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- EMDB-70536: sx20S complex (NSF-alphaSNAP-syntaxin-1a), 4:4 alphaSNAP-syntaxin... -

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Basic information

Entry
Database: EMDB / ID: EMD-70536
Titlesx20S complex (NSF-alphaSNAP-syntaxin-1a), 4:4 alphaSNAP-syntaxin-1a subcomplex local refinement, non-hydrolyzing, class 1
Map dataSharpened map from cryoSPARC new-local-refine, B = 148.3
Sample
  • Complex: The sx20S complex of NSF, alphaSNAP, and soluble syntaxin-1a
    • Complex: Subcomplex of alphaSNAP-syntaxin-1a
      • Complex: Homotetrameric Syntaxin-1a
        • Protein or peptide: Syntaxin-1A
      • Complex: alphaSNAP
        • Protein or peptide: Alpha-soluble NSF attachment protein
    • Complex: Homohexameric NSF
  • Ligand: water
KeywordsATPase / SNARE / hydrolysis / disassembly / translocation / exocytosis / neurotransmitter release / synapse / synaptic transmission / membrane fusion / HYDROLASE
Function / homology
Function and homology information


Intra-Golgi traffic / Retrograde transport at the Trans-Golgi-Network / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / soluble NSF attachment protein activity / lamellar body / myosin head/neck binding / Other interleukin signaling / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex ...Intra-Golgi traffic / Retrograde transport at the Trans-Golgi-Network / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / soluble NSF attachment protein activity / lamellar body / myosin head/neck binding / Other interleukin signaling / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / protein-containing complex disassembly / positive regulation of catecholamine secretion / positive regulation of norepinephrine secretion / Dopamine Neurotransmitter Release Cycle / COPII-mediated vesicle transport / hormone secretion / regulation of synaptic vesicle priming / Golgi Associated Vesicle Biogenesis / : / regulated exocytosis / secretion by cell / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / calcium-ion regulated exocytosis / SNARE complex disassembly / positive regulation of calcium ion-dependent exocytosis / positive regulation of neurotransmitter secretion / : / chloride channel inhibitor activity / regulation of exocytosis / protein carrier activity / SNARE complex / SNAP receptor activity / vesicle fusion / actomyosin / LGI-ADAM interactions / positive regulation of ATP-dependent activity / ATP-dependent protein binding / cytoplasmic side of membrane / insulin secretion / apical protein localization / syntaxin binding / protein localization to membrane / exocytosis / myosin binding / SNARE complex assembly / synaptic vesicle priming / response to gravity / synaptic vesicle exocytosis / neurotransmitter transport / positive regulation of exocytosis / response to hyperoxia / regulation of dopamine secretion / modulation of excitatory postsynaptic potential / protein sumoylation / synaptic vesicle endocytosis / calcium channel inhibitor activity / presynaptic active zone membrane / secretory granule / acrosomal vesicle / positive regulation of excitatory postsynaptic potential / brain development / SNARE binding / synaptic membrane / neuromuscular junction / synaptic transmission, glutamatergic / intracellular protein transport / postsynaptic density membrane / Schaffer collateral - CA1 synapse / kinase binding / calcium-dependent protein binding / terminal bouton / synaptic vesicle membrane / neuron differentiation / presynapse / synaptic vesicle / nuclear membrane / cytoplasmic vesicle / presynaptic membrane / membrane fusion / perikaryon / transmembrane transporter binding / postsynapse / protein-macromolecule adaptor activity / postsynaptic membrane / neuron projection / axon / dendrite / protein-containing complex binding / glutamatergic synapse / protein-containing complex / mitochondrion / membrane / identical protein binding / plasma membrane
Similarity search - Function
NSF attachment protein / Soluble NSF attachment protein, SNAP / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / SNARE domain ...NSF attachment protein / Soluble NSF attachment protein, SNAP / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / SNARE domain / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Syntaxin-1A / Alpha-soluble NSF attachment protein
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.07 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: Nat Commun / Year: 2025
Title: Structural remodeling of target-SNARE protein complexes by NSF 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: Synaptic vesicles containing neurotransmitters fuse with the plasma membrane upon the arrival of an action potential at the active zone. Multiple proteins organize trans-SNARE complex assembly and ...Synaptic vesicles containing neurotransmitters fuse with the plasma membrane upon the arrival of an action potential at the active zone. 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 reveal mechanistic details of AAA+ protein NSF (N-ethylmaleimide sensitive factor) and SNAP (soluble NSF attachment protein) action before fusion. We show that syntaxin clusters are conserved, that NSF colocalizes with them, and characterize SNARE populations that may exist within or near them using cryo-EM. Supercomplexes of NSF, α-SNAP, and either a syntaxin tetramer or one of 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
DepositionMay 7, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70536.png

