SAXSdb — 9tbi

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1. Structure Basics

entry_id	9tbi
deposition_date	2025-11-20
title	Hepatitis A Virus in complex with GD1a
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	31.65 Å
rg_electron	30.76 Å
i0	101384000.00
molecular_weight	80788.0 kDa
excluded_volume	101450 Å³
envelope_volume	133370 Å³
shell_volume	36649 Å³
envelope_diameter	127.2 Å
shell_rg	36.67 Å
envelope_rg	33.23 Å
shape_rg	30.69 Å
total_rg	31.53 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	119.1 Å
rg_real	31.88 Å
rg_real_error	1.31 Å
i0_real	1.0140e+08
i0_real_error	1.6420e+06
rg_reciprocal	31.78 Å
i0_reciprocal	101400000.0000
total_estimate	0.7388
solution_quality	REASONABLE a REASONABLE solution
n_peaks	3
r_peak_primary	33.3 Å
skewness	0.572
kurtosis	0.045
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	20450000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.587; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.841; Smooth: 0.000

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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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resolution	1.700 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	1.70 Å
resolution_method	—
num_particles	93507

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

Hepatitis A Virus in complex with GD1a

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Refinement

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)