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Electron cryomicroscopy structure of N-ethyl maleimide sensitive factor at 11 A resolution.

by single particle reconstruction, at 11.0 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.736926654, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.736926654, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1059
AuthorsFurst J, Sutton RB, Chen J, Brunger AT, Grigorieff N
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.736926654, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.736926654, Made by UCSF CHIMERA

Supplemental images

1059.gif
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)

Diagram

EMDB-1913

EMDB-1734

EMDB-1676

EMDB-1241
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleEMBO J., Vol. 22, Issue 17, Page 4365-74, Year 2003
TitleElectron cryomicroscopy structure of N-ethyl maleimide sensitive factor at 11 A resolution.
AuthorsJohannes Furst, R Bryan Sutton, James Chen, Axel T Brunger, Nikolaus Grigorieff
Howard Hughes Medical Institute and Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, 415 South Street, Waltham, MA 02454, USA.
KeywordsAdenosine Triphosphatases (chemistry, 3.6.1.-), Animals, Carrier Proteins (chemistry), Cricetinae, Cryoelectron Microscopy, Crystallography, X-Ray, Hydrolysis, Models, Molecular, Mutagenesis, Site-Directed, N-Ethylmaleimide-Sensitive Proteins (3.6.4.6), Protein Conformation, Recombinant Proteins (chemistry), Vesicular Transport Proteins
LinksPubMed: 12941689, DOI: 10.1093/emboj/cdg420, PMC: PMC202363
Map
FileEMD-1059.map ( map file in CCP4 format, 2917 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:0.144, 0.7369267 (movie #1):
Minimum - Maximum: -0.681735 - 1.45625
Average (Standard dev.): 0.0257073 (0.145834)
Data Typefloat (32-bit)
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 90 90 90
Origin : 1 1 1
Limit : 90 90 90
Spacing : 90 90 90
Unit CellA = 315 A , B = 315 A , C = 315 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 3.5 A , Y = 3.5 A , Z = 3.5 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z3.53.53.5
M x/y/z909090
origin x/y/z0.0000.0000.000
length x/y/z315.000315.000315.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ0052
NX/NY/NZ12812855
MAP C/R/S123
start NC/NR/NS111
NC/NR/NS909090
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.6821.4560.026
Annotation Details3D density map of NSF?alpha-SNAP?SNARE (20S)
Supplement
Images
Images

1059.gif
Sample
NameNSF alpha-SNAP SNARE 20S
Number of Components3
Experimental Mass0.68 MDa
Mass-estimation Methodgel permeation chromatography
DetailsThe sample was monodisperse. Some domains were disordered.
Component #1: protein - NSF
Scientific nameN-ethyl Maleimide Sensitive Factor
Common NameNSF
Experimental Mass0.0828 MDa
Details6 subunits
Oligomeric Detailshexamer
Number of Copies6
Scientific Name of SpeciesCricetulus griseus (NCBI Taxonomy: 10029)
Common Name of SpeciesChinese Hamster
Recombinant expressionYes
Engineered SourceExp System: Escherichia coli (NCBI Taxonomy: 562)
Component #2: protein - alpha-SNAP
Scientific nameSoluble NSF Attachment Protein
Common Namealpha-SNAP
Experimental Mass0.0334 MDa
Scientific Name of SpeciesBos taurus (NCBI Taxonomy: 9913)

Common Name of SpeciesCattle
Recombinant expressionYes
Component #3: protein - SNARE
Scientific nameSoluble NSF Attachment Protein Receptor
Common NameSNARE
Experimental Mass0.0823 MDa
Scientific Name of Speciesunidentified (NCBI Taxonomy: 32644)
Common Name of SpeciesChinese Hamster
Recombinant expressionYes
Experiment
Sample Preparation
Specimen Conc0.2 mg/ml
Stainingcryo (no stain)
Specimen Support Detailsholey carbon film
Specimen Stateparticle
BufferDetails: 20mM HEPES, pH 7.4, 300 mM NACl, 2 mM MgCl2, 5mM b-mercaptoethanol, 0.01/0.1 mM ADP/ATP nucleotide
pH: 7.4
Vitrification
Cryogen NameETHANE
Humidity80
Temperature85 Kelvin
InstrumentHOMEMADE PLUNGER
DetailsVitrification instrument: Technion plunger
Imaging
MicroscopeFEI TECNAI 20
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose10 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 62000 X,
Nominal Cs2.0 mm
Imaging ModeBRIGHT FIELD
Defocus2000 nm - 4000 nm
Specimen Holder
HolderEucentric ( GATAN LIQUID NITROGEN )
Tilt Angle0 degrees - 0 degrees
Temperature85 Kelvin
Camera
DetectorKodak SO163
Image Acquisition
Sampling Size7 microns
Od Range1.4
Quant Bit Number8
ScannerZEISS SCAI
Details3 x 3 averaging, final step size = 27 microns
Processing
Methodsingle particle reconstruction
3 D reconstruction
AlgorithmCommon lines
SoftwareIMAGIC, FREALIGN
CTF CorrectionFREALIGN
Resolution By Author11.0
Resolution MethodFSC at 0.5 cut-off
DetailsFinal map was calculated from three data sets
Single Particle
Number of Projections31592
Detailsmanual particle selection
Download
Data from EMDB
Header (meta data in XML format)emd-1059.xml (8.6 KB)
Map dataemd_1059.map.gz (1.7 MB)
Images1059.gif (76.8 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1059
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 20.1 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5 MB
Session file for UCSF-Chimera, 20.3 KB