[English] 日本語
- PDB-6mdn: The 20S supercomplex engaging the SNAP-25 N-terminus (class 2) -

Open data

ID or keywords:


no data

Basic information

Database: PDB / ID: 6mdn
TitleThe 20S supercomplex engaging the SNAP-25 N-terminus (class 2)
  • Alpha-soluble NSF attachment protein
  • Synaptosomal-associated protein 25SNAP25
  • Syntaxin-1A
  • Vesicle-associated membrane protein 2Vesicle-associated membrane protein
  • Vesicle-fusing ATPase
KeywordsHYDROLASE / SNARE / NSF / SNAP / ATPase / AAA / disassembly / synapse / membrane fusion / exocytosis
Function / homologyAAA+ lid domain / CDC48, N-terminal subdomain / SNAP-25 / Synaptobrevin / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48), N-terminal domain / Synaptobrevin / SNAP-25 family / Syntaxin / ATPase family associated with various cellular activities (AAA) ...AAA+ lid domain / CDC48, N-terminal subdomain / SNAP-25 / Synaptobrevin / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48), N-terminal domain / Synaptobrevin / SNAP-25 family / Syntaxin / ATPase family associated with various cellular activities (AAA) / Vesicle-fusing ATPase / Synaptosomal-associated protein 25 / AAA+ ATPase domain / Synaptobrevin signature. / CDC48 domain 2-like superfamily / Vesicle-associated membrane protein 2 / Syntaxin 1A / P-loop containing nucleoside triphosphate hydrolase / Synaptobrevin/Vesicle-associated membrane protein / Tetratricopeptide-like helical domain superfamily / SNARE / Aspartate decarboxylase-like domain superfamily / Syntaxin/epimorphin, conserved site / Syntaxin, N-terminal domain / CDC48, domain 2 / SNARE domain / AAA-protein family signature. / ATPase, AAA-type, core / Syntaxin / epimorphin family signature. / GABA synthesis, release, reuptake and degradation / Target SNARE coiled-coil homology domain / Clathrin-mediated endocytosis / Cargo recognition for clathrin-mediated endocytosis / Retrograde transport at the Trans-Golgi-Network / Intra-Golgi traffic / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / LGI-ADAM interactions / Other interleukin signaling / Golgi Associated Vesicle Biogenesis / Lysosome Vesicle Biogenesis / Clathrin derived vesicle budding / Acetylcholine Neurotransmitter Release Cycle / NSF attachment protein / Dopamine Neurotransmitter Release Cycle / Glutamate Neurotransmitter Release Cycle / COPII-mediated vesicle transport / Norepinephrine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / v-SNARE coiled-coil homology domain profile. / t-SNARE coiled-coil homology domain profile. / ATPase, AAA-type, conserved site / soluble NSF attachment protein activity / regulation of delayed rectifier potassium channel activity / SNARE complex disassembly / storage vacuole / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / anchored component of presynaptic membrane / myosin head/neck binding / regulation of synaptic vesicle priming / zymogen granule membrane / growth hormone secretion / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / neurotransmitter transport / positive regulation of norepinephrine secretion / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / synaptic vesicle fusion to presynaptic active zone membrane / presynaptic active zone membrane / positive regulation of catecholamine secretion / synaptic vesicle docking / SNARE complex assembly / regulation of synaptic vesicle recycling / synaptic vesicle priming / intracellular organelle / positive regulation of neurotransmitter secretion / apical protein localization / regulation of synapse assembly / protein-containing complex disassembly / Golgi to plasma membrane protein transport / calcium ion-regulated exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis / vesicle docking / vesicle-fusing ATPase / response to gravity / protein localization to membrane / positive regulation of hormone secretion / integral component of synaptic vesicle membrane / sleep / chloride channel inhibitor activity / SNAP receptor activity / vesicle fusion / synaptic vesicle exocytosis / positive regulation of ATPase activity / regulation of exocytosis / regulation of neuron projection development / positive regulation of receptor recycling / SNARE complex / positive regulation of intracellular protein transport / membrane fusion
Function and homology information
Specimen sourceCricetulus griseus (Chinese hamster)
Rattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.4 Å resolution
AuthorsWhite, K.I. / Zhao, M. / Brunger, A.T.
CitationJournal: Elife / Year: 2018
Title: Structural principles of SNARE complex recognition by the AAA+ protein NSF.
Authors: K Ian White / Minglei Zhao / Ucheor B Choi / Richard A Pfuetzner / Axel T Brunger
Abstract: The recycling of SNARE proteins following complex formation and membrane fusion is an essential process in eukaryotic trafficking. A highly conserved AAA+ protein, NSF (-ethylmaleimide sensitive ...The recycling of SNARE proteins following complex formation and membrane fusion is an essential process in eukaryotic trafficking. A highly conserved AAA+ protein, NSF (-ethylmaleimide sensitive factor) and an adaptor protein, SNAP (soluble NSF attachment protein), disassemble the SNARE complex. We report electron-cryomicroscopy structures of the complex of NSF, αSNAP, and the full-length soluble neuronal SNARE complex (composed of syntaxin-1A, synaptobrevin-2, SNAP-25A) in the presence of ATP under non-hydrolyzing conditions at ~3.9 Å resolution. These structures reveal electrostatic interactions by which two αSNAP molecules interface with a specific surface of the SNARE complex. This interaction positions the SNAREs such that the 15 N-terminal residues of SNAP-25A are loaded into the D1 ring pore of NSF via a spiral pattern of interactions between a conserved tyrosine NSF residue and SNAP-25A backbone atoms. This loading process likely precedes ATP hydrolysis. Subsequent ATP hydrolysis then drives complete disassembly.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 4, 2018 / Release: Sep 19, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 19, 2018Structure modelrepositoryInitial release
1.1Sep 26, 2018Structure modelData collection / Database referencescitation / citation_author_citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

