[English] 日本語
Yorodumi
- EMDB-71533: 22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydroly... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-71533
Title22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 29
Map dataSharpened map from CryoSPARC NU-Refine, B = 129.0
Sample
  • Complex: The 22bin20S complex of NSF, alphaSNAP, and the soluble 2:2 binary SNARE complex of syntaxin-1a and SNAP-25
    • Complex: Subcomplex of alpha-SNAP with poorly defined SNARE bundle
      • RNA: Unknown SNARE protein
      • Protein or peptide: Alpha-soluble NSF attachment protein
    • Complex: Homohexameric NSF
      • Protein or peptide: Vesicle-fusing ATPase
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: PHOSPHATE ION
  • Ligand: MAGNESIUM ION
KeywordsATPase / SNARE / hydrolysis / disassembly / translocation / exocytosis / neurotransmitter release / synapse / synaptic transmission / membrane fusion / HYDROLASE
Function / homology
Function and homology information


soluble NSF attachment protein activity / Intra-Golgi traffic / Retrograde transport at the Trans-Golgi-Network / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / SNARE complex disassembly / synaptobrevin 2-SNAP-25-syntaxin-1a complex / COPII-mediated vesicle transport / Golgi Associated Vesicle Biogenesis / regulation of synaptic vesicle priming ...soluble NSF attachment protein activity / Intra-Golgi traffic / Retrograde transport at the Trans-Golgi-Network / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / SNARE complex disassembly / synaptobrevin 2-SNAP-25-syntaxin-1a complex / COPII-mediated vesicle transport / Golgi Associated Vesicle Biogenesis / regulation of synaptic vesicle priming / protein-containing complex disassembly / ATP-dependent protein disaggregase activity / intra-Golgi vesicle-mediated transport / Golgi to plasma membrane protein transport / positive regulation of ATP-dependent activity / Golgi stack / apical protein localization / syntaxin binding / vesicle-fusing ATPase / syntaxin-1 binding / synaptic vesicle priming / positive regulation of receptor recycling / presynaptic active zone membrane / ionotropic glutamate receptor binding / SNARE binding / synaptic transmission, glutamatergic / PDZ domain binding / intracellular protein transport / brain development / neuromuscular junction / potassium ion transport / terminal bouton / neuron differentiation / positive regulation of protein catabolic process / presynapse / midbody / membrane fusion / postsynapse / protein kinase binding / protein-containing complex binding / glutamatergic synapse / ATP hydrolysis activity / ATP binding / metal ion binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
NSF attachment protein / Soluble NSF attachment protein, SNAP / : / 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 ...NSF attachment protein / Soluble NSF attachment protein, SNAP / : / 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 / Tetratricopeptide-like helical domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Vesicle-fusing ATPase / Alpha-soluble NSF attachment protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Cricetulus griseus (Chinese hamster)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.16 Å
AuthorsWhite KI / Brunger AT
Funding support United States, 3 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Helen Hay Whitney Foundation United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH063105 United States
CitationJournal: bioRxiv / Year: 2024
Title: Pre-fusion AAA+ remodeling of target-SNARE protein complexes enables synaptic transmission.
Authors: K Ian White / Yousuf A Khan / Kangqiang Qiu / Ashwin Balaji / Sergio Couoh-Cardel / Luis Esquivies / Richard A Pfuetzner / Jiajie Diao / Axel T Brunger
Abstract: Membrane fusion is driven by SNARE complex formation across cellular contexts, including vesicle fusion during synaptic transmission. Multiple proteins organize trans-SNARE complex assembly and ...Membrane fusion is driven by SNARE complex formation across cellular contexts, including vesicle fusion during synaptic transmission. Multiple proteins organize trans-SNARE complex assembly and priming, leading to fusion. One target membrane SNARE, syntaxin, forms nanodomains at the active zone, and another, SNAP-25, enters non-fusogenic complexes with it. Here, we show that the AAA+ protein NSF (N-ethylmaleimide sensitive factor) and SNAP (soluble NSF attachment protein) must act prior to fusion. We show that syntaxin clusters are conserved, that NSF colocalizes with them, and characterize SNARE populations within and near these clusters using cryo-EM. Supercomplexes of NSF, α-SNAP, and either a syntaxin tetramer or two binary complexes of syntaxin-SNAP-25 reveal atomic details of SNARE processing and show how sequential ATP hydrolysis drives disassembly. These results suggest a functional role for syntaxin clusters as reservoirs and a corresponding role for NSF in syntaxin liberation and SNARE protein quality control preceding fusion.
History
DepositionJun 30, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_71533.png

Downloads & links

-
Map

FileDownload / File: emd_71533.map.gz / Format: CCP4 / Size: 96.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map from CryoSPARC NU-Refine, B = 129.0
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 294 pix.
= 322.224 Å		1.1 Å/pix.
x 294 pix.
= 322.224 Å		1.1 Å/pix.
x 294 pix.
= 322.224 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.096 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.89817065 - 1.6620429
Average (Standard dev.)0.0007713381 (±0.05719177)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions294294294
Spacing294294294
CellA=B=C: 322.224 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Unsharpened map from CryoSPARC NU-Refine

Fileemd_71533_additional_1.map
AnnotationUnsharpened map from CryoSPARC NU-Refine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A from CryoSPARC NU-Refine

Fileemd_71533_half_map_1.map
AnnotationHalf map A from CryoSPARC NU-Refine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B from CryoSPARC NU-Refine

Fileemd_71533_half_map_2.map
AnnotationHalf map B from CryoSPARC NU-Refine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : The 22bin20S complex of NSF, alphaSNAP, and the soluble 2:2 binar...

