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- EMDB-49758: Structure of Synaptic Vesicle Protein 2A Bound to Brivaracetam an... -

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Basic information

Entry
Database: EMDB / ID: EMD-49758
TitleStructure of Synaptic Vesicle Protein 2A Bound to Brivaracetam and UCB1244283
Map dataSharpened map
Sample
  • Complex: SV2A bound to brivaracetam and UCB1244283
    • Protein or peptide: Synaptic vesicle glycoprotein 2A
  • Ligand: (3R)-4-(3,5-dimethylphenyl)-N-(2-methoxyphenyl)-3-methylbutanamide
  • Ligand: (2S)-2-[(4R)-2-oxidanylidene-4-propyl-pyrrolidin-1-yl]butanamide
  • Ligand: CHOLESTEROL
  • Ligand: (3S)-4-(3,5-dimethylphenyl)-N-(2-methoxyphenyl)-3-methylbutanamide
KeywordsSynaptic vesicle / SLC22 / Inhibitor / Positive allosteric modulator / MEMBRANE 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: 3.05 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
DepositionMar 18, 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_49758.png

Downloads & links

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Map

FileDownload / File: emd_49758.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: 0.5
Minimum - Maximum-1.1656541 - 1.6856767
Average (Standard dev.)0.0010684362 (±0.036088604)
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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Mask #1

Fileemd_49758_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_49758_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_49758_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 B

Fileemd_49758_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : SV2A bound to brivaracetam and UCB1244283

EntireName: SV2A bound to brivaracetam and UCB1244283
Components
  • Complex: SV2A bound to brivaracetam and UCB1244283
    • Protein or peptide: Synaptic vesicle glycoprotein 2A
  • Ligand: (3R)-4-(3,5-dimethylphenyl)-N-(2-methoxyphenyl)-3-methylbutanamide
  • Ligand: (2S)-2-[(4R)-2-oxidanylidene-4-propyl-pyrrolidin-1-yl]butanamide
  • Ligand: CHOLESTEROL
  • Ligand: (3S)-4-(3,5-dimethylphenyl)-N-(2-methoxyphenyl)-3-methylbutanamide

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Supramolecule #1: SV2A bound to brivaracetam and UCB1244283

SupramoleculeName: SV2A bound to brivaracetam and UCB1244283 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.319047 KDa
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

UniProtKB: Synaptic vesicle glycoprotein 2A

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Macromolecule #2: (3R)-4-(3,5-dimethylphenyl)-N-(2-methoxyphenyl)-3-methylbutanamide

MacromoleculeName: (3R)-4-(3,5-dimethylphenyl)-N-(2-methoxyphenyl)-3-methylbutanamide
type: ligand / ID: 2 / Number of copies: 1 / Formula: A1B1J
Molecular weightTheoretical: 311.418 Da

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Macromolecule #3: (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: 3 / Number of copies: 1 / Formula: VLX
Molecular weightTheoretical: 212.289 Da

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Macromolecule #4: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 4 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #5: (3S)-4-(3,5-dimethylphenyl)-N-(2-methoxyphenyl)-3-methylbutanamide

MacromoleculeName: (3S)-4-(3,5-dimethylphenyl)-N-(2-methoxyphenyl)-3-methylbutanamide
type: ligand / ID: 5 / Number of copies: 1 / Formula: A1B1I
Molecular weightTheoretical: 311.418 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

Concentration8.13 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/1 / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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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: PDB ENTRY
PDB model - PDB ID:

8uo9


Details: Structure of synaptic vesicle protein 2A in complex with a nanobody. PDB DOI: https://doi.org/10.2210/pdb8UO9/pdbEM Map EMD-42431: EMDB EMDataResource Deposited: 2023-10-19 Released: 2024-05- ...Details: Structure of synaptic vesicle protein 2A in complex with a nanobody. PDB DOI: https://doi.org/10.2210/pdb8UO9/pdbEM Map EMD-42431: EMDB EMDataResource Deposited: 2023-10-19 Released: 2024-05-22 Deposition Author(s): Mittal, A., Martin, M.F., Levin, E., Adams, C., Yang, M., Ledecq, M., Horanyi, P.S., Coleman, J.A.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36477
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8uo9


Chain - Chain ID: A / Chain - Residue range: 144-738 / Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: PDB 8UO9 was used for building initial model.
Output model

PDB-9ntc:
Structure of Synaptic Vesicle Protein 2A Bound to Brivaracetam and UCB1244283

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