconstruction of nucleotide-free MsbA in lipid nanodisc
Methodsingle particle reconstruction, at 4.2 Å resolution
AuthorsMi W / Walz T
CitationNature, 2017

Nature, 2017 StrPapers
Structural basis of MsbA-mediated lipopolysaccharide transport.
Wei Mi / Yanyan Li / Sung Hwan Yoon / Robert K Ernst / Thomas Walz / Maofu Liao

Validation ReportPDB-ID: 5tv4

SummaryFull reportAbout validation report
DateDeposition: Nov 8, 2016 / Header (metadata) release: Jan 25, 2017 / Map release: Sep 20, 2017 / Last update: Sep 20, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.045
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5tv4
  • Surface level: 0.045
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_8469.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.23 Å/pix.
= 236.16 Å
192 pix
1.23 Å/pix.
= 236.16 Å
192 pix
1.23 Å/pix.
= 236.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.23 Å
Density
Contour Level:0.045 (by author), 0.045 (movie #1):
Minimum - Maximum-0.10215455 - 0.17202976
Average (Standard dev.)9.394499E-6 (0.011065408)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin-96-96-96
Limit959595
Spacing192192192
CellA=B=C: 236.16 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z236.160236.160236.160
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-0.1020.1720.000

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Supplemental data

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Sample components

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Entire MsbA reconstituted in lipid nanodisc

EntireName: MsbA reconstituted in lipid nanodisc / Number of components: 9

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Component #1: protein, MsbA reconstituted in lipid nanodisc

ProteinName: MsbA reconstituted in lipid nanodisc / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli 'bl21-gold(de3)plyss ag' / bacteria / image: Escherichia coli
Vector: pET-19a

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Component #2: protein, Lipid A export ATP-binding/permease protein MsbA

ProteinName: Lipid A export ATP-binding/permease protein MsbA / Recombinant expression: No
MassTheoretical: 67.310445 kDa
Source (engineered)Expression System: Escherichia coli o157:h7 / bacteria / image: Escherichia coli

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Component #3: ligand, 2-amino-2-deoxy-alpha-D-glucopyranose

LigandName: 2-amino-2-deoxy-alpha-D-glucopyranose / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.179171 kDa

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Component #4: ligand, 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID

LigandName: 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.238192 kDa

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Component #5: ligand, L-GLYCERO-D-MANNO-HEPTOPYRANOSE

LigandName: L-GLYCERO-D-MANNO-HEPTOPYRANOSE / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.210182 kDa

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Component #6: ligand, PHOSPHATE ION

LigandName: PHOSPHATE ION / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 9.497105 MDa

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Component #7: ligand, 3-HYDROXY-TETRADECANOIC ACID

LigandName: 3-HYDROXY-TETRADECANOIC ACID / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.24437 kDa

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Component #8: ligand, MYRISTIC ACID

LigandName: MYRISTIC ACID / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.228371 kDa

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Component #9: ligand, LAURIC ACID

LigandName: LAURIC ACID / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.200318 kDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 47 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 67220
3D reconstructionSoftware: RELION / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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