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9pv5

10E8-GT10.2 immunogen in complex with Rhesus macaque Fab W3-05 and mouse Fab W6-03

Method: ELECTRON MICROSCOPY D_max: 109.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pv5
deposition_date	2025-08-01
title	10E8-GT10.2 immunogen in complex with Rhesus macaque Fab W3-05 and mouse Fab W6-03
keywords	HIV, Germline targeting, MPER, broadly neutralizing antibody, vaccine design, 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	31.94 Å
rg_electron	31.81 Å
i0	78247000.00
molecular_weight	70311.0 kDa
excluded_volume	87918 Å³
envelope_volume	112330 Å³
shell_volume	31038 Å³
envelope_diameter	119.8 Å
shell_rg	36.85 Å
envelope_rg	32.00 Å
shape_rg	31.75 Å
total_rg	32.45 Å
total_atoms	4963
n_residues	630
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	109.5 Å
rg_real	32.18 Å
rg_real_error	0.98 Å
i0_real	7.8250e+07
i0_real_error	1.2710e+06
rg_reciprocal	32.08 Å
i0_reciprocal	78240000.0000
total_estimate	0.8505
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.5 Å
skewness	0.442
kurtosis	-0.538
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	21480000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.759; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.811; Smooth: 0.966

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	10E8-GT10.2 immunogen
formula_weight	17828.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C
atom_count	4963

TGNVTQEDIIRALASPLIKDGMVDEDFAEYVIARENRSPTGLQAKGVGVAIPHTLGDYVRDNAISVGILDKPVNFSGWYQSPDPVPVRVVFMLAGRTWDDIVIVLKWIKDVILDEEFMKRLLNMSDEEIYRQIYTRISKAPNLSGINFSREYVRHLN

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Homo sapiens

Entity 2 polymer

description	W6-03 mouse Fab heavy chain
formula_weight	14537.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

DVQLQESGPGLVKPSQSLSLTCSVTGYSITSGYYWNWIRQFPGNKLEWMGYISYDGSNNYNPSLKNRISITRDTSQNQFFLKLNSVTTEDTASYYCAREGPYYDFWSGYYAYYMDVWGKGTTVTVSS

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 3 polymer

description	W6-03 mouse Fab light chain
formula_weight	12411.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

DIVMSQSPSSLAVSVGEKVTMSCKSSQSLLYSSNQKNYLAWYQQKPGQSPKLLIYWASTRKSGVPDRFTGSGSGTDFTLTISSVKAEDLAVYYCQQYFGYPLTFGAGTKLELK

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 4 polymer

description	W3-05 rhesus macaque Fab heavy chain
formula_weight	14346.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

EVQLVESGGGLVQPGGSLRLSCAASGFTFSNYWMSWVRQAPGKGLEWVGFIKNKADGGTAAYAESVKGRFTISRDDSKNTLYLQMNSLKTEDTAVYYCARDLGRYNFWSGFYSQNRFDVWGPGVLVTVSS

Source

organism	Macaca mulatta
ncbi_taxonomy_id	9544
host_organism	Homo sapiens

Entity 5 polymer

description	W3-05 rhesus macaque Fab light chain
formula_weight	11580.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

SYEVTQPPSVSVSPGQMARITCGGDNLGSKYVHWYQQKPAQAPVLVIYDDSERPSGIPERFSGSKSGNTATLTISGVEAGDEADYYCQVWDSSSDHPLFGGGTRLTVL

Source

organism	Macaca mulatta
ncbi_taxonomy_id	9544
host_organism	Homo sapiens

Entity 6 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	1

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6. Citations (2)

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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	3.900 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.90 Å
resolution_method	—
num_particles	41951

fit	/app/data/saxs_computation/pv/9pv5/9pv5.fit
pddf	/app/data/pr_computation/pv/9pv5/9pv5.pr.out
profile	/app/data/saxs_computation/pv/9pv5/9pv5.dat

10E8-GT10.2 immunogen in complex with Rhesus macaque Fab W3-05 and mouse Fab W6-03

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 (6)

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 non-polymer

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)