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9prs

Cryo-EM structure of human SV2A in complex with Levetiracetam and UCB1244283

Method: ELECTRON MICROSCOPY D_max: 81.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9prs
deposition_date	2025-07-24
last_revision	2025-12-10
title	Cryo-EM structure of human SV2A in complex with Levetiracetam and UCB1244283
keywords	SLC transporter, SLC22 family, MEMBRANE PROTEIN, inhibitor; MEMBRANE PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	23.90 Å
rg_electron	23.05 Å
i0	83403600.00
molecular_weight	49659.0 kDa
excluded_volume	48977 Å³
envelope_volume	78438 Å³
shell_volume	27992 Å³
envelope_diameter	84.9 Å
shell_rg	30.72 Å
envelope_rg	23.53 Å
shape_rg	23.05 Å
total_rg	23.72 Å
total_atoms	3768
n_residues	479
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	81.2 Å
rg_real	23.85 Å
rg_real_error	0.59 Å
i0_real	8.3400e+07
i0_real_error	1.2490e+06
rg_reciprocal	23.86 Å
i0_reciprocal	83400000.0000
total_estimate	0.8750
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.9 Å
skewness	0.333
kurtosis	-0.304
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	11010000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.801; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.981

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Synaptic vesicle glycoprotein 2A
formula_weight	67822.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3768

AQRRKEREELAQQYEAILRECGHGRFQWTLYFVLGLALMADGVEVFVVGFVLPSAEKDMCLSDSNKGMLGLIVYLGMMVGAFLWGGLADRLGRRQCLLISLSVNSVFAFFSSFVQGYGTFLFCRLLSGVGIGGSIPIVFSYFSEFLAQEKRGEHLSWLCMFWMIGGVYAAAMAWAIIPHYGWSFQMGSAYQFHSWRVFVLVCAFPSVFAIGALTTQPESPRFFLENGKHDEAWMVLKQVHDTNMRAKGHPERVFSVTHIKTIHQEDELIEIQSDTGTWYQRWGVRALSLGGQVWGNFLSCFGPEYRRITLMMMGVWFTMSFSYYGLTVWFPDMIRHLQAVDYASRTKVFPGERVEHVTFNFTLENQIHRGGQYFNDKFIGLRLKSVSFEDSLFEECYFEDVTSSNTFFRNCTFINTVFYNTDLFEYKFVNSRLINSTFLHNKEGCPLDVTGTGEGAYMVYFVSFLGTLAVLPGNIVSALLMDKIGRLRMLAGSSVMSCVSCFFLSFGNSESAMIALLCLFGGVSIASWNALDVLTVELYPSDKRTTAFGFLNALCKLAAVLGISIFTSFVGITKAAPILFASAALALGSSLALKLPETRGQVLQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 non-polymer

description	(2S)-2-(2-oxidanylidenepyrrolidin-1-yl)butanamide
formula_weight	170.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	(3R)-4-(3,5-dimethylphenyl)-N-(2-methoxyphenyl)-3-methylbutanamide
formula_weight	311.4 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.030 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.03 Å
resolution_method	—
num_particles	157236

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

Cryo-EM structure of human SV2A in complex with Levetiracetam and UCB1244283

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D