Downloads & links

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Map

FileDownload / File: emd_70536.map.gz / Format: CCP4 / Size: 96.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map from cryoSPARC new-local-refine, B = 148.3
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-0.55728894 - 1.4413855
Average (Standard dev.)0.0030359288 (±0.04488734)
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 new-local-refine

Fileemd_70536_additional_1.map
AnnotationUnsharpened map from cryoSPARC new-local-refine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A from cryoSPARC new-local-refine

Fileemd_70536_half_map_1.map
AnnotationHalf map A from cryoSPARC new-local-refine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B from cryoSPARC new-local-refine

Fileemd_70536_half_map_2.map
AnnotationHalf map B from cryoSPARC new-local-refine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The sx20S complex of NSF, alphaSNAP, and soluble syntaxin-1a

EntireName: The sx20S complex of NSF, alphaSNAP, and soluble syntaxin-1a
Components
  • Complex: The sx20S complex of NSF, alphaSNAP, and soluble syntaxin-1a
    • Complex: Subcomplex of alphaSNAP-syntaxin-1a
      • Complex: Homotetrameric Syntaxin-1a
        • Protein or peptide: Syntaxin-1A
      • Complex: alphaSNAP
        • Protein or peptide: Alpha-soluble NSF attachment protein
    • Complex: Homohexameric NSF
  • Ligand: water

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Supramolecule #1: The sx20S complex of NSF, alphaSNAP, and soluble syntaxin-1a

SupramoleculeName: The sx20S complex of NSF, alphaSNAP, and soluble syntaxin-1a
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Subcomplex of alphaSNAP-syntaxin-1a

SupramoleculeName: Subcomplex of alphaSNAP-syntaxin-1a / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2

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Supramolecule #3: Homohexameric NSF

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

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Supramolecule #4: Homotetrameric Syntaxin-1a

SupramoleculeName: Homotetrameric Syntaxin-1a / type: complex / ID: 4 / Parent: 2 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Supramolecule #5: alphaSNAP

SupramoleculeName: alphaSNAP / type: complex / ID: 5 / Parent: 2 / Macromolecule list: #2
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Syntaxin-1A

MacromoleculeName: Syntaxin-1A / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 29.350803 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKDRTQELRT AKDSDDDDDV TVTVDRDRFM DEFFEQVEEI RGFIDKIAEN VEEVKRKHSA ILASPNPDEK TKEELEELMS DIKKTANKV RSKLKSIEQS IEQEEGLNRS SADLRIRKTQ HSTLSRKFVE VMSEYNATQS DYRERCKGRI QRQLEITGRT T TSEELEDM ...String:
MKDRTQELRT AKDSDDDDDV TVTVDRDRFM DEFFEQVEEI RGFIDKIAEN VEEVKRKHSA ILASPNPDEK TKEELEELMS DIKKTANKV RSKLKSIEQS IEQEEGLNRS SADLRIRKTQ HSTLSRKFVE VMSEYNATQS DYRERCKGRI QRQLEITGRT T TSEELEDM LESGNPAIFA SGIIMDSSIS KQALSEIETR HSEIIKLENS IRELHDMFMD MAMLVESQGE MIDRIEYNVE HA VDYVERA VSDTKK

UniProtKB: Syntaxin-1A

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Macromolecule #2: Alpha-soluble NSF attachment protein

MacromoleculeName: Alpha-soluble NSF attachment protein / type: protein_or_peptide / ID: 2 / 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 #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 9 / 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 / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: OTHER
Details: 15 mA with PELCO easiGlow Glow Discharge Cleaning System
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: 27.608 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: 975203
CTF correctionSoftware: (Name: CTFFIND (ver. 4), RELION (ver. 3.1.4)) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Software - details: new-local-refine was used
Details: Reconstruction performed using cryoSPARC local refinement following signal subtraction of all NSF domains.
Number images used: 53244
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

1n7s

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9ojj:
sx20S complex (NSF-alphaSNAP-syntaxin-1a), 4:4 alphaSNAP-syntaxin-1a subcomplex local refinement, non-hydrolyzing, class 1

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