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- EMDB-8669: CryoEM map of MsbA in POPG nanodisc -

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Basic information

Entry
Database: EMDB / ID: 8669
TitleCryoEM map of MsbA in POPG nanodisc
SampleMsbA with LPS in POPG nanodisc
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map datamap of MsbA with LPS in POPG nanodisc, filtered to 5A and sharpened with -280 B-factor
Methodsingle particle reconstruction, at 5 Å resolution
AuthorsMi W / Walz T / Liao M
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

DateDeposition: Apr 11, 2017 / Header (metadata) release: Jul 19, 2017 / 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: 0.04
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.04
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_8669.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.28 Å/pix.
= 245.76 Å
192 pix
1.28 Å/pix.
= 245.76 Å
192 pix
1.28 Å/pix.
= 245.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.28 Å
Density
Contour Level:0.034 (by author), 0.04 (movie #1):
Minimum - Maximum-0.06834029 - 0.14602281
Average (Standard dev.)3.7362337E-5 (0.00919677)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin-96-96-96
Limit959595
Spacing192192192
CellA=B=C: 245.76 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.281.281.28
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z245.760245.760245.760
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-0.0680.1460.000

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Supplemental data

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Sample components

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Entire MsbA with LPS in POPG nanodisc

EntireName: MsbA with LPS in POPG nanodisc / Number of components: 2
MassTheoretical: 67.2 kDa

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Component #1: protein, MsbA with LPS in POPG nanodisc

ProteinName: MsbA with LPS in POPG nanodisc / Recombinant expression: No
MassTheoretical: 67.2 kDa
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

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Component #2: protein, MsbA

ProteinName: MsbA / Recombinant expression: No
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml / pH: 7.5
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: 55199
3D reconstructionResolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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