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- EMDB-71502: Structure of Synaptic Vesicle Protein 2A Bound to Levetiracetam a... -

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Basic information

Entry
Database: EMDB / ID: EMD-71502
TitleStructure of Synaptic Vesicle Protein 2A Bound to Levetiracetam and UCB1244283
Map dataSharpened map
Sample
  • Complex: SV2A bound to levetiracetam and UCB1244283
    • Protein or peptide: Synaptic vesicle glycoprotein 2A
KeywordsSynaptic vesicle / SLC22 / Inhibitor / LEV / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.93 Å
AuthorsMittal A / Martin MF / Ledecq M / Horanyi PS / Coleman JA
Funding support United States, 1 items
OrganizationGrant numberCountry
Brain & Behavior Research Foundation30153 United States
CitationJournal: To Be Published
Title: Molecular structure of a biomolecule.
Authors: Mittal A / Martin MF / Ledecq M / Horanyi PS / Coleman JA
History
DepositionJun 27, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71502.png

Downloads & links

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Map

FileDownload / File: emd_71502.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 336 pix.
= 241.584 Å		0.72 Å/pix.
x 336 pix.
= 241.584 Å		0.72 Å/pix.
x 336 pix.
= 241.584 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.719 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.088
Minimum - Maximum-0.19918822 - 0.31361946
Average (Standard dev.)0.0009779984 (±0.012104508)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 241.584 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_71502_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_71502_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_71502_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SV2A bound to levetiracetam and UCB1244283

EntireName: SV2A bound to levetiracetam and UCB1244283
Components
  • Complex: SV2A bound to levetiracetam and UCB1244283
    • Protein or peptide: Synaptic vesicle glycoprotein 2A

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Supramolecule #1: SV2A bound to levetiracetam and UCB1244283

SupramoleculeName: SV2A bound to levetiracetam and UCB1244283 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75.5 kDa/nm

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Macromolecule #1: Synaptic vesicle glycoprotein 2A

MacromoleculeName: Synaptic vesicle glycoprotein 2A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGYYRGEGTQ DEEEGGASSD ATEGHDEDDE IYEGEYQGIP RAESGGKGER MADGAPLAGV RGGLSDGEGP PGGRGEAQRR KEREELAQQ YEAILRECGH GRFQWTLYFV LGLALMADGV EVFVVGFVLP SAEKDMCLSD SNKGMLGLIV YLGMMVGAFL W GGLADRLG ...String:
MGYYRGEGTQ DEEEGGASSD ATEGHDEDDE IYEGEYQGIP RAESGGKGER MADGAPLAGV RGGLSDGEGP PGGRGEAQRR KEREELAQQ YEAILRECGH GRFQWTLYFV LGLALMADGV EVFVVGFVLP SAEKDMCLSD SNKGMLGLIV YLGMMVGAFL W GGLADRLG RRQCLLISLS VNSVFAFFSS FVQGYGTFLF CRLLSGVGIG GSIPIVFSYF SEFLAQEKRG EHLSWLCMFW MI GGVYAAA MAWAIIPHYG WSFQMGSAYQ FHSWRVFVLV CAFPSVFAIG ALTTQPESPR FFLENGKHDE AWMVLKQVHD TNM RAKGHP ERVFSVTHIK TIHQEDELIE IQSDTGTWYQ RWGVRALSLG GQVWGNFLSC FGPEYRRITL MMMGVWFTMS FSYY GLTVW FPDMIRHLQA VDYASRTKVF PGERVEHVTF NFTLENQIHR GGQYFNDKFI GLRLKSVSFE DSLFEECYFE DVTSS NTFF RNCTFINTVF YNTDLFEYKF VNSRLINSTF LHNKEGCPLD VTGTGEGAYM VYFVSFLGTL AVLPGNIVSA LLMDKI GRL RMLAGSSVMS CVSCFFLSFG NSESAMIALL CLFGGVSIAS WNALDVLTVE LYPSDKRTTA FGFLNALCKL AAVLGIS IF TSFVGITKAA PILFASAALA LGSSLALKLP ETRGQVLQLE VLFQ

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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

Concentration5.3 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/1 / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (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: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 194000
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: 6.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 39638
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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