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- EMDB-39207: Cryo-EM structure of human SV2A in complex with Brivaracetam -

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Basic information

Entry
Database: EMDB / ID: EMD-39207
TitleCryo-EM structure of human SV2A in complex with Brivaracetam
Map data
Sample
  • Complex: Synaptic vesicle glycoprotein 2A in complex with Brivaracetam
    • Protein or peptide: Synaptic vesicle glycoprotein 2A
  • Ligand: (2S)-2-[(4R)-2-oxidanylidene-4-propyl-pyrrolidin-1-yl]butanamide
KeywordsSynaptic vesicle glycoprotein 2A / Brivaracetam / TRANSPORT PROTEIN
Function / homology
Function and homology information


regulation of gamma-aminobutyric acid secretion / 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) / synaptic vesicle priming / presynaptic active zone / transmembrane transporter activity / GABA-ergic synapse / neuromuscular junction ...regulation of gamma-aminobutyric acid secretion / 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) / synaptic vesicle priming / presynaptic active zone / transmembrane transporter activity / GABA-ergic synapse / neuromuscular junction / synaptic vesicle membrane / intracellular calcium ion homeostasis / cell-cell junction / synaptic vesicle / neuron projection / neuronal cell body / glutamatergic synapse / dendrite / protein kinase binding / endoplasmic reticulum / plasma membrane
Similarity search - Function
Synaptic vesicle protein SV2 / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Sugar transporter, conserved site / 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: 3.38 Å
AuthorsQu Q / Liu S / Zhou Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171194 China
CitationJournal: To Be Published
Title: Cryo-EM structure of human SV2A in complex with Brivaracetam
Authors: Qu Q / Liu S / Zhou Z
History
DepositionFeb 23, 2024-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39207.png

Downloads & links

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Map

FileDownload / File: emd_39207.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.932 Å
Density
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-3.3937733 - 4.1471024
Average (Standard dev.)-0.0001429882 (±0.09043016)
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_39207_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39207_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_39207_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 in complex with Brivaracetam

EntireName: Synaptic vesicle glycoprotein 2A in complex with Brivaracetam
Components
  • Complex: Synaptic vesicle glycoprotein 2A in complex with Brivaracetam
    • Protein or peptide: Synaptic vesicle glycoprotein 2A
  • Ligand: (2S)-2-[(4R)-2-oxidanylidene-4-propyl-pyrrolidin-1-yl]butanamide

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Supramolecule #1: Synaptic vesicle glycoprotein 2A in complex with Brivaracetam

SupramoleculeName: Synaptic vesicle glycoprotein 2A in complex with Brivaracetam
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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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Macromolecule #2: (2S)-2-[(4R)-2-oxidanylidene-4-propyl-pyrrolidin-1-yl]butanamide

MacromoleculeName: (2S)-2-[(4R)-2-oxidanylidene-4-propyl-pyrrolidin-1-yl]butanamide
type: ligand / ID: 2 / Number of copies: 2 / Formula: VLX
Molecular weightTheoretical: 212.289 Da

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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: 60 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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 112317
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-8yf1:
Cryo-EM structure of human SV2A in complex with Brivaracetam

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