SAXSdb — 9pc9

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Synaptic vesicle glycoprotein 2A

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–742	Not recorded	A1CHN (4S)-1-{[(4S)-2-(methoxymethyl)-6-(trifluoromethyl)imidazo[2,1-b][1,3,4]thiadiazol-5-yl]methyl}-4-(3,3,3-trifluoropropyl)pyrrolidin-2-one × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.91 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9PC9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4V11 Structure of Synaptotagmin-1 with SV2A peptide phosphorylated at Thr84 Deposited 2014-09-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 81–90（10 aa） Fragment：UNP RESIDUES 81-90	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1 M HEPES PH 7.5, 18 % PEG 3350, 0.05 M CACL2	Resolution 1.95 Å R-free 0.196
8JLC Cryo-EM structure of SV2A in complex with BoNT/A2 Hc and levetiracetam Deposited 2023-06-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–742（741 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 UKX (2S)-2-(2-oxidanylidenepyrrolidin-1-yl)butanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes (pH7.5), 150 mM NaCl, 0.001% LMNG, 0.0002% cholesterol hemisuccinate cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.88 Å
8JLE Cryo-EM structure of SV2A LD4 in complex with BoNT/A2 Hc in the SV2A-levetiracetam-BoNT/A2 Hc complex Deposited 2023-06-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 480–587（108 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes (pH7.5), 150 mM NaCl, 0.001% LMNG, 0.0002% cholesterol hemisuccinate cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.82 Å
8JLF Cryo-EM structure of SV2A in complex with BoNT/A2 Hc Deposited 2023-06-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–742（741 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes (pH7.5), 150 mM NaCl, 0.001% LMNG, 0.0002% cholesterol hemisuccinate cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
8JLG Cryo-EM structure of SV2A in complex with BoNT/A2 Hc Deposited 2023-06-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 480–590（111 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes (pH7.5), 150 mM NaCl, 0.001% LMNG, 0.0002% cholesterol hemisuccinate cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.87 Å
8JLH Cryo-EM structure of SV2A dimer in complex with BoNT/A2 Hc and levetiracetam Deposited 2023-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–742（741 aa） Chain C 2–742（741 aa）	Not recorded	UKX (2S)-2-(2-oxidanylidenepyrrolidin-1-yl)butanamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes (pH7.5), 150 mM NaCl, 0.001% LMNG, 0.0002% cholesterol hemisuccinate cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8JLI Cryo-EM structure of SV2A dimer in complex levetiracetam Deposited 2023-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–742（741 aa） Chain B 2–742（741 aa）	Not recorded	UKX (2S)-2-(2-oxidanylidenepyrrolidin-1-yl)butanamide × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes (pH7.5), 150 mM NaCl, 0.001% LMNG, 0.0002% cholesterol hemisuccinate cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.38 Å
8JS8 Cryo-EM structure of SV2A in complex with BoNT/A2 Hc and levetiracetam Deposited 2023-06-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–742（741 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 UKX (2S)-2-(2-oxidanylidenepyrrolidin-1-yl)butanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes (pH7.5), 150 mM NaCl, 0.001% LMNG, 0.0002% cholesterol hemisuccinate cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.88 Å
8JS9 Cryo-EM structure of SV2A in complex with BoNT/A2 Hc Deposited 2023-06-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–742（741 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
8K77 Cryo-EM structure of SV2A in complex with BoNT/A2 Hc and brivaracetam Deposited 2023-07-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–742（741 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 VLX (2S)-2-[(4R)-2-oxidanylidene-4-propyl-pyrrolidin-1-yl]butanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.11 Å
8UO9 Structure of synaptic vesicle protein 2A in complex with a nanobody Deposited 2023-10-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 64–742（679 aa）	Not recorded	X49 (4S)-1-{[(4S)-2-(methoxymethyl)-6-(trifluoromethyl)imidazo[2,1-b][1,3,4]thiadiazol-5-yl]methyl}-4-(4,4,4-trifluorobutyl)pyrrolidin-2-one × 1 Y01 CHOLESTEROL HEMISUCCINATE × 1 PS1 1,2-DIDECANOYL-SN-GLYCERO-3-[PHOSPHO-L-SERINE] × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.30 Å
8UOA Structure of the synaptic vesicle protein 2A Luminal domain in complex with a nanobody Deposited 2023-10-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 64–742（679 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；150 mM NaCl, 20 mM Tris pH 8.0, 0.02 mM LMNG, 0.020 mM CHS, 0.050mM GDN, and 1 micromolar of UCB-2500 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
8YF0 Cryo-EM structure of human SV2A Deposited 2024-02-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–734（734 aa） Chain C 1–734（734 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.49 Å
8YF1 Cryo-EM structure of human SV2A in complex with Brivaracetam Deposited 2024-02-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–734（734 aa） Chain B 1–734（734 aa）	Not recorded	VLX (2S)-2-[(4R)-2-oxidanylidene-4-propyl-pyrrolidin-1-yl]butanamide × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.38 Å
9NTC Structure of Synaptic Vesicle Protein 2A Bound to Brivaracetam and UCB1244283 Deposited 2025-03-18	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 64–742（679 aa）	Not recorded	A1B1J (3R)-4-(3,5-dimethylphenyl)-N-(2-methoxyphenyl)-3-methylbutanamide × 1 VLX (2S)-2-[(4R)-2-oxidanylidene-4-propyl-pyrrolidin-1-yl]butanamide × 1 CLR CHOLESTEROL × 1 A1B1I (3S)-4-(3,5-dimethylphenyl)-N-(2-methoxyphenyl)-3-methylbutanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.05 Å
9PCB Structure of Synaptic Vesicle Protein 2A Bound to UCB-J Deposited 2025-06-27	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 64–742（679 aa）	Not recorded	A1CCA (4R)-1-[(3-methylpyridin-4-yl)methyl]-4-(3,4,5-trifluorophenyl)pyrrolidin-2-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.42 Å
9PRS Cryo-EM structure of human SV2A in complex with Levetiracetam and UCB1244283 Deposited 2025-07-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 139–742（604 aa）	Not recorded	UKX (2S)-2-(2-oxidanylidenepyrrolidin-1-yl)butanamide × 1 A1B1J (3R)-4-(3,5-dimethylphenyl)-N-(2-methoxyphenyl)-3-methylbutanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.03 Å

