8UO8

Structure of synaptic vesicle protein 2B with padsevonil


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of synaptic vesicle protein 2A and 2B bound to anticonvulsants.

Mittal, A.Martin, M.F.Levin, E.J.Adams, C.Yang, M.Provins, L.Hall, A.Procter, M.Ledecq, M.Hillisch, A.Wolff, C.Gillard, M.Horanyi, P.S.Coleman, J.A.

(2024) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-024-01335-1
  • Primary Citation of Related Structures:  
    8UO8, 8UO9, 8UOA

  • PubMed Abstract: 

    Epilepsy is a common neurological disorder characterized by abnormal activity of neuronal networks, leading to seizures. The racetam class of anti-seizure medications bind specifically to a membrane protein found in the synaptic vesicles of neurons called synaptic vesicle protein 2 (SV2) A (SV2A). SV2A belongs to an orphan subfamily of the solute carrier 22 organic ion transporter family that also includes SV2B and SV2C. The molecular basis for how anti-seizure medications act on SV2s remains unknown. Here we report cryo-electron microscopy structures of SV2A and SV2B captured in a luminal-occluded conformation complexed with anticonvulsant ligands. The conformation bound by anticonvulsants resembles an inhibited transporter with closed luminal and intracellular gates. Anticonvulsants bind to a highly conserved central site in SV2s. These structures provide blueprints for future drug design and will facilitate future investigations into the biological function of SV2s.


  • Organizational Affiliation

    Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Synaptic vesicle glycoprotein 2B683Homo sapiensMutation(s): 0 
Gene Names: SV2B
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L1I2 (Homo sapiens)
Explore Q7L1I2 
Go to UniProtKB:  Q7L1I2
PHAROS:  Q7L1I2
GTEx:  ENSG00000185518 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7L1I2
Glycosylation
Glycosylation Sites: 3Go to GlyGen: Q7L1I2-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PS1
Query on PS1

Download Ideal Coordinates CCD File 
F [auth A]1,2-DIDECANOYL-SN-GLYCERO-3-[PHOSPHO-L-SERINE]
C26 H49 N O10 P
LRIPXDCMGANCAE-PKTZIBPZSA-M
9Z9
Query on 9Z9

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
C34 H56 O5
CEEBZAXXSRFQIC-GZSGZGDASA-N
Y01
Query on Y01

Download Ideal Coordinates CCD File 
J [auth A]CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
X3U (Subject of Investigation/LOI)
Query on X3U

Download Ideal Coordinates CCD File 
E [auth A](4R)-4-(2-chloro-2,2-difluoroethyl)-1-{[(4R)-2-(methoxymethyl)-6-(trifluoromethyl)imidazo[2,1-b][1,3,4]thiadiazol-5-yl]methyl}pyrrolidin-2-one
C14 H14 Cl F5 N4 O2 S
DCXFIOLWWRXEQH-SSDOTTSWSA-N
43Y
Query on 43Y

Download Ideal Coordinates CCD File 
I [auth A][(2R)-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-2-propanoyloxy-propyl] propanoate
C14 H29 N O8 P
LMBVWVMURYPSQM-GFCCVEGCSA-O
NAG
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Brain & Behavior Research FoundationUnited States30153

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release
  • Version 1.1: 2024-06-26
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary