Cryo-EM structure of the aspartate:alanine antiporter AspT WT

Method: ELECTRON MICROSCOPY D_max: 103.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vdc
deposition_date	2025-06-08
title	Cryo-EM structure of the aspartate:alanine antiporter AspT WT
keywords	amino acid, antiporter, elevator mechanism, TRANSPORT PROTEIN; TRANSPORT 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	33.79 Å
rg_electron	33.10 Å
i0	172940000.00
molecular_weight	114920.0 kDa
excluded_volume	148340 Å³
envelope_volume	198320 Å³
shell_volume	49593 Å³
envelope_diameter	106.0 Å
shell_rg	40.40 Å
envelope_rg	32.30 Å
shape_rg	33.06 Å
total_rg	33.92 Å
total_atoms	16540
n_residues	1086
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	103.6 Å
rg_real	33.64 Å
rg_real_error	0.79 Å
i0_real	1.7290e+08
i0_real_error	2.9040e+06
rg_reciprocal	33.74 Å
i0_reciprocal	173000000.0000
total_estimate	0.9044
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	44.1 Å
skewness	0.127
kurtosis	-0.528
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	34000000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.902

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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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	3.40 Å
resolution_method	—
num_particles	125465

description	Aspartate/alanine antiporter
formula_weight	58084.0 kDa
src_method	man
entity_count	2

type	polypeptide(L)
strand_id	A,B
atom_count	16540

Cryo-EM structure of the aspartate:alanine antiporter AspT WT

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

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Tetragenococcus halophilus
ncbi_taxonomy_id	51669
host_organism	Escherichia coli BL21(DE3)

description	ASPARTIC ACID
formula_weight	133.1 kDa
src_method	syn
entity_count	2

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