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- EMDB-8467: Cryo-EM structure of MsbA-nanodisc with ADP-vanadate -

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Basic information

Entry
Database: EMDB / ID: 8467
TitleCryo-EM structure of MsbA-nanodisc with ADP-vanadate
SampleMsbA reconstituted in lipid nanodiscs
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map data3D cryo-EM density map of MsbA-nanodisc with ADP-vanadate
Methodsingle particle reconstruction, at 4.8 Å resolution
AuthorsMi W / Walz T
CitationNature, 2017, 549, 233-237

Nature, 2017, 549, 233-237 Yorodumi Papers
Structural basis of MsbA-mediated lipopolysaccharide transport.
Wei Mi / Yanyan Li / Sung Hwan Yoon / Robert K Ernst / Thomas Walz / Maofu Liao

Validation ReportPDB-ID: 5ttp

SummaryFull reportAbout validation report
DateDeposition: Nov 4, 2016 / Header (metadata) release: Dec 21, 2016 / Map release: Sep 20, 2017 / Last update: Sep 27, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.026
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.026
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5ttp
  • Surface level: 0.026
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_8467.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

Image control

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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:0.026 (by author), 0.026 (movie #1):
Minimum - Maximum-0.036314443 - 0.07850477
Average (Standard dev.)1.5757078E-5 (0.0040237997)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin000
Limit191191191
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/NS000
NC/NR/NS192192192
D min/max/mean-0.0360.0790.000

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Supplemental data

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Sample components

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Entire MsbA reconstituted in lipid nanodiscs

EntireName: MsbA reconstituted in lipid nanodiscs / Number of components: 2

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Component #1: protein, MsbA reconstituted in lipid nanodiscs

ProteinName: MsbA reconstituted in lipid nanodiscs / 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-19b

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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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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: C2 (2 fold cyclic) / Number of projections: 36732
3D reconstructionResolution: 4.8 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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