SAXSdb — 9q0w

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1. Structure Basics

entry_id	9q0w
deposition_date	2025-08-13
last_revision	2025-12-10
title	Cryo-EM Structure of HIV-1 BG505DS-SOSIP.664 Env Trimer Bound to DFPH-a.01_10R59P_LC Fab
keywords	antibody improvement, broadly neutralizing antibody, epitope, fusion peptide, HIV-1 vaccine, paratope, 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	56.30 Å
rg_electron	56.13 Å
i0	1841790000.00
molecular_weight	352650.0 kDa
excluded_volume	438960 Å³
envelope_volume	667310 Å³
shell_volume	100840 Å³
envelope_diameter	202.4 Å
shell_rg	56.98 Å
envelope_rg	55.74 Å
shape_rg	56.12 Å
total_rg	56.18 Å
total_atoms	24735
n_residues	3042
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	190.8 Å
rg_real	56.28 Å
rg_real_error	1.64 Å
i0_real	1.8420e+09
i0_real_error	3.7900e+07
rg_reciprocal	56.30 Å
i0_reciprocal	1842000000.0000
total_estimate	0.6551
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	68.2 Å
skewness	0.322
kurtosis	-0.280
angular_range	— – 0.1400 Å⁻¹
current_alpha	0.0001
highest_alpha	88570000.0000
n_real_points	29
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.852; Stabil: 1.000; Sysdev: 0.041; Positv: 1.000; Valcen: 0.997; Smooth: 0.836

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	HIV-1 BG505 DS-SOSIP gp120
formula_weight	54086.3 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,C,E
atom_count	24735

AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR

Source

organism	Human immunodeficiency virus 1
ncbi_taxonomy_id	11676
host_organism	Homo sapiens

Entity 2 polymer

description	BG505 DS-SOSIP GP41
formula_weight	17146.5 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	B,D,F

AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Source

organism	Human immunodeficiency virus 1
ncbi_taxonomy_id	11676
host_organism	Homo sapiens

Entity 3 polymer

description	DFPH-a.01_10R59P_LC Fab heavy chain
formula_weight	24875.8 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	G,I,K

QVQLQVSGPGVVKASETLSLTCDVSSASNTRDYFYWSWVRQSPGKGLEWIGGVYSNSDTSNKNPSLESRVTISKDTSKNRFFLRLNSVTAADTAVYYCSSRAKIYFAVGYDSGGRIDVWGPGVLVTVATASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPVTVSWNSGSLTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYVCNVNHKPSNTKVDKRVEIKTCG

Source

organism	Macaca
ncbi_taxonomy_id	9539
host_organism	Homo sapiens

Entity 4 polymer

description	DFPH-a.01_10R59P_LC Fab light chain
formula_weight	23266.8 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	H,J,L

DIQMTQSPSRLSASVGDRVTVTCRASQDIDKDLSWFQQKPGKAPTLLIFTASSLQTGVPSRFSGSGSGTEFTLTISSLQPEDFATYFCQQDYSFPLTFGGGTKVDLKRTVAAPSVFIFPPSEDQVKSGTVSVVCLLNNFYPREASVKWKVDGALKTGNSQESVTEQDSKDNTYSLSSTLTLSSTEYQSHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Macaca
ncbi_taxonomy_id	9539
host_organism	Homo sapiens

Entity 5 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	27

Entity 6 branched

description	;alpha-D-mannopyranose-(1-2)-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	910.8 kDa
src_method	man
entity_count	3

Entity 7 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	18

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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	3.00 Å
resolution_method	—
num_particles	347691

fit	/app/data/saxs_computation/q0/9q0w/9q0w.fit
pddf	/app/data/pr_computation/q0/9q0w/9q0w.pr.out
profile	/app/data/saxs_computation/q0/9q0w/9q0w.dat

Cryo-EM Structure of HIV-1 BG505DS-SOSIP.664 Env Trimer Bound to DFPH-a.01_10R59P_LC Fab

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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 branched

Entity 6 branched

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)