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

by single particle reconstruction, at 11 A resolution

Movie

Orientation:

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

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

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1059
TitleElectron cryomicroscopy structure of N-ethyl maleimide sensitive factor at 11 A resolution.
Map3D density map of NSF?alpha-SNAP?SNARE (20S)
SampleNSF alpha-SNAP SNARE 20S
AuthorsFurst J, Sutton RB, Chen J, Brunger AT, Grigorieff N
DateDeposition: 2003-10-10, Header release: 2003-10-10, Map release: 2003-10-10, Last update: 2012-10-24
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

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

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

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)
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.gz ( map file in CCP4 format, 2849 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
90 pix
3.5 A/pix
= 315. A
90 pix
3.5 A/pix
= 315. A
90 pix
3.5 A/pix
= 315. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.144, 0.7369267 (movie #1):
Minimum - Maximum: -0.681735 - 1.45625
Average (Standard dev.): 0.0257073 (0.145834)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions909090
Origin111
Limit909090
Spacing909090
Unit CellA= B= C: 315 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= 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
Sample
NameNSF alpha-SNAP SNARE 20S
Number of Components3
Experimental Mass0.68MDa
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
Common Name of SpeciesChinese Hamster
NCBI taxonomy10029
Recombinant expressionYes
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Component #2: protein - alpha-SNAP
Scientific nameSoluble NSF Attachment Protein
Common Namealpha-SNAP
Experimental Mass0.0334 MDa
Scientific Name of SpeciesBos taurus

Common Name of SpeciesCattle
NCBI taxonomy9913
Recombinant expressionYes
Component #3: protein - SNARE
Scientific nameSoluble NSF Attachment Protein Receptor
Common NameSNARE
Experimental Mass0.0823 MDa
Scientific Name of Speciesunidentified
Common Name of SpeciesChinese Hamster
NCBI taxonomy32644
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
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus2000 nm - 4000 nm
Specimen Holder
HolderEucentric
ModelGATAN LIQUID NITROGEN
Tilt Angle0 degrees - 0 degrees
Temperature85 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
Sampling Size7
Od Range1.4
Quant Bit Number8
ScannerZEISS SCAI
Details3 x 3 averaging, final step size = 27 microns
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmCommon lines
SoftwareIMAGIC, FREALIGN
CTF CorrectionFREALIGN
Resolution By Author11 A
Resolution MethodFSC 0.5
DetailsFinal map was calculated from three data sets
Single Particle
Number of Projections31592
Detailsmanual particle selection
Applied SymmetryC6 (6 fold cyclic)
Download
Data from EMDB
Header (meta data in XML format)emd-1059.xml (8.7 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