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

by single particle reconstruction, at 4.2 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.045, Imaged by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.045, Imaged by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-5tv4, Surface level: 0.045, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 8469
Title3D cryo-EM reconstruction of nucleotide-free MsbA in lipid nanodisc
Map3D cryo-EM reconstruction of nucleotide-free MsbA in lipid nanodisc
SampleMsbA reconstituted in lipid nanodisc
AuthorsMi W, Walz T
DateDeposition: 2016-11-08, Header release: 2017-01-25, Map release: 2017-09-20, Last update: 2017-11-08
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.045, Imaged by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.045, Imaged by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-5tv4, Surface level: 0.045, Imaged by UCSF CHIMERA

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

PDB-5tv4

CiteFit

Cite: data citing same article

Fit: output model of fitting

Similar-shape strucutres
Search for similar-shape assemblies throgh:
EMDB + EM entries in PDB
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Article
Citation - Primary
ArticleNature, Vol. 549, Issue 7671, Page 233-237, 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_8469.map.gz ( map file in CCP4 format, 28312 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.23 A/pix
= 236.16 A
192 pix
1.23 A/pix
= 236.16 A
192 pix
1.23 A/pix
= 236.16 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

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)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin-96-96-96
Limit959595
Spacing192192192
Unit CellA= B= C: 236.16 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.23 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.1020.1720.000
Annotation Details3D cryo-EM reconstruction of nucleotide-free MsbA in lipid nanodisc
Supplement
Images
Images
FSC
FSC
Sample
NameMsbA reconstituted in lipid nanodisc
Number of Components9
Component #1: protein - MsbA reconstituted in lipid nanodisc
Scientific nameMsbA reconstituted in lipid nanodisc
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 866768
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
Vector: pET-19a
Component #2: protein - Lipid A export ATP-binding/permease protein MsbA
Scientific nameLipid A export ATP-binding/permease protein MsbA
Theoretical Mass0.067310445 MDa
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 83334
Expression system: Escherichia coli O157:H7
Component #3: ligand - 2-amino-2-deoxy-alpha-D-glucopyranose
Scientific name2-amino-2-deoxy-alpha-D-glucopyranose
Theoretical Mass0.000179171 MDa
Number of Copies2
Recombinant expressionNo
Component #4: ligand - 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
Scientific name3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
Theoretical Mass0.000238192 MDa
Number of Copies2
Recombinant expressionNo
Component #5: ligand - L-GLYCERO-D-MANNO-HEPTOPYRANOSE
Scientific nameL-GLYCERO-D-MANNO-HEPTOPYRANOSE
Theoretical Mass0.000210182 MDa
Number of Copies3
Recombinant expressionNo
Component #6: ligand - PHOSPHATE ION
Scientific namePHOSPHATE ION
Theoretical Mass9.4971e-05 MDa
Number of Copies4
Recombinant expressionNo
Component #7: ligand - 3-HYDROXY-TETRADECANOIC ACID
Scientific name3-HYDROXY-TETRADECANOIC ACID
Theoretical Mass0.00024437 MDa
Number of Copies4
Recombinant expressionNo
Component #8: ligand - MYRISTIC ACID
Scientific nameMYRISTIC ACID
Theoretical Mass0.000228371 MDa
Number of Copies1
Recombinant expressionNo
Component #9: ligand - LAURIC ACID
Scientific nameLAURIC ACID
Theoretical Mass0.000200318 MDa
Number of Copies1
Recombinant expressionNo
Experiment
Sample Preparation
Specimen Stateparticle
BufferpH: 7.4
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
4.2 A
Resolution MethodFSC 0.143 CUT-OFF
Single Particle
Applied SymmetryC1 (asymmetric)
Number of Projections67220
Atomic Model Fitting
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-8469-v19.xml (8.9 KB)
emd-8469-v20.xml (14.5 KB)
emd-8469.xml (8.9 KB)
Map dataemd_8469.map.gz (25.1 MB)
Imagesemd_8469.png (56.2 KB)
FSC (resolution estimation)emd_8469_fsc.xml (8 KB)
Othersemd_8469_additional.map.gz (20.7 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-8469
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 6.6 MB
Session file for UCSF-Chimera, 26.9 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 6.6 MB
Session file for UCSF-Chimera, 26.5 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 7.1 MB
Session file for UCSF-Chimera, 753.7 KB