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9q3s

Cryo-EM structure of PGT121 Fab and Rhesus macaque Ab4 Fab in complex with HIV-1 Env trimer BG505 SOSIP.664

Method: ELECTRON MICROSCOPY D_max: 186.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q3s
deposition_date	2025-08-19
title	Cryo-EM structure of PGT121 Fab and Rhesus macaque Ab4 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-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	58.06 Å
rg_electron	57.79 Å
i0	2068270000.00
molecular_weight	375080.0 kDa
excluded_volume	466760 Å³
envelope_volume	707120 Å³
shell_volume	103210 Å³
envelope_diameter	188.0 Å
shell_rg	58.48 Å
envelope_rg	56.67 Å
shape_rg	57.84 Å
total_rg	57.66 Å
total_atoms	26322
n_residues	3018
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	186.6 Å
rg_real	57.82 Å
rg_real_error	1.71 Å
i0_real	2.0680e+09
i0_real_error	4.1490e+07
rg_reciprocal	58.25 Å
i0_reciprocal	2070000000.0000
total_estimate	0.8584
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	76.0 Å
skewness	0.111
kurtosis	-0.425
angular_range	— – 0.1350 Å⁻¹
current_alpha	0.0000
highest_alpha	69430000.0000
n_real_points	28
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.539

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4. Crystallography & Experiment

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5. Entities & Polymer Info (12)

Entity 1 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
atom_count	26619

AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Source

organism	Human immunodeficiency virus 1
ncbi_taxonomy_id	11676
host_organism	Homo sapiens

Entity 2 polymer

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

Polymer

type	polypeptide(L)
strand_id	G,A,I

AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR

Source

organism	Human immunodeficiency virus 1
ncbi_taxonomy_id	11676
host_organism	Homo sapiens

Entity 3 polymer

description	Ab 4 Fab heavy chain
formula_weight	24438.2 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	H,D,K

QLQLQESGPGLVKPSETLSVTCDVSGGSISDNFWIWIRQAPGQGLEWIGYMYGTNGGTNVNPSFKGRVTLSADTSKNQLSLKVDSVTVADTAVYYCVRYWNRWGTGYFDYWGQGVLVTVSSASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPVTVSWNSGSLTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYVCNVNHKPSNTKVDKRVEIKTCGGGSK

Source

organism	Macaca mulatta
common_name	Rhesus macaque
ncbi_taxonomy_id	9544
host_organism	Homo sapiens

Entity 4 polymer

description	Ab 4 Fab light chain
formula_weight	22666.2 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	L,E,M

QAVVTQEPSMTVSPGGTVTLTCASSTGAVAIGHTPHWFQQKPGQVPRALIYHSDQKHSGTPARFSGSLLGDKAALTLSGALPEDEAEYYCWLAFSSGGVFGSGTKLTVLGQPKASPLVTLFPPSSEELQANKATLVCLISDFYPGVVKVAWKADGNSVNTGVETTTPSKQSNNKYAASSYLSLTSDQWKSHKSYSCQVTHEGSTVEKTVAPTECS

Source

organism	Macaca mulatta
common_name	Rhesus macaque
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	;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 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 9 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	30

Entity 10 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 11 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 12 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	man
entity_count	21

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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	3.010 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

fit	/app/data/saxs_computation/q3/9q3s/9q3s.fit
pddf	/app/data/pr_computation/q3/9q3s/9q3s.pr.out
profile	/app/data/saxs_computation/q3/9q3s/9q3s.dat

Cryo-EM structure of PGT121 Fab and Rhesus macaque Ab4 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

Refinement

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)