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- EMDB-9698: NSF-D1D2 part in the whole 20S complex -

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Basic information

Entry
Database: EMDB / ID: EMD-9698
TitleNSF-D1D2 part in the whole 20S complex
Map data
Sample
  • Complex: NSF-D1D2 part in the whole 20S complex
    • Protein or peptide: Vesicle-fusing ATPase
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywordsmembrane fusion / ATPase / HYDROLASE
Function / homology
Function and homology information


SNARE complex disassembly / ATP-dependent protein disaggregase activity / intra-Golgi vesicle-mediated transport / Golgi to plasma membrane protein transport / Golgi stack / vesicle-fusing ATPase / syntaxin-1 binding / positive regulation of receptor recycling / ionotropic glutamate receptor binding / SNARE binding ...SNARE complex disassembly / ATP-dependent protein disaggregase activity / intra-Golgi vesicle-mediated transport / Golgi to plasma membrane protein transport / Golgi stack / vesicle-fusing ATPase / syntaxin-1 binding / positive regulation of receptor recycling / ionotropic glutamate receptor binding / SNARE binding / PDZ domain binding / intracellular protein transport / potassium ion transport / positive regulation of protein catabolic process / midbody / protein kinase binding / protein-containing complex binding / ATP hydrolysis activity / ATP binding / metal ion binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
: / NSF, AAA+ ATPase lid domain / Vesicle-fusing ATPase / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily ...: / NSF, AAA+ ATPase lid domain / Vesicle-fusing ATPase / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Vesicle-fusing ATPase
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHuang X / Sun S
CitationJournal: Sci Adv / Year: 2019
Title: Mechanistic insights into the SNARE complex disassembly.
Authors: Xuan Huang / Shan Sun / Xiaojing Wang / Fenghui Fan / Qiang Zhou / Shan Lu / Yong Cao / Qiu-Wen Wang / Meng-Qiu Dong / Jun Yao / Sen-Fang Sui /
Abstract: NSF (-ethylmaleimide-sensitive factor) and α-SNAP (α-soluble NSF attachment protein) bind to the SNARE (soluble NSF attachment protein receptor) complex, the minimum machinery to mediate membrane ...NSF (-ethylmaleimide-sensitive factor) and α-SNAP (α-soluble NSF attachment protein) bind to the SNARE (soluble NSF attachment protein receptor) complex, the minimum machinery to mediate membrane fusion, to form a 20S complex, which disassembles the SNARE complex for reuse. We report the cryo-EM structures of the α-SNAP-SNARE subcomplex and the NSF-D1D2 domain in the 20S complex at 3.9- and 3.7-Å resolutions, respectively. Combined with the biochemical and electrophysiological analyses, we find that α-SNAPs use R116 through electrostatic interactions and L197 through hydrophobic interactions to apply force mainly on two positions of the VAMP protein to execute disassembly process. Furthermore, we define the interaction between the amino terminus of the SNARE helical bundle and the pore loop of the NSF-D1 domain and demonstrate its essential role as a potential anchor for SNARE complex disassembly. Our studies provide a rotation model of α-SNAP-mediated disassembly of the SNARE complex.
History
DepositionNov 1, 2018-
Header (metadata) releaseApr 24, 2019-
Map releaseApr 24, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.062
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.062
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ip2
  • Surface level: 0.062
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9698.png

Downloads & links

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Map

FileDownload / File: emd_9698.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 160 pix.
= 209.046 Å		1.31 Å/pix.
x 160 pix.
= 209.046 Å		1.31 Å/pix.
x 160 pix.
= 209.046 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.30654 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.062 / Movie #1: 0.062
Minimum - Maximum-0.23277421 - 0.36905763
Average (Standard dev.)0.0011960381 (±0.020084916)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 209.0464 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.30653751.30653751.3065375
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z209.046209.046209.046
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.2330.3690.001

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Supplemental data

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Sample components

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Entire : NSF-D1D2 part in the whole 20S complex

EntireName: NSF-D1D2 part in the whole 20S complex
Components
  • Complex: NSF-D1D2 part in the whole 20S complex
    • Protein or peptide: Vesicle-fusing ATPase
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: NSF-D1D2 part in the whole 20S complex

SupramoleculeName: NSF-D1D2 part in the whole 20S complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Cricetulus griseus (Chinese hamster)

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Macromolecule #1: Vesicle-fusing ATPase

MacromoleculeName: Vesicle-fusing ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: vesicle-fusing ATPase
Source (natural)Organism: Cricetulus griseus (Chinese hamster)
Molecular weightTheoretical: 85.441133 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRGSHHHHHH TDPLDVDSEP DVSAKMAGRS MQAARCPTDE LSLSNCAVVS EKDYQSGQHV IVRTSPNHKY IFTLRTHPSV VPGSVAFSL PQRKWAGLSI GQEIEVALYS FDKAKQCIGT MTIEIDFLQK KNIDSNPYDT DKMAAEFIQQ FNNQAFSVGQ Q LVFSFNDK ...String:
MRGSHHHHHH TDPLDVDSEP DVSAKMAGRS MQAARCPTDE LSLSNCAVVS EKDYQSGQHV IVRTSPNHKY IFTLRTHPSV VPGSVAFSL PQRKWAGLSI GQEIEVALYS FDKAKQCIGT MTIEIDFLQK KNIDSNPYDT DKMAAEFIQQ FNNQAFSVGQ Q LVFSFNDK LFGLLVKDIE AVDPSILKGE PASGKRQKIE VGLVVGNSQV AFEKAENSSL NLIGKAKTKE NRQSIINPDW NF EKMGIGG LDKEFSDIFR RAFASRVFPP EIVEQMGCKH VKGILLYGPP GCGKTLLARQ IGKMLNAREP KVVNGPEILN KYV GESEAN IRKLFADAEE EQRRLGANSG LHIIIFDEID AICKQRGSMA GSTGVHDTVV NQLLSKIDGV EQLNNILVIG MTNR PDLID EALLRPGRLE VKMEIGLPDE KGRLQILHIH TARMRGHQLL SADVDIKELA VETKNFSGAE LEGLVRAAQS TAMNR HIKA STKVEVDMEK AESLQVTRGD FLASLENDIK PAFGTNQEDY ASYIMNGIIK WGDPVTRVLD DGELLVQQTK NSDRTP LVS VLLEGPPHSG KTALAAKIAE ESNFPFIKIC SPDKMIGFSE TAKCQAMKKI FDDAYKSQLS CVVVDDIERL LDYVPIG PR FSNLVLQALL VLLKKAPPQG RKLLIIGTTS RKDVLQEMEM LNAFSTTIHV PNIATGEQLL EALELLGNFK DKERTTIA Q QVKGKKVWIG IKKLLMLIEM SLQMDPEYRV RKFLALLREE GASPLDFD

UniProtKB: Vesicle-fusing ATPase

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 12 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 163942
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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