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9zry

Cryo-EM structure of SHIV-elicited CN81-2029 Fab in complex with HIV Env trimer Q23-SCT27

Method: ELECTRON MICROSCOPY D_max: 144.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zry
deposition_date	2025-12-21
title	Cryo-EM structure of SHIV-elicited CN81-2029 Fab in complex with HIV Env trimer Q23-SCT27
keywords	Immune complex, HIV V2 apex, neutralizing antibody, SHIV, 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	44.66 Å
rg_electron	43.99 Å
i0	923127000.00
molecular_weight	246420.0 kDa
excluded_volume	306620 Å³
envelope_volume	437930 Å³
shell_volume	80347 Å³
envelope_diameter	158.1 Å
shell_rg	51.12 Å
envelope_rg	43.46 Å
shape_rg	43.99 Å
total_rg	44.28 Å
total_atoms	17248
n_residues	1954
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	144.1 Å
rg_real	44.44 Å
rg_real_error	1.06 Å
i0_real	9.2310e+08
i0_real_error	1.6240e+07
rg_reciprocal	44.66 Å
i0_reciprocal	923400000.0000
total_estimate	0.8789
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	61.8 Å
skewness	0.143
kurtosis	-0.389
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	126300000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.832

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	CN81-2029 heavy chain
formula_weight	26292.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	17248

EVQLAQSGGGLVQPGGSLRLSCAASGFIFSDYEMYWVRQAPGKGLEAVSGIGNDGSYTHYIDSVKGRFTISRDNAKNSVSLQMNSLRVEDTAVYYCARREFSYFDDDYAVSYTKRSLDSWGQGVVVTVSSASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPVTVSWNSGSLTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYVCNVNHKPSNTKVDKRVEIKTCGGHHHHHHHH

Source

organism	Macaca mulatta
ncbi_taxonomy_id	9544
host_organism	Homo sapiens

Entity 2 polymer

description	CN81-2029 light chain
formula_weight	24050.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

DIVMTQTPLSLPVTPGEPASISCRSSQSLLDSDDGNTYLDWFLQKPGQPPQLLIYEVSNRASGVPDRFSGSGSDTDFTLKIRRVEAEDVGVYYCMQGREFPLSFGGGTKVEIKRTVAAPSVFIFPPSEDQVKSGTVSVVCLLNNFYPREASVKWKVDGALKTGNSQESVTEQDSKDNTYSLSSTLTLSSTEYQSHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Macaca mulatta
ncbi_taxonomy_id	9544
host_organism	Homo sapiens

Entity 3 polymer

description	Envelope gp120
formula_weight	56731.6 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	b,d,f

MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAENLWVTVYYGVPVWRDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLDNVTEKFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLHCTNVTSVNTTGDREELKNCSFNMTTELRDKRQKVYSLFYRLDIVPINENQGSEYRLINCNTSACTQACPKVSFEPIPIHYCAPAGFAILKCKDEGFNGTGLCKNVSTVQCTHGIKPVVSTQLLLNGSLAEKNITIRSENITNNAKIIIVQLVQPVTIKCIRPNNYTRKSIRIGPGQAFYAMGDIIGDIRQAHCNVSRSRWNKTLQEVAEKLRTYFGNKTIIFANSSGGDLEITTHSFNCGGEFFYCNTSGLFNSTWYVNSTWNDTDSTQESNDTITLPCRIKQIINMWQRAGQCMYAPPIPGVIKCESNITGLLLTRDGGKDