SAXSdb — 9pq2

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1. Structure Basics

entry_id	9pq2
deposition_date	2025-07-22
title	Cryo-EM structure of HIV-1 459C-WT DS-SOSIP RnS Env trimer
keywords	Envelope trimer, 459C-WT, RnS DS-SOSIP immunogen, VIRAL PROTEIN; VIRAL 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	42.56 Å
rg_electron	41.53 Å
i0	825382000.00
molecular_weight	231340.0 kDa
excluded_volume	287380 Å³
envelope_volume	414170 Å³
shell_volume	78630 Å³
envelope_diameter	126.8 Å
shell_rg	50.20 Å
envelope_rg	41.16 Å
shape_rg	41.51 Å
total_rg	42.02 Å
total_atoms	16167
n_residues	1749
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	128.7 Å
rg_real	42.27 Å
rg_real_error	0.97 Å
i0_real	8.2540e+08
i0_real_error	1.5520e+07
rg_reciprocal	42.56 Å
i0_reciprocal	825700000.0000
total_estimate	0.9020
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	59.1 Å
skewness	-0.022
kurtosis	-0.647
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	151100000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.949

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	459C-WT RnS DS-SOSIP gp120
formula_weight	54848.9 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	C,G,I
atom_count	16167

GNLWVTVYYGVPVWREAKTTLFCASDAKAYDREVHNVWATHACVPTDPNPQEIVLENVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLNCTNVTSSAANVTSNVTNDANNASNANGRNVINEDMKNCSFNATTEIRDRKKEMYALFYKLDIVPLDGEKSDNRYRLINCNTSTITQACPKVSFDPIPIHYCTPAGFAILKCNNKTFNGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEDIIIRSENLTNNAKTIIVHLNESVEIVCTRPNNMTRKSIRIGPGQTFYALNDIIGDIRQAHCNISEEKWNNTLHRVWKKLVEHFPNKTTIRFDRHSGGDLEITTHSFNCGGEFFYCNTSGLFNITYNSNYTYNDTKHNGTKVITLPCRIKQIINMWQEVGRAMYAPPIAGNITCTSNITGLLLTRDGGNNSTETETFRPGGGDMRDNWRSELYKYKVVEIKPLGIAPTGCKRRVVER

Source

organism	Human immunodeficiency virus 1
ncbi_taxonomy_id	11676
host_organism	Homo sapiens

Entity 2 polymer

description	459C-WT RnS DS-SOSIP gp41
formula_weight	17164.4 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,F

AVGIGAVFLGFLGAAGSTMGAASNTLTVQARQLLSGIVQQQSNLPKAPEAQQHLLQLTVWGIKQLQTRVLAIERYLEVQQLLGLWGCSGKLICCTAVPWNSSWSNKSETEIWNNMTWMQWDREINNYTNTIYRLLEESQFQQEINEVDLLALD

Source

organism	Human immunodeficiency virus 1
ncbi_taxonomy_id	11676
host_organism	Homo sapiens

Entity 3 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	15

Entity 4 branched

description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	910.8 kDa
src_method	man
entity_count	6

Entity 5 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	24

Entity 6 branched

description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1073.0 kDa
src_method	man
entity_count	3

Entity 7 branched

description	;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	748.7 kDa
src_method	man
entity_count	3

Entity 8 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	9

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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	triclinic

resolution	3.33 Å
resolution_method	—
num_particles	207797

fit	/app/data/saxs_computation/pq/9pq2/9pq2.fit
pddf	/app/data/pr_computation/pq/9pq2/9pq2.pr.out
profile	/app/data/saxs_computation/pq/9pq2/9pq2.dat

Cryo-EM structure of HIV-1 459C-WT DS-SOSIP RnS Env trimer

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 (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 branched

Entity 4 branched

Entity 5 branched

Entity 6 branched

Entity 7 branched

Entity 8 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)