[English] 日本語
Yorodumi
- EMDB-9698: NSF-D1D2 part in the whole 20S complex -

+
Open data


ID or keywords:

Loading...

-
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 / 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 ...SNARE complex disassembly / ATP-dependent protein disaggregase activity / 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-containing complex binding / protein kinase binding / Golgi apparatus / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
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 ...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

-
Structure visualization

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

emd_9698.png

Downloads & links

-
Map

FileDownload / File: emd_9698.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.30654 Å
Density
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

-
Supplemental data

-
Sample components

-
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

-
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)

-
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

-
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 / Adenosine triphosphate

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

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

-
Image processing

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more