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- EMDB-5371: Cryo-EM structure of full-length NSF in the ADP state -

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Basic information

Entry
Database: EMDB / ID: EMD-5371
TitleCryo-EM structure of full-length NSF in the ADP state
Map dataNSF hexamer in the ADP state
Sample
  • Sample: N-ethylmaleimide-sensitive factor (NSF)
  • Protein or peptide: N-ethylmaleimide-sensitive factor
Keywordsmembrane fusion / AAA+ ATPase
Biological speciesCricetulus griseus (Chinese hamster)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsChang LF / Chen S / Liu CC / Pan X / Jiang J / Bai XC / Xie X / Wang HW / Sui SF
CitationJournal: Nat Struct Mol Biol / Year: 2012
Title: Structural characterization of full-length NSF and 20S particles.
Authors: Lei-Fu Chang / Song Chen / Cui-Cui Liu / Xijiang Pan / Jiansen Jiang / Xiao-Chen Bai / Xin Xie / Hong-Wei Wang / Sen-Fang Sui /
Abstract: The 20S particle, which is composed of the N-ethylmaleimide-sensitive factor (NSF), soluble NSF attachment proteins (SNAPs) and the SNAP receptor (SNARE) complex, has an essential role in ...The 20S particle, which is composed of the N-ethylmaleimide-sensitive factor (NSF), soluble NSF attachment proteins (SNAPs) and the SNAP receptor (SNARE) complex, has an essential role in intracellular vesicle fusion events. Using single-particle cryo-EM and negative stain EM, we reconstructed four related three-dimensional structures: Chinese hamster NSF hexamer in the ATPγS, ADP-AlFx and ADP states, and the 20S particle. These structures reveal a parallel arrangement between the D1 and D2 domains of the hexameric NSF and characterize the nucleotide-dependent conformational changes in NSF. The structure of the 20S particle shows that it holds the SNARE complex at two interaction interfaces around the C terminus and N-terminal half of the SNARE complex, respectively. These findings provide insight into the molecular mechanism underlying disassembly of the SNARE complex by NSF.
History
DepositionDec 15, 2011-
Header (metadata) releaseJan 3, 2012-
Map releaseFeb 1, 2012-
UpdateFeb 1, 2012-
Current statusFeb 1, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5371_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5371.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNSF hexamer in the ADP state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.8 Å/pix.
x 128 pix.
= 230.4 Å		1.8 Å/pix.
x 128 pix.
= 230.4 Å		1.8 Å/pix.
x 128 pix.
= 230.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.6 / Movie #1: 3.5
Minimum - Maximum-5.46910524 - 9.450402260000001
Average (Standard dev.)0.1477396 (±1.22013593)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 230.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.81.81.8
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z230.400230.400230.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-5.4699.4500.148

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Supplemental data

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Sample components

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Entire : N-ethylmaleimide-sensitive factor (NSF)

EntireName: N-ethylmaleimide-sensitive factor (NSF)
Components
  • Sample: N-ethylmaleimide-sensitive factor (NSF)
  • Protein or peptide: N-ethylmaleimide-sensitive factor

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Supramolecule #1000: N-ethylmaleimide-sensitive factor (NSF)

SupramoleculeName: N-ethylmaleimide-sensitive factor (NSF) / type: sample / ID: 1000 / Details: The sample was freshly purified. / Oligomeric state: homohexamer / Number unique components: 1

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Macromolecule #1: N-ethylmaleimide-sensitive factor

MacromoleculeName: N-ethylmaleimide-sensitive factor / type: protein_or_peptide / ID: 1 / Name.synonym: NSF / Recombinant expression: Yes
Source (natural)Organism: Cricetulus griseus (Chinese hamster) / synonym: Chinese hamster
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
DateNov 15, 2010
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: CT3500 / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.5 CUT-OFF

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Atomic model buiding 1

Initial modelPDB ID:

1nsf

RefinementSpace: REAL

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