17 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SV2A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–742； UniProt 1–742

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9pc9
Deposition date deposition_date	2025-06-27
Structure title title	Structure of Synaptic Vesicle Protein 2A Bound to UCB7361
Keywords keywords	Synaptic vesicle, SLC22, Inhibitor, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	22.53 Å
Radius of gyration Rg (electron density) rg_electron	21.37 Å
Forward intensity I(0) i0	33089800.00
Molecular weight molecular_weight	47313.0 kDa
Excluded volume excluded_volume	60246 Å³
Envelope volume envelope_volume	67332 Å³
Hydration-shell volume shell_volume	25626 Å³
Envelope diameter envelope_diameter	80.9 Å
Shell Rg shell_rg	28.99 Å
Envelope Rg envelope_rg	22.04 Å
Shape Rg shape_rg	21.30 Å
Total Rg total_rg	22.54 Å
Total atoms total_atoms	6600
Residues n_residues	435
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	84.8 Å
Rg (real space) rg_real	22.50 Å
Rg uncertainty (real space) rg_real_error	0.87 Å
I(0) (real space) i0_real	3.3090e+07
I(0) uncertainty (real space) i0_real_error	4.8440e+05
Rg (reciprocal space) rg_reciprocal	22.51 Å
I(0) (reciprocal space) i0_reciprocal	33090000.0000
Solution quality estimate total_estimate	0.7455
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	27.0 Å
Skewness Skewness skewness	0.355
Kurtosis Kurtosis kurtosis	-0.206
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8514000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.585; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.935; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Synaptic vesicle glycoprotein 2A
Molecular weight formula_weight	82777.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6600

MEEGFRDRAAFIRGAKDIAKEVKKHAAKKVVKGLDRVQDEYSRRSYSRFEEEDDDDDFPAPSDGYYRGEGTQDEEEGGASSDATEGHDEDDEIYEGEYQGIPRAESGGKGERMADGAPLAGVRGGLSDGEGPPGGRGEAQRRKEREELAQQYEAILRECGHGRFQWTLYFVLGLALMADGVEVFVVGFVLPSAEKDMCLSDSNKGMLGLIVYLGMMVGAFLWGGLADRLGRRQCLLISLSVNSVFAFFSSFVQGYGTFLFCRLLSGVGIGGSIPIVFSYFSEFLAQEKRGEHLSWLCMFWMIGGVYAAAMAWAIIPHYGWSFQMGSAYQFHSWRVFVLVCAFPSVFAIGALTTQPESPRFFLENGKHDEAWMVLKQVHDTNMRAKGHPERVFSVTHIKTIHQEDELIEIQSDTGTWYQRWGVRALSLGGQVWGNFLSCFGPEYRRITLMMMGVWFTMSFSYYGLTVWFPDMIRHLQAVDYASRTKVFPGERVEHVTFNFTLENQIHRGGQYFNDKFIGLRLKSVSFEDSLFEECYFEDVTSSNTFFRNCTFINTVFYNTDLFEYKFVNSRLINSTFLHNKEGCPLDVTGTGEGAYMVYFVSFLGTLAVLPGNIVSALLMDKIGRLRMLAGSSVMSCVSCFFLSFGNSESAMIALLCLFGGVSIASWNALDVLTVELYPSDKRTTAFGFLNALCKLAAVLGISIFTSFVGITKAAPILFASAALALGSSLALKLPETRGQVLQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	;(4S)-1-{[(4S)-2-(methoxymethyl)-6-(trifluoromethyl)imidazo[2,1-b][1,3,4]thiadiazol-5-yl]methyl}-4-(3,3,3-trifluoropropyl)pyrrolidin-2-one ;
Molecular weight formula_weight	430.4 kDa
Source method src_method	syn
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.91 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	22999

fit	/app/data/saxs_computation/pc/9pc9/9pc9.fit
pddf	/app/data/pr_computation/pc/9pc9/9pc9.pr.out
profile	/app/data/saxs_computation/pc/9pc9/9pc9.dat

Structure of Synaptic Vesicle Protein 2A Bound to UCB7361

1. Protein Identity and Related Structures Protein Identity & Related Structures

Synaptic vesicle glycoprotein 2A

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)