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- EMDB-39206: Cryo-EM structure of human SV2A -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-39206
TitleCryo-EM structure of human SV2A
Map data
Sample
  • Complex: Synaptic vesicle glycoprotein 2A
    • Protein or peptide: Synaptic vesicle glycoprotein 2A
KeywordsSynaptic vesicle glycoprotein 2A / TRANSPORT PROTEIN
Function / homology
Function and homology information


Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type D (botD) / Toxicity of botulinum toxin type E (botE) / Toxicity of botulinum toxin type A (botA) / presynaptic active zone / synaptic vesicle priming / transmembrane transporter activity / neuromuscular junction / GABA-ergic synapse / intracellular calcium ion homeostasis ...Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type D (botD) / Toxicity of botulinum toxin type E (botE) / Toxicity of botulinum toxin type A (botA) / presynaptic active zone / synaptic vesicle priming / transmembrane transporter activity / neuromuscular junction / GABA-ergic synapse / intracellular calcium ion homeostasis / synaptic vesicle / cell-cell junction / synaptic vesicle membrane / neuron projection / protein kinase binding / glutamatergic synapse / endoplasmic reticulum / plasma membrane
Similarity search - Function
: / SV2A/B/C luminal domain / Synaptic vesicle protein SV2 / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Synaptic vesicle glycoprotein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsQu Q / Liu S / Zhou Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171194 China
CitationJournal: Cell Discov / Year: 2024
Title: Recognition of antiepileptic brivaracetam by synaptic vesicle protein 2A.
Authors: Shujin Liu / Yulin Chao / Zixuan Zhou / Chuanhui Yang / Zhini Zhu / Yuwei Wang / Qianhui Qu /
History
DepositionFeb 23, 2024-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39206.png

Downloads & links

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Map

FileDownload / File: emd_39206.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 270 pix.
= 251.64 Å		0.93 Å/pix.
x 270 pix.
= 251.64 Å		0.93 Å/pix.
x 270 pix.
= 251.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-2.074018 - 2.523872
Average (Standard dev.)-0.0014394254 (±0.04277665)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 251.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_39206_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39206_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39206_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Synaptic vesicle glycoprotein 2A

EntireName: Synaptic vesicle glycoprotein 2A
Components
  • Complex: Synaptic vesicle glycoprotein 2A
    • Protein or peptide: Synaptic vesicle glycoprotein 2A

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Supramolecule #1: Synaptic vesicle glycoprotein 2A

SupramoleculeName: Synaptic vesicle glycoprotein 2A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Synaptic vesicle glycoprotein 2A

MacromoleculeName: Synaptic vesicle glycoprotein 2A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.394883 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEEGFRDRAA FIRGAKDIAK EVKKHAAKKV VKGLDRVQDE YSRRSYSRFE EEDDDDDFPA PSDGYYRGEG TQDEEEGGAS SDATEGHDE DDEIYEGEYQ GIPRAESGGK GERMADGAPL AGVRGGLSDG EGPPGGRGEA QRRKEREELA QQYEAILREC G HGRFQWTL ...String:
MEEGFRDRAA FIRGAKDIAK EVKKHAAKKV VKGLDRVQDE YSRRSYSRFE EEDDDDDFPA PSDGYYRGEG TQDEEEGGAS SDATEGHDE DDEIYEGEYQ GIPRAESGGK GERMADGAPL AGVRGGLSDG EGPPGGRGEA QRRKEREELA QQYEAILREC G HGRFQWTL YFVLGLALMA DGVEVFVVGF VLPSAEKDMC LSDSNKGMLG LIVYLGMMVG AFLWGGLADR LGRRQCLLIS LS VNSVFAF FSSFVQGYGT FLFCRLLSGV GIGGSIPIVF SYFSEFLAQE KRGEHLSWLC MFWMIGGVYA AAMAWAIIPH YGW SFQMGS AYQFHSWRVF VLVCAFPSVF AIGALTTQPE SPRFFLENGK HDEAWMVLKQ VHDTNMRAKG HPERVFSVTH IKTI HQEDE LIEIQSDTGT WYQRWGVRAL SLGGQVWGNF LSCFGPEYRR ITLMMMGVWF TMSFSYYGLT VWFPDMIRHL QAVDY ASRT KVFPGERVEH VTFNFTLENQ IHRGGQYFND KFIGLRLKSV SFEDSLFEEC YFEDVTSSNT FFRNCTFINT VFYNTD LFE YKFVNSRLIN STFLHNKEGC PLDVTGTGEG AYMVYFVSFL GTLAVLPGNI VSALLMDKIG RLRMLAGSSV MSCVSCF FL SFGNSESAMI ALLCLFGGVS IASWNALDVL TVELYPSDKR TTAFGFLNAL CKLAAVLGIS IFTSFVGITK AAPILFAS A ALALGSSLAL KLPSRLEEEL RRRTEPGSLE VLFQ

UniProtKB: Synaptic vesicle glycoprotein 2A

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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

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 50 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 260.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 119837
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8yf0:
Cryo-EM structure of human SV2A

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