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- EMDB-71601: Min22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a H3:SNAP-25 SN1... -

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Entry
Database: EMDB / ID: EMD-71601
TitleMin22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a H3:SNAP-25 SN1), 4:2:2 alphaSNAP-syntaxin-1a H3-SNAP-25 SN1 subcomplex local refinement, non-hydrolyzing, class 28
Map dataSharpened map from CryoSPARC local_refine_new, B = 126.7
Sample
  • Complex: The spire of the min22bin20S complex of NSF, alphaSNAP, and the soluble 2:2 binary SNARE complex of the syntaxin-1a H3 and SNAP-25 SN1 domains
    • Complex: Subcomplex of alphaSNAP, syntaxin-1a H3, and SNAP-25 SN1
      • Complex: 2:2 binary complex of SNAP-25 SN1 and syntaxin-1a H3
        • Protein or peptide: Syntaxin-1A
        • Protein or peptide: Alpha-soluble NSF attachment protein
      • Protein or peptide: Synaptosomal-associated protein 25
    • Complex: Homohexameric NSF
      • Protein or peptide: Vesicle-fusing ATPase
  • Ligand: water
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 / BLOC-1 complex / myosin head/neck binding / SNARE complex disassembly / synaptic vesicle fusion to presynaptic active zone membrane / Other interleukin signaling ...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 / BLOC-1 complex / myosin head/neck binding / SNARE complex disassembly / synaptic vesicle fusion to presynaptic active zone membrane / Other interleukin signaling / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / presynaptic dense core vesicle exocytosis / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / extrinsic component of presynaptic membrane / calcium ion-regulated exocytosis of neurotransmitter / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / COPII-mediated vesicle transport / GABA synthesis, release, reuptake and degradation / regulated exocytosis / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / Dopamine Neurotransmitter Release Cycle / synaptic vesicle docking / Golgi Associated Vesicle Biogenesis / regulation of synaptic vesicle priming / regulation of establishment of protein localization / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / protein-containing complex disassembly / positive regulation of calcium ion-dependent exocytosis / vesicle docking / ribbon synapse / secretion by cell / regulation of exocytosis / SNAP receptor activity / chloride channel inhibitor activity / SNARE complex / vesicle fusion / calcium-ion regulated exocytosis / ATP-dependent protein disaggregase activity / actomyosin / LGI-ADAM interactions / hormone secretion / intra-Golgi vesicle-mediated transport / Golgi to plasma membrane protein transport / positive regulation of hormone secretion / positive regulation of ATP-dependent activity / Golgi stack / ATP-dependent protein binding / neurotransmitter secretion / apical protein localization / protein localization to membrane / syntaxin binding / vesicle-fusing ATPase / syntaxin-1 binding / insulin secretion / endosomal transport / Neutrophil degranulation / SNARE complex assembly / positive regulation of neurotransmitter secretion / neurotransmitter transport / synaptic vesicle priming / regulation of synapse assembly / response to gravity / myosin binding / regulation of neuron projection development / positive regulation of receptor recycling / exocytosis / modulation of excitatory postsynaptic potential / positive regulation of exocytosis / synaptic vesicle exocytosis / associative learning / protein sumoylation / synaptic vesicle endocytosis / voltage-gated potassium channel activity / positive regulation of excitatory postsynaptic potential / long-term memory / axonal growth cone / calcium channel inhibitor activity / presynaptic active zone membrane / photoreceptor inner segment / voltage-gated potassium channel complex / somatodendritic compartment / ionotropic glutamate receptor binding / endomembrane system / axonogenesis / secretory granule / acrosomal vesicle / SNARE binding / synaptic transmission, glutamatergic / PDZ domain binding / filopodium / intracellular protein transport / locomotory behavior / trans-Golgi network / postsynaptic density membrane / brain development
Similarity search - Function
NSF attachment protein / Soluble NSF attachment protein, SNAP / : / NSF, AAA+ ATPase lid domain / Vesicle-fusing ATPase / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Syntaxin / Syntaxin N-terminal domain ...NSF attachment protein / Soluble NSF attachment protein, SNAP / : / NSF, AAA+ ATPase lid domain / Vesicle-fusing ATPase / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / SNARE domain / Syntaxin / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / 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 / Syntaxin-1A / Alpha-soluble NSF attachment protein / Synaptosomal-associated protein 25
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Cricetulus griseus (Chinese hamster)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.58 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
DepositionJul 4, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71601.png

