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9yqo

AMC008 v4.2 SOSIP Env trimer in complex with PGT121 and VRC01 Fabs

Method: ELECTRON MICROSCOPY D_max: 161.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yqo
deposition_date	2025-10-15
title	AMC008 v4.2 SOSIP Env trimer in complex with PGT121 and VRC01 Fabs
keywords	HIV-1 Envelope glycoprotein, broadly neutralizing antibodies, IMMUNE SYSTEM; 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	52.00 Å
rg_electron	51.42 Å
i0	2123220000.00
molecular_weight	377010.0 kDa
excluded_volume	468470 Å³
envelope_volume	691120 Å³
shell_volume	109220 Å³
envelope_diameter	163.0 Å
shell_rg	56.90 Å
envelope_rg	50.66 Å
shape_rg	51.44 Å
total_rg	51.53 Å
total_atoms	26433
n_residues	3102
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	161.3 Å
rg_real	51.78 Å
rg_real_error	1.06 Å
i0_real	2.1230e+09
i0_real_error	4.1500e+07
rg_reciprocal	52.17 Å
i0_reciprocal	2124000000.0000
total_estimate	0.8715
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	64.5 Å
skewness	0.128
kurtosis	-0.469
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0000
highest_alpha	128700000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.585

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4. Crystallography & Experiment

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5. Entities & Polymer Info (12)

Entity 1 polymer

description	VRC01 Fab heavy chain
formula_weight	24395.7 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	M,C,I
atom_count	26433

QVQLVQSGGQMKKPGESMRISCRASGYEFIDCTLNWIRLAPGKRPEWMGWLKPRGGAVNYARPLQGRVTMTRDVYSDTAFLELRSLTVDDTAVYFCTRGKNCDYNWDFEHWGRGTPVIVSSPSTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	VRC01 Fab light chain
formula_weight	23172.7 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	N,D,J

EIVLTQSPGTLSLSPGETAIISCRTSQYGSLAWYQQRPGQAPRLVIYSGSTRAAGIPDRFSGSRWGPDYNLTISNLESGDFGVYYCQQYEFFGQGTKVQVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	PGT121 Fab light chain
formula_weight	22574.9 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	Q,E,K

SDISVAPGETARISCGEKSLGSRAVQWYQHRAGQAPSLIIYNNQDRPSGIPERFSGSPDSPFGTTATLTITSVEAGDEADYYCHIWDSRVPTKWVFGGGTTLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 polymer

description	PGT121 Fab heavy chain
formula_weight	25169.2 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	R,F,L

QMQLQESGPGLVKPSETLSLTCSVSGASISDSYWSWIRRSPGKGLEWIGYVHKSGDTNYSPSLKSRVNLSLDTSKNQVSLSLVAATAADSGKYYCARTLHGRRIYGIVAFNEWFTYFYMDVWGNGTQVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 5 polymer

description	HIV-1 envelope glycoprotein gp120
formula_weight	55212.5 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,G,O

MDWTWILFLVAAATRVHSTEKLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVRNVWATHACVPTDPSPQEVILENVTENFNMWTNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTNELKNTTKTNNSSWGGEMKNCSFNVTTSIRDKVQKEYALFYKLDIVPIDDDNNTSNYRLINCNTSVITQACPKITFEPIPIQFCTPAGFAILKCNNKKFNGKGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVIIRSDNFTDNAKTIIVQLNESVVINCTRPNNNTRKSINIGPGRWFYTTGEIIGDIRQAHCNLSRTQWNNTLKQIAIKLREQFENKTIVFNQSSGGDPEIVMHSFNCGGEFFYCNTTKLFNSTWNDTDIRGNNTEGNDTITIPCRIKQIVNMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGSESNTTEIFRPGGGDMRDNWRSELYKYKVVRIEPLGVAPTKCKRRVVQ

Source

organism	Human immunodeficiency virus 1
ncbi_taxonomy_id	11676
host_organism	Homo sapiens

Entity 6 polymer

description	Envelope glycoprotein gp41
formula_weight	17428.8 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	B,H,P

AVGTIGAMFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQNNLLRAPEAQQHLLQLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTSVPWNTSWSNKSLDKIWNNMTWMEWEREIDNYTSLIYTLLEESQNQQEKNEQELLELD

Source

organism	Human immunodeficiency virus 1
ncbi_taxonomy_id	11676
host_organism	Homo sapiens

Entity 7 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	33

Entity 8 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 9 branched

description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	1559.4 kDa
src_method	man
entity_count	3

Entity 10 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 11 branched

description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 12 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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resolution	3.26 Å
resolution_method	—
num_particles	56692

fit	/app/data/saxs_computation/yq/9yqo/9yqo.fit
pddf	/app/data/pr_computation/yq/9yqo/9yqo.pr.out
profile	/app/data/saxs_computation/yq/9yqo/9yqo.dat

AMC008 v4.2 SOSIP Env trimer in complex with PGT121 and VRC01 Fabs

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (12)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

Entity 7 branched

Entity 8 branched

Entity 9 branched

Entity 10 branched

Entity 11 branched

Entity 12 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)