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- EMDB-8944: 20S supercomplex consisting of linked neuronal SNARE complex, alp... -

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Basic information

Entry
Database: EMDB / ID: EMD-8944
Title20S supercomplex consisting of linked neuronal SNARE complex, alpha-SNAP, and N-ethylmaleimide sensitive factor (NSF)
Map data20S supercomplex with linked SNARE
Sample
  • Complex: 20S Supercomplex with linked SNARE complex
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsZhao M / Choi UB / Brunger AT
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)not applicable United States
CitationJournal: Elife / Year: 2018
Title: NSF-mediated disassembly of on- and off-pathway SNARE complexes and inhibition by complexin.
Authors: Ucheor B Choi / Minglei Zhao / K Ian White / Richard A Pfuetzner / Luis Esquivies / Qiangjun Zhou / Axel T Brunger /
Abstract: SNARE complex disassembly by the ATPase NSF is essential for neurotransmitter release and other membrane trafficking processes. We developed a single-molecule FRET assay to monitor repeated rounds of ...SNARE complex disassembly by the ATPase NSF is essential for neurotransmitter release and other membrane trafficking processes. We developed a single-molecule FRET assay to monitor repeated rounds of NSF-mediated disassembly and reassembly of individual SNARE complexes. For ternary neuronal SNARE complexes, disassembly proceeds in a single step within 100 msec. We observed short- (<0.32 s) and long-lived (≥0.32 s) disassembled states. The long-lived states represent fully disassembled SNARE complex, while the short-lived states correspond to failed disassembly or immediate reassembly. Either high ionic strength or decreased αSNAP concentration reduces the disassembly rate while increasing the frequency of short-lived states. NSF is also capable of disassembling anti-parallel ternary SNARE complexes, implicating it in quality control. Finally, complexin-1 competes with αSNAP binding to the SNARE complex; addition of complexin-1 has an effect similar to that of decreasing the αSNAP concentration, possibly differentially regulating cis and trans SNARE complexes disassembly.
History
DepositionJul 6, 2018-
Header (metadata) releaseJul 25, 2018-
Map releaseJul 25, 2018-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0282
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0282
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8944.png

Downloads & links

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Map

FileDownload / File: emd_8944.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation20S supercomplex with linked SNARE
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.02 Å/pix.
x 150 pix.
= 303. Å		2.02 Å/pix.
x 150 pix.
= 303. Å		2.02 Å/pix.
x 150 pix.
= 303. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0282 / Movie #1: 0.0282
Minimum - Maximum-0.017321697 - 0.057110235
Average (Standard dev.)0.00032873152 (±0.0049185315)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 303.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.022.022.02
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z303.000303.000303.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-51-35-11
NX/NY/NZ11110799
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-0.0170.0570.000

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Supplemental data

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Additional map: Sharpened map of 20S supercomplex with linked SNARE

Fileemd_8944_additional.map
AnnotationSharpened map of 20S supercomplex with linked SNARE
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 20S Supercomplex with linked SNARE complex

EntireName: 20S Supercomplex with linked SNARE complex
Components
  • Complex: 20S Supercomplex with linked SNARE complex

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Supramolecule #1: 20S Supercomplex with linked SNARE complex

SupramoleculeName: 20S Supercomplex with linked SNARE complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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

Concentration15 mg/mL
BufferpH: 8
GridSupport film - Material: CARBON / Support film - topology: HOLEY / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 78.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3j96

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 45194
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.3)

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