8YF1 | pdb_00008yf1

Cryo-EM structure of human SV2A in complex with Brivaracetam

• PDB DOI: https://doi.org/10.2210/pdb8YF1/pdb
• EM Map EMD-39207: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2024-02-23 Released: 2024-06-12 
• Deposition Author(s): Qu, Q., Liu, S., Zhou, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.38 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Recognition of antiepileptic brivaracetam by synaptic vesicle protein 2A.

Liu, S., Chao, Y., Zhou, Z., Yang, C., Zhu, Z., Wang, Y., Qu, Q.

(2024) Cell Discov 10: 56-56

• PubMed: 38773074 
• DOI: https://doi.org/10.1038/s41421-024-00686-9
• Primary Citation of Related Structures:  
  8YF0, 8YF1

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Organizational Affiliation: 
• Shanghai Stomatological Hospital, School of Stomatology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Systems Biology for Medicine, Fudan University, Shanghai, China.
Shanghai Stomatological Hospital, School of Stomatology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China. [e-mail].
Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Systems Biology for Medicine, Fudan University, Shanghai, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 169.21 kDa 
• Atom Count: 9,187 
• Modeled Residue Count: 1,156 
• Deposited Residue Count: 1,510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptic vesicle glycoprotein 2A	A [auth B], B [auth A]	755	Homo sapiens	Mutation(s): 0  Gene Names: SV2A, KIAA0736, PSEC0174 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L0J3 (Homo sapiens) Explore Q7L0J3  Go to UniProtKB:  Q7L0J3
PHAROS:  Q7L0J3 GTEx:  ENSG00000159164

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VLX (Subject of Investigation/LOI)	C [auth B], D [auth A]	(2S)-2-[(4R)-2-oxidanylidene-4-propyl-pyrrolidin-1-yl]butanamide C11 H20 N2 O2 MSYKRHVOOPPJKU-BDAKNGLRSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
VLX	BindingDB:  8YF1	IC50: 100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.38 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-12 
Deposition Author(s): Qu, Q., Liu, S., Zhou, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32171194

Revision History  

• Version 1.0: 2024-06-12
  Type: Initial release
  
• Version 1.1: 2025-07-02
  Changes: Data collection, Database references, Structure summary