SAXSdb — 9tbh

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1. Structure Basics

entry_id	9tbh
deposition_date	2025-11-20
title	Hepatitis A Virus in Complex with LDLR Receptor
keywords	Hepatitis A Virus GD1a, VIRUS; VIRUS
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	31.71 Å
rg_electron	30.81 Å
i0	101337000.00
molecular_weight	80788.0 kDa
excluded_volume	101450 Å³
envelope_volume	134030 Å³
shell_volume	36751 Å³
envelope_diameter	127.9 Å
shell_rg	36.79 Å
envelope_rg	33.29 Å
shape_rg	30.74 Å
total_rg	31.58 Å
total_atoms	5700
n_residues	723
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	121.2 Å
rg_real	31.94 Å
rg_real_error	1.17 Å
i0_real	1.0130e+08
i0_real_error	1.7850e+06
rg_reciprocal	31.84 Å
i0_reciprocal	101300000.0000
total_estimate	0.8042
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.9 Å
skewness	0.573
kurtosis	0.048
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	21010000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.565; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.806; Smooth: 0.949

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Capsid protein VP1
formula_weight	30244.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5773

VGDDSGGFSTTVSTEQNVPDPQVGITTMKDLKGKANRGKMDVSGVQAPVGAITTIEDPVLAKKVPETFPELKPGESRHTSDHMSIYKFMGRSHFLCTFTFNSNNKEYTFPITLSSTSNPPHGLPSTLRWFFNLFQLYRGPLDLTIIITGATDVDGMAWFTPVGLAVDTPWVEKESALSIDYKTALGAVRFNTRRTGNIQIRLPWYSYLYAVSGALDGLGDKTDSTFGLVSIQIANYNHSDEYLSFSCYLSVTEQSEFYFPRAPLNSNAMLSTES

Source

organism	Human hepatitis A virus
ncbi_taxonomy_id	208726
host_organism	Chlorocebus aethiops aethiops

Entity 2 polymer

description	Capsid protein VP2
formula_weight	24870.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

DIEEEQMIQSVDRTAVTGASYFTSVDQSSVHTAEVGSHQVEPLRTSVDKPGSKKTQGEKFFLIHSADWLTTHALFHEVAKLDVVKLLYNEQFAVQGLLRYHTYARFGIEIQVQINPTPFQQGGLICAMVPGDQSYGSIASLTVYPHGLLNCNINNVVRIKVPFIYTRGAYHFKDPQYPVWELTIRVWSELNIGTGTSAYTSLNVLARFTDLELHGLTPLSTQ

Source

organism	Human hepatitis A virus
ncbi_taxonomy_id	208726
host_organism	Chlorocebus aethiops aethiops

Entity 3 polymer

description	Capsid protein VP3
formula_weight	27835.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MMRNETRVSTTENVVNLSNYEDARAKMSFALDQEDWKSDPSQGGGIKITHFTTWTSIPTLAAQFPFNASDSVGQQIKVIPVDPYFFQMTNTNPDQKCITALASICQMFCFWRGDLVFDFQVFPTKYHSGRLLFCFVPGNELIDVTGITLKQATTAPCAVMDIAGVQSTLRFRVPWISDTPYRVNRYTKEAHQKGEYTAIGKLIVYCYNRLTSPSNVAHHVRVNVYLSAINLECFAPLYHAMDVTTQ

Source

organism	Human hepatitis A virus
ncbi_taxonomy_id	208726
host_organism	Chlorocebus aethiops aethiops

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	73

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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	1.70 Å
resolution_method	—
num_particles	27762

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

Hepatitis A Virus in Complex with LDLR Receptor

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)