3D Electron Microscopy (3D-EM) Data Navigator [English / [日本語]]
Top Gallery List Statistics Shape search Viewer
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - EMDB-8670

This page is a legacy version and will be discarded in future. The new page is here.

CryoEM map of MsbA with lipid A in POPG nanodisc

by single particle reconstruction, at 4.5 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.04, Imaged by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.04, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 8670
TitleCryoEM map of MsbA with lipid A in POPG nanodisc
MapMsbA with lipid A in POPG nanodisc filtered to 4.5 A and with -220 B-factor sharpening
SampleMsbA with lipid A in POPG nanodisc
AuthorsMi W, Walz T, Liao M
DateDeposition: 2017-04-11, Header release: 2017-07-19, Map release: 2017-09-20, Last update: 2017-09-20
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.04, Imaged by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.04, Imaged by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

Cite: data citing same article

Similar-shape strucutres
Search for similar-shape assemblies throgh:
EMDB + EM entries in PDB
all of EMDB & PDB (Omokage search)
Article
Citation - Primary
ArticleNature, Year 2017
TitleStructural basis of MsbA-mediated lipopolysaccharide transport.
AuthorsWei Mi, Yanyan Li, Sung Hwan Yoon, Robert K Ernst, Thomas Walz, Maofu Liao
Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.
State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, USA.
Laboratory of Molecular Electron Microscopy, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA.
LinksPubMed: 28869968, DOI: 10.1038/nature23649
Map
Fileemd_8670.map.gz ( map file in CCP4 format, 16385 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
1.28 A/pix
= 204.8 A
160 pix
1.28 A/pix
= 204.8 A
160 pix
1.28 A/pix
= 204.8 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.0235 (by author), 0.04 (movie #1):
Minimum - Maximum: -0.061054986 - 0.14212495
Average (Standard dev.): 0.000107734224 (0.008882276)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin-80-80-80
Limit797979
Spacing160160160
Unit CellA= B= C: 204.79999 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.28 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.281.281.28
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z204.800204.800204.800
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0610.1420.000
Annotation DetailsMsbA with lipid A in POPG nanodisc filtered to 4.5 A and with -220 B-factor sharpening
Supplement
Images
Images
FSC
FSC
Sample
NameMsbA with lipid A in POPG nanodisc
Number of Components2
DetailsMsbA expressed from special E.coli strain ClearColi (which has no LPS), mixed with lipid A and reconstituted into POPG nanodisc
Component #1: protein - MsbA with lipid A in POPG nanodisc
Scientific nameMsbA with lipid A in POPG nanodisc
DetailsMsbA expressed from special E.coli strain ClearColi (which has no LPS), mixed with lipid A and reconstituted into POPG nanodisc
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 866768
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
Exp System Strain: ClearColi
Component #2: protein - MsbA with lipid A in POPG nanodisc
Scientific nameMsbA with lipid A in POPG nanodisc
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Experiment
Sample Preparation
Specimen Stateparticle
BufferpH: 7.5
Vitrification
Cryogen NameETHANE
Imaging
MicroscopeFEI POLARA 300
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose47 e/A**2
Illumination ModeFLOOD BEAM
Lens
Imaging ModeBRIGHT FIELD
Specimen Holder
ModelOTHER
Camera
DetectorGATAN K2 (4k x 4k)
Processing
Methodsingle particle reconstruction
3D reconstruction
SoftwareRELION
Resolution By Author
4.5 A
Resolution MethodFSC 0.143 CUT-OFF
Single Particle
Applied SymmetryC1 (asymmetric)
Number of Projections85496
Download
Data from EMDB
Header (meta data in XML format)emd-8670-v19.xml (6.2 KB)
emd-8670-v20.xml (11.9 KB)
emd-8670.xml (6.2 KB)
Map dataemd_8670.map.gz (14.3 MB)
Imagesemd_8670.png (50.6 KB)
FSC (resolution estimation)emd_8670_fsc.xml (6.7 KB)
Othersemd_8670_additional.map.gz (11.8 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-8670
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 6.2 MB
Session file for UCSF-Chimera, 27 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 6.3 MB
Session file for UCSF-Chimera, 27.1 KB