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9q09

Cryo-EM structure of PGT121 Fab and Rhesus macaque Ab76 Fab in complex with HIV-1 Env trimer BG505 SOSIP.664

Method: ELECTRON MICROSCOPY D_max: 170.1 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q09
deposition_date	2025-08-12
title	Cryo-EM structure of PGT121 Fab and Rhesus macaque Ab76 Fab in complex with HIV-1 Env trimer BG505 SOSIP.664
keywords	HIV-1 Env, Broadly-neutralizing antibodies (bNAbs), glycan hole, CD4-binding site (CD4bs), 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	54.43 Å
rg_electron	53.91 Å
i0	2185130000.00
molecular_weight	383500.0 kDa
excluded_volume	476600 Å³
envelope_volume	716090 Å³
shell_volume	109170 Å³
envelope_diameter	171.7 Å
shell_rg	58.40 Å
envelope_rg	52.46 Å
shape_rg	53.94 Å
total_rg	53.94 Å
total_atoms	26904
n_residues	3182
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	170.1 Å
rg_real	55.08 Å
rg_real_error	0.61 Å
i0_real	2.1450e+09
i0_real_error	3.4520e+07
rg_reciprocal	54.65 Å
i0_reciprocal	2187000000.0000
total_estimate	0.7227
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	70.4 Å
skewness	0.145
kurtosis	-0.364
angular_range	— – 0.1450 Å⁻¹
current_alpha	1.6030
highest_alpha	101600000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 0.923; Sysdev: 0.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.842

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4. Crystallography & Experiment

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5. Entities & Polymer Info (14)

Entity 1 polymer

description	BG505 SOSIP.664 gp120
formula_weight	54064.3 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,G,I
atom_count	26930

AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR

Source

organism	Human immunodeficiency virus 1
ncbi_taxonomy_id	11676
host_organism	Homo sapiens

Entity 2 polymer

description	BG505 SOSIP.664 gp41
formula_weight	17146.5 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	B,C,J

AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Source

organism	Human immunodeficiency virus 1
ncbi_taxonomy_id	11676
host_organism	Homo sapiens

Entity 3 polymer

description	Ab76 Fab heavy chain
formula_weight	24511.4 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	D,H,K

DVQLVESGGGLVKPGGSLRLSCVASGFSFSSYEMHWVRQAPGKGLEWVSYFSDTGGITYYADSVKGRFTISRDNAENSLFLQMNNLRVEDTAVYYCARGGYTGSWIDLFDLWGQGVLVTVSSASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPVTVSWNSGSLTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYVCNVNHKPSNTKVDKRVEIKTCGGGSK

Source

organism	Macaca mulatta
ncbi_taxonomy_id	9544
host_organism	Homo sapiens

Entity 4 polymer

description	Ab76 Fab light chain
formula_weight	23473.0 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	E,L,M

KAILTQPASLSASPGASASLTCTFSGGIHVAGYHIFWYQQKPGSPPRYLLRYKSDSDKAQGSGVPSRFSGSKDASANTGILRISGLQSEDEADYYCAIGHSDGHGLFGGGTRLTVLGQPKASPLVTLFPPSSEELQANKATLVCLISDFYPGVVKVAWKADGNSVNTGVETTTPSKQSNNKYAASSYLSLTSDQWKSHKSYSCQVTHEGSTVEKTVAPTECS

Source

organism	Macaca mulatta
ncbi_taxonomy_id	9544
host_organism	Homo sapiens

Entity 5 polymer

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

Polymer

type	polypeptide(L)
strand_id	h,d,k

QMQLQESGPGLVKPSETLSLTCSVSGASISDSYWSWIRRSPGKGLEWIGYVHKSGDTNYSPSLKSRVNLSLDTSKNQVSLSLVAATAADSGKYYCARTLHGRRIYGIVAFNEWFTYFYMDVWGNGTQVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 6 polymer

description	PGT121 Fab light chain
formula_weight	22869.3 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	l,e,m

QVQIDISVAPGETARISCGEKSLGSRAVQWYQHRAGQAPSLIIYNNQDRPSGIPERFSGSPDSPFGTTATLTITSVEAGDEADYYCHIWDSRVPTKWVFGGGTTLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTEC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
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	26

Entity 8 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	6

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	4

Entity 10 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 11 branched

description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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	1073.0 kDa
src_method	man
entity_count	3

Entity 12 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	1

Entity 13 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	1

Entity 14 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	man
entity_count	17

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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	3.23 Å
resolution_method	—
num_particles	332541

fit	/app/data/saxs_computation/q0/9q09/9q09.fit
pddf	/app/data/pr_computation/q0/9q09/9q09.pr.out
profile	/app/data/saxs_computation/q0/9q09/9q09.dat

Cryo-EM structure of PGT121 Fab and Rhesus macaque Ab76 Fab in complex with HIV-1 Env trimer BG505 SOSIP.664

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 (14)

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 branched

Entity 13 branched

Entity 14 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)