EntireName: The 22bin20S complex of NSF, alphaSNAP, and the soluble 2:2 binary SNARE complex of syntaxin-1a and SNAP-25
Components
  • Complex: The 22bin20S complex of NSF, alphaSNAP, and the soluble 2:2 binary SNARE complex of syntaxin-1a and SNAP-25
    • Complex: Subcomplex of alpha-SNAP with poorly defined SNARE bundle
      • RNA: Unknown SNARE protein
      • Protein or peptide: Alpha-soluble NSF attachment protein
    • Complex: Homohexameric NSF
      • Protein or peptide: Vesicle-fusing ATPase
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: PHOSPHATE ION
  • Ligand: MAGNESIUM ION

+
Supramolecule #1: The 22bin20S complex of NSF, alphaSNAP, and the soluble 2:2 binar...

SupramoleculeName: The 22bin20S complex of NSF, alphaSNAP, and the soluble 2:2 binary SNARE complex of syntaxin-1a and SNAP-25
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

+
Supramolecule #2: Subcomplex of alpha-SNAP with poorly defined SNARE bundle

SupramoleculeName: Subcomplex of alpha-SNAP with poorly defined SNARE bundle
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Rattus norvegicus (Norway rat)

+
Supramolecule #3: Homohexameric NSF

SupramoleculeName: Homohexameric NSF / type: complex / ID: 3 / Parent: 1 / 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: 82.90743 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAHMAGRSMQ AARCPTDELS LSNCAVVSEK DYQSGQHVIV RTSPNHKYIF TLRTHPSVVP GSVAFSLPQR KWAGLSIGQE IEVALYSFD KAKQCIGTMT IEIDFLQKKN IDSNPYDTDK MAAEFIQQFN NQAFSVGQQL VFSFNDKLFG LLVKDIEAMD P SILKGEPA ...String:
GAHMAGRSMQ AARCPTDELS LSNCAVVSEK DYQSGQHVIV RTSPNHKYIF TLRTHPSVVP GSVAFSLPQR KWAGLSIGQE IEVALYSFD KAKQCIGTMT IEIDFLQKKN IDSNPYDTDK MAAEFIQQFN NQAFSVGQQL VFSFNDKLFG LLVKDIEAMD P SILKGEPA SGKRQKIEVG LVVGNSQVAF EKAENSSLNL IGKAKTKENR QSIINPDWNF EKMGIGGLDK EFSDIFRRAF AS RVFPPEI VEQMGCKHVK GILLYGPPGC GKTLLARQIG KMLNAREPKV VNGPEILNKY VGESEANIRK LFADAEEEQR RLG ANSGLH IIIFDEIDAI CKQRGSMAGS TGVHDTVVNQ LLSKIDGVEQ LNNILVIGMT NRPDLIDEAL LRPGRLEVKM EIGL PDEKG RLQILHIHTA RMRGHQLLSA DVDIKELAVE TKNFSGAELE GLVRAAQSTA MNRHIKASTK VEVDMEKAES LQVTR GDFL ASLENDIKPA FGTNQEDYAS YIMNGIIKWG DPVTRVLDDG ELLVQQTKNS DRTPLVSVLL EGPPHSGKTA LAAKIA EES NFPFIKICSP DKMIGFSETA KCQAMKKIFD DAYKSQLSCV VVDDIERLLD YVPIGPRFSN LVLQALLVLL KKAPPQG RK LLIIGTTSRK DVLQEMEMLN AFSTTIHVPN IATGEQLLEA LELLGNFKDK ERTTIAQQVK GKKVWIGIKK LLMLIEMS L QMDPEYRVRK FLALLREEGA SPLDFD

UniProtKB: Vesicle-fusing ATPase

+
Macromolecule #3: Alpha-soluble NSF attachment protein

MacromoleculeName: Alpha-soluble NSF attachment protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 33.290715 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GMDTSGKQAE AMALLAEAER KVKNSQSFFS GLFGGSSKIE EACEIYARAA NMFKMAKNWS AAGNAFCQAA QLHLQLQSKH DAATCFVDA GNAFKKADPQ EAINCLMRAI EIYTDMGRFT IAAKHHISIA EIYETELVDV EKAIAHYEQS ADYYKGEESN S SANKCLLK ...String:
GMDTSGKQAE AMALLAEAER KVKNSQSFFS GLFGGSSKIE EACEIYARAA NMFKMAKNWS AAGNAFCQAA QLHLQLQSKH DAATCFVDA GNAFKKADPQ EAINCLMRAI EIYTDMGRFT IAAKHHISIA EIYETELVDV EKAIAHYEQS ADYYKGEESN S SANKCLLK VAGYAAQLEQ YQKAIDIYEQ VGTSAMDSPL LKYSAKDYFF KAALCHFCID MLNAKLAVQK YEELFPAFSD SR ECKLMKK LLEAHEEQNV DSYTESVKEY DSISRLDQWL TTMLLRIKKT IQGDEEDLR

UniProtKB: Alpha-soluble NSF attachment protein

+
Macromolecule #2: Unknown SNARE protein

MacromoleculeName: Unknown SNARE protein / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 1.061405 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

+
Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 5 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

+
Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 7 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

+
Macromolecule #6: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

+
Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration15 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
50.0 mMTris-HCl
150.0 mMsodium chlorideNaCl
1.0 mMmagnesium chlorideMgCl2
1.0 mMadenosine triphosphate
1.0 mMTCEP
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 33.96 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 / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1889717
CTF correctionSoftware: (Name: CTFFIND (ver. 4), RELION (ver. 3.1.4)) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: EXACT BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 35805
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.1.4)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6mdm


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9pdd:
22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 29

+
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