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- EMDB-1059: Electron cryomicroscopy structure of N-ethyl maleimide sensitive ... -

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Basic information

Entry
Database: EMDB / ID: 1059
TitleElectron cryomicroscopy structure of N-ethyl maleimide sensitive factor at 11 A resolution.
SampleNSF alpha-SNAP SNARE 20S
SourceCricetulus griseus / mammal / Chinese Hamster / モンゴルキヌゲネズミ
Bos taurus / mammal / Cattle / ウシ /
Unidentified / Chinese Hamster
Map data3D density map of NSF?alpha-SNAP?SNARE (20S)
Methodsingle particle reconstruction, at 11 A resolution
AuthorsFurst J / Sutton RB / Chen J / Brunger AT / Grigorieff N
CitationEMBO J., 2003, 22, 4365-4374

EMBO J., 2003, 22, 4365-4374 StrPapers
Electron cryomicroscopy structure of N-ethyl maleimide sensitive factor at 11 A resolution.
Johannes Furst / R Bryan Sutton / James Chen / Axel T Brunger / Nikolaus Grigorieff

DateDeposition: Oct 10, 2003 / Header (metadata) release: Oct 10, 2003 / Map release: Oct 10, 2003 / Last update: Oct 10, 2003

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.736926654
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.736926654
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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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.

Voxel sizeX=Y=Z: 3.5 A
Density
Contour Level:0.144, 0.7369267 (movie #1):
Minimum - Maximum-0.681735 - 1.45625
Average (Standard dev.)0.0257073 (0.145834)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions909090
Origin111
Limit909090
Spacing909090
CellA=B=C: 315 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

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
D min/max/mean-0.6821.4560.026

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Supplemental data

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Sample components

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Entire NSF alpha-SNAP SNARE 20S

EntireName: NSF alpha-SNAP SNARE 20S
Details: The sample was monodisperse. Some domains were disordered.
Number of components: 3
MassExperimental: 680 kDa / Measured by: gel permeation chromatography

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Component #1: protein, N-ethyl Maleimide Sensitive Factor

ProteinName: N-ethyl Maleimide Sensitive Factor / a.k.a: NSF / Oligomeric Details: hexamer / Details: 6 subunits / Number of Copies: 6 / Recombinant expression: Yes
MassExperimental: 82.8 kDa
SourceSpecies: Cricetulus griseus / mammal / Chinese Hamster / モンゴルキヌゲネズミ
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: protein, Soluble NSF Attachment Protein

ProteinName: Soluble NSF Attachment Protein / a.k.a: alpha-SNAP / Recombinant expression: Yes
MassExperimental: 33.4 kDa
SourceSpecies: Bos taurus / mammal / Cattle / ウシ /

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Component #3: protein, Soluble NSF Attachment Protein Receptor

ProteinName: Soluble NSF Attachment Protein Receptor / a.k.a: SNARE / Recombinant expression: Yes
MassExperimental: 82.3 kDa
SourceSpecies: Unidentified / Chinese Hamster

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.2 mg/ml
Buffer solution: 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
Support filmholey carbon film
Stainingcryo (no stain)
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 85 K / Humidity: 80 % / Details: Vitrification instrument: Technion plunger

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 62000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 4000 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 85 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionScanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8 / OD range: 1.4 / Details: 3 x 3 averaging, final step size = 27 microns

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 31592 / Details: manual particle selection / Applied symmetry: C6 (6 fold cyclic)
3D reconstructionAlgorithm: Common lines / Software: IMAGIC, FREALIGN / CTF correction: FREALIGN / Resolution: 11 A / Resolution method: FSC 0.5 / Details: Final map was calculated from three data sets

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