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- PDB-9pcb: Structure of Synaptic Vesicle Protein 2A Bound to UCB-J -

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Basic information

Entry
Database: PDB / ID: 9pcb
TitleStructure of Synaptic Vesicle Protein 2A Bound to UCB-J
ComponentsSynaptic vesicle glycoprotein 2A
KeywordsMEMBRANE PROTEIN / Synaptic vesicle / SLC22 / PET tracer
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsMittal, A. / Martin, M.F. / Ledecq, M. / Horanyi, P.S. / Coleman, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Brain & Behavior Research Foundation30153 United States
CitationJournal: To Be Published
Title: Molecular structure of a biomolecule.
Authors: Mittal, A. / Martin, M.F. / Ledecq, M. / Horanyi, P.S. / Coleman, J.A.
History
DepositionJun 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Synaptic vesicle glycoprotein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6392
Polymers76,3191
Non-polymers3201
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Synaptic vesicle glycoprotein 2A


Mass: 76319.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SV2A, KIAA0736, PSEC0174 / Cell line (production host): tsA201 / Production host: Homo sapiens (human) / References: UniProt: Q7L0J3
#2: Chemical ChemComp-A1CCA / (4R)-1-[(3-methylpyridin-4-yl)methyl]-4-(3,4,5-trifluorophenyl)pyrrolidin-2-one


Mass: 320.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15F3N2O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SV2A bound to UCB-J / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 75.5 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: tsa201
Buffer solutionpH: 8
SpecimenConc.: 5.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 194000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARCparticle selection
7Coot0.9.8.95 ELmodel fittingModel Building
12cryoSPARC3D reconstruction
13PHENIX1.20.1-4487model refinementReal Space refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119776 / Symmetry type: POINT
Atomic model buildingPDB-ID: 8UO9

8uo9


Pdb chain-ID: A / Accession code: 8UO9 / Chain residue range: 144-738 / Details: PDB 8UO9 was used for building initial model. / Pdb chain residue range: 144-738 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0024030
ELECTRON MICROSCOPYf_angle_d0.5115475
ELECTRON MICROSCOPYf_dihedral_angle_d6.903577
ELECTRON MICROSCOPYf_chiral_restr0.035617
ELECTRON MICROSCOPYf_plane_restr0.003682

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