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9pnn

Cryo-EM structure of J601-A6 Fab in complex with HIV-1 BG505 DS-SOSIP Env trimer

Method: ELECTRON MICROSCOPY D_max: 147.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pnn
deposition_date	2025-07-21
title	Cryo-EM structure of J601-A6 Fab in complex with HIV-1 BG505 DS-SOSIP Env trimer
keywords	;antibody-antigen complex, fusion peptide directed, viral surface glycoprotein, ANTIVIRAL 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	47.94 Å
rg_electron	47.19 Å
i0	1384630000.00
molecular_weight	302990.0 kDa
excluded_volume	376540 Å³
envelope_volume	547730 Å³
shell_volume	93463 Å³
envelope_diameter	153.2 Å
shell_rg	54.19 Å
envelope_rg	46.29 Å
shape_rg	47.16 Å
total_rg	47.55 Å
total_atoms	21225
n_residues	2412
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	147.2 Å
rg_real	47.56 Å
rg_real_error	1.02 Å
i0_real	1.3850e+09
i0_real_error	2.4300e+07
rg_reciprocal	47.94 Å
i0_reciprocal	1385000000.0000
total_estimate	0.8828
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	66.9 Å
skewness	0.046
kurtosis	-0.495
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0000
highest_alpha	128600000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.782

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4. Crystallography & Experiment

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5. Entities & Polymer Info (11)

Entity 1 polymer

description	Envelope glycoprotein BG505 DS-SOSIP gp41
formula_weight	17162.5 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	B,A,F
atom_count	21225

AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAIEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Source

organism	Human immunodeficiency virus 1
ncbi_taxonomy_id	11676
host_organism	Cricetulus griseus

Entity 2 polymer

description	Envelope glycoprotein BG505 DS-SOSIP gp120
formula_weight	52987.0 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	G,C,I

AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRV

Source

organism	Human immunodeficiency virus 1
ncbi_taxonomy_id	11676
host_organism	Cricetulus griseus

Entity 3 polymer

description	antibody J601-A6 heavy chain
formula_weight	25058.9 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	H,D,J

QVQLEESGPGIVKPSETLSLTCAASRGPFSGGHFYWNWFRQPPGKGLEWIGGIYSDGDAADYNPSLESRVAISRDRSANRFSLKLISVTATDTAVYYCSSTYSWNNVWFDQWGQGVLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

Source

organism	Macaca mulatta
ncbi_taxonomy_id	9544
host_organism	Homo sapiens

Entity 4 polymer

description	antibody J601-A6 light chain
formula_weight	23630.1 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	L,E,K

EDIQLTQSPSSLSASVGDRVTITCRASQDINTDLSWYYQKSGEAPKLLIYRASNLQSGAPSRFSGTGSGTEFTLTISSLQPEDFITYYCQQRYSFPITFGAGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Macaca mulatta
ncbi_taxonomy_id	9544
host_organism	Homo sapiens

Entity 5 branched

description	;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	748.7 kDa
src_method	man
entity_count	3

Entity 6 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	9

Entity 7 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	3

Entity 8 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 9 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 10 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 11 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	15

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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	3.50 Å
resolution_method	—
num_particles	46939

fit	/app/data/saxs_computation/pn/9pnn/9pnn.fit
pddf	/app/data/pr_computation/pn/9pnn/9pnn.pr.out
profile	/app/data/saxs_computation/pn/9pnn/9pnn.dat

Cryo-EM structure of J601-A6 Fab in complex with HIV-1 BG505 DS-SOSIP 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 (11)

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 branched

Entity 8 branched

Entity 9 branched

Entity 10 branched

Entity 11 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)