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9q3x

The CryoEM structure of Rhesus macaque 1G3 and PGT121 Fabs in complex with BG505 SOSIP.664

Method: ELECTRON MICROSCOPY D_max: 192.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q3x
deposition_date	2025-08-19
title	The CryoEM structure of Rhesus macaque 1G3 and PGT121 Fabs in complex with BG505 SOSIP.664
keywords	;HIV-1, envelope trimer, GP120, GP41, viral entry, type-1 membrane fusion glycoprotein, Rhesus macaque IgG, PGT121, VIRAL PROTEIN-IMMUNE SYSTEM complex, VIRAL PROTEIN ;; 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	57.98 Å
rg_electron	57.66 Å
i0	2004550000.00
molecular_weight	368930.0 kDa
excluded_volume	459120 Å³
envelope_volume	725560 Å³
shell_volume	105930 Å³
envelope_diameter	187.1 Å
shell_rg	58.88 Å
envelope_rg	56.40 Å
shape_rg	57.69 Å
total_rg	57.57 Å
total_atoms	25890
n_residues	2994
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	192.6 Å
rg_real	57.71 Å
rg_real_error	1.78 Å
i0_real	2.0050e+09
i0_real_error	4.0360e+07
rg_reciprocal	58.19 Å
i0_reciprocal	2006000000.0000
total_estimate	0.8652
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	78.5 Å
skewness	0.103
kurtosis	-0.403
angular_range	— – 0.1350 Å⁻¹
current_alpha	0.0000
highest_alpha	80950000.0000
n_real_points	28
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.808; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.829

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4. Crystallography & Experiment

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5. Entities & Polymer Info (12)

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	G,A,I
atom_count	25890

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	1G3 Fab heavy chain
formula_weight	12346.7 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	H,D,K

QVQLQESGPGLVKPSETLSLTCAVSGGSISDDHYWSWIRQPPGKGLEWIGYIYGAYGGTNYNPSLSNRLTISKDTSKNQFSLKLTSVTAADTAVYYCARSPTGNWGQGVLVTVSS

Source

organism	Macaca mulatta
common_name	Rhesus macaque
ncbi_taxonomy_id	9544
host_organism	Homo sapiens

Entity 4 polymer

description	1G3 Fab light chain
formula_weight	11728.1 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	L,E,M

DIVMTQTPSSLSASVGDRVTITCRASQDISSYLSWYQQKPGKAPKLLIYYSNRLESGVPSRFSGSGSGTEFTLTISSLQPEDFATYYCLQYHSLFTFGPGTRLDIK

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	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	24

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	3

Entity 9 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 10 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 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	24

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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	3.640 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.64 Å
resolution_method	—
num_particles	425978

fit	/app/data/saxs_computation/q3/9q3x/9q3x.fit
pddf	/app/data/pr_computation/q3/9q3x/9q3x.pr.out
profile	/app/data/saxs_computation/q3/9q3x/9q3x.dat

The CryoEM structure of Rhesus macaque 1G3 and PGT121 Fabs in complex with 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

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)