Structure visualization

  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9101
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:

Downloads & links


Deposited unit
A: Vesicle-fusing ATPase
B: Vesicle-fusing ATPase
C: Vesicle-fusing ATPase
D: Vesicle-fusing ATPase
E: Vesicle-fusing ATPase
F: Vesicle-fusing ATPase
H: Synaptosomal-associated protein 25
I: Syntaxin-1A
J: Vesicle-associated membrane protein 2
K: Alpha-soluble NSF attachment protein
L: Alpha-soluble NSF attachment protein
hetero molecules

Theoretical massNumber of molelcules
Total (without water)655,79922

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1


Protein/peptide , 5 types, 11 molecules ABCDEFHIJKL

#1: Protein/peptide
Vesicle-fusing ATPase / / N-ethylmaleimide-sensitive fusion protein / NEM-sensitive fusion protein / Vesicular-fusion protein NSF

Mass: 85509.227 Da / Num. of mol.: 6 / Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: NSF / Production host: Escherichia coli (E. coli) / References: UniProt: P18708, vesicle-fusing ATPase
#2: Protein/peptide Synaptosomal-associated protein 25 / SNAP25 / SNAP-25 / Super protein / SUP / Synaptosomal-associated 25 kDa protein

Mass: 23512.387 Da / Num. of mol.: 1 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25, Snap / Production host: Escherichia coli (E. coli) / References: UniProt: P60881
#3: Protein/peptide Syntaxin-1A / Neuron-specific antigen HPC-1 / Synaptotagmin-associated 35 kDa protein / P35A

Mass: 29634.129 Da / Num. of mol.: 1 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stx1a, Sap / Production host: Escherichia coli (E. coli) / References: UniProt: P32851
#4: Protein/peptide Vesicle-associated membrane protein 2 / Vesicle-associated membrane protein / VAMP-2 / Synaptobrevin-2

Mass: 12981.304 Da / Num. of mol.: 1 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vamp2, Syb2 / Production host: Escherichia coli (E. coli) / References: UniProt: P63045
#5: Protein/peptide Alpha-soluble NSF attachment protein / SNAP-alpha / N-ethylmaleimide-sensitive factor attachment protein alpha

Mass: 35598.223 Da / Num. of mol.: 2 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Napa, Snap, Snapa / Production host: Escherichia coli (E. coli) / References: UniProt: P54921

Non-polymers , 2 types, 11 molecules

#6: Chemical

Mass: 507.181 Da / Num. of mol.: 9 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#7: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE

Mass: 427.201 Da / Num. of mol.: 2 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

Sample preparation

IDNameTypeEntity IDParent IDSource
120S supercomplex consisting of soluble neuronal SNARE complex, alpha-SNAP, and N-ethylmaleimide sensitive factor (NSF)COMPLEX1, 2, 3, 4, 50MULTIPLE SOURCES
2N-ethylmaleimide sensitive factorCOMPLEX11RECOMBINANT
3Synaptosomal-associated protein 25COMPLEX21RECOMBINANT
5Vesicle-associated membrane protein 2COMPLEX41RECOMBINANT
6Alpha-soluble NSF attachment proteinCOMPLEX51RECOMBINANT
Molecular weight
IDValueEntity assembly IDExperimental value
10.628533 MDa1NO
20.496812 MDa2NO
30.023625 MDa3NO
40.030726 MDa4NO
50.010870 MDa5NO
60.033250 MDa6NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
2210029Cricetulus griseus (Chinese hamster)
3310116Rattus norvegicus (Norway rat)
4410116Rattus norvegicus (Norway rat)
5510116Rattus norvegicus (Norway rat)
6610116Rattus norvegicus (Norway rat)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
22562Escherichia coli (E. coli)
33562Escherichia coli (E. coli)
44562Escherichia coli (E. coli)
55562Escherichia coli (E. coli)
66562Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer ID
10.05 MTris HClC4H11NO31
20.150 MSodium chlorideNaCl1
30.001 MAdenosine triphosphateC10H16N5O13P31
40.001 MEthylenediaminetetraacetic acidC10H16N2O81
50.001 MDithiothreitolC4H10O2S21
60.05 % v/vNonidet P-401
SpecimenConc.: 15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 kelvins / Details: Blot for 3.5 seconds before plunging.

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 58 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 2 / Number of real images: 5418
Image scansMovie frames/image: 40 / Used frames/image: 2-40


EM software
2SerialEMimage acquisition
4RELION2.1CTF correction
7PHENIXmodel fitting
8Cootmodel fitting
10PHENIXmodel refinement
11Cootmodel refinement
12RELION2.1initial Euler assignment
13RELION2.1final Euler assignment
15RELION2.13D reconstruction
CTF correctionDetails: CTF correction was carried out in Relion with reconstruction step.
Particle selectionNumber of particles selected: 475680
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 62723 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL
Atomic model buildingPDB-ID: 3J96

About Yorodumi


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. See below links for details.
  • 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

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more


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.

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