Downloads & links

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Map

FileDownload / File: emd_71601.map.gz / Format: CCP4 / Size: 96.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map from CryoSPARC local_refine_new, B = 126.7
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-1.5966408 - 2.6555703
Average (Standard dev.)0.0018228374 (±0.05782651)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Additional map: Unsharpened map from CryoSPARC local refine new

Fileemd_71601_additional_1.map
AnnotationUnsharpened map from CryoSPARC local_refine_new
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A from CryoSPARC local refine new

Fileemd_71601_half_map_1.map
AnnotationHalf map A from CryoSPARC local_refine_new
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B from CryoSPARC local refine new

Fileemd_71601_half_map_2.map
AnnotationHalf map B from CryoSPARC local_refine_new
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : The spire of the min22bin20S complex of NSF, alphaSNAP, and the s...

EntireName: The spire of the min22bin20S complex of NSF, alphaSNAP, and the soluble 2:2 binary SNARE complex of the syntaxin-1a H3 and SNAP-25 SN1 domains
Components
  • Complex: The spire of the min22bin20S complex of NSF, alphaSNAP, and the soluble 2:2 binary SNARE complex of the syntaxin-1a H3 and SNAP-25 SN1 domains
    • Complex: Subcomplex of alphaSNAP, syntaxin-1a H3, and SNAP-25 SN1
      • Complex: 2:2 binary complex of SNAP-25 SN1 and syntaxin-1a H3
        • Protein or peptide: Syntaxin-1A
        • Protein or peptide: Alpha-soluble NSF attachment protein
      • Protein or peptide: Synaptosomal-associated protein 25
    • Complex: Homohexameric NSF
      • Protein or peptide: Vesicle-fusing ATPase
  • Ligand: water

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Supramolecule #1: The spire of the min22bin20S complex of NSF, alphaSNAP, and the s...

SupramoleculeName: The spire of the min22bin20S complex of NSF, alphaSNAP, and the soluble 2:2 binary SNARE complex of the syntaxin-1a H3 and SNAP-25 SN1 domains
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: Subcomplex of alphaSNAP, syntaxin-1a H3, and SNAP-25 SN1

SupramoleculeName: Subcomplex of alphaSNAP, syntaxin-1a H3, and SNAP-25 SN1
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Supramolecule #3: Homohexameric NSF

SupramoleculeName: Homohexameric NSF / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Cricetulus griseus (Chinese hamster)

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Supramolecule #4: 2:2 binary complex of SNAP-25 SN1 and syntaxin-1a H3

SupramoleculeName: 2:2 binary complex of SNAP-25 SN1 and syntaxin-1a H3 / type: complex / ID: 4 / Parent: 2 / Macromolecule list: #2-#3
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Synaptosomal-associated protein 25

MacromoleculeName: Synaptosomal-associated protein 25 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 9.741827 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SMAEDADMRN ELEEMQRRAD QLADESLEST RRMLQLVEES KDAGIRTLVM LDEQGEQLER IEEGMDQINK DMKEAEKNLT DLGK

UniProtKB: Synaptosomal-associated protein 25

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Macromolecule #2: Syntaxin-1A

MacromoleculeName: Syntaxin-1A / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 9.233696 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MALSEIETRH SEIIKLENSI RELHDMFMDM AMLVESQGEM IDRIEYNVEH AVDYVERAVS DTKKAVKYQS KARRKKIM

UniProtKB: Syntaxin-1A

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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

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Macromolecule #4: Vesicle-fusing ATPase

MacromoleculeName: Vesicle-fusing ATPase / type: protein_or_peptide / ID: 4 / Number of copies: 2 / 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

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 24 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
Component:
ConcentrationNameFormula
50.0 mMTris-HCl
150.0 mMsodium chlorideNaCl
1.0 mMEDTA
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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 33.992 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

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Image processing

Particle selectionNumber selected: 1473284
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: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Software - details: new_local_refine / Number images used: 341427
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)

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Atomic model buiding 1

Initial model
PDB IDChain

6mdm

source_name: PDB, initial_model_type: experimental model

1jth

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9pfg:
Min22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a H3:SNAP-25 SN1), 4:2:2 alphaSNAP-syntaxin-1a H3-SNAP-25 SN1 subcomplex local refinement, non-hydrolyzing, class 28

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