SAXSdb — 9yik

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1. Structure Basics

entry_id	9yik
deposition_date	2025-10-01
title	HIV-1 Env del4-3fill SOSIP
keywords	HIV-1, Envelope protein, Vaccine, Immunogen, Antibody, bNAb, Viral Protein, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
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	40.91 Å
rg_electron	39.95 Å
i0	613379000.00
molecular_weight	198950.0 kDa
excluded_volume	247250 Å³
envelope_volume	338980 Å³
shell_volume	67808 Å³
envelope_diameter	120.6 Å
shell_rg	48.31 Å
envelope_rg	39.15 Å
shape_rg	39.95 Å
total_rg	40.40 Å
total_atoms	13926
n_residues	1659
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	117.6 Å
rg_real	40.64 Å
rg_real_error	0.63 Å
i0_real	6.1340e+08
i0_real_error	7.9510e+06
rg_reciprocal	40.91 Å
i0_reciprocal	613600000.0000
total_estimate	0.8943
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	57.3 Å
skewness	-0.069
kurtosis	-0.690
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	89060000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.971; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.732

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Transmembrane protein gp41
formula_weight	17134.3 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	C,B,A
atom_count	13926

AVGIGAVSLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEPQQHLLKDTHWGIKQLQARVLAVEHYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Source

organism	Human immunodeficiency virus 1
ncbi_taxonomy_id	11676
host_organism	Homo sapiens

Entity 2 polymer

description	Envelope glycoprotein gp160
formula_weight	53501.6 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	G,F,E

NLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLQCTNYTNDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSFEPIPIHYCAPAGFAILKCKNKTFNGTGPCPNVSTVQCTHGIKPVVSTQLLLNGSLAEEEVIIRSENITNNAKNILVQLNTPVQINCTRPNNNTVKSIRIGPGQAFYYTGDIIGDIRQAHCNVSKATWNETLGNVSKQLRKHFGNNTIIRFAQSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR

Source

organism	Human immunodeficiency virus 1
ncbi_taxonomy_id	11676
host_organism	Homo sapiens

Entity 3 branched

description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	586.5 kDa
src_method	man
entity_count	3

Entity 4 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	3

Entity 5 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	42

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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	3.900 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.90 Å
resolution_method	—
num_particles	172278

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

HIV-1 Env del4-3fill SOSIP

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

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 branched

Entity 4 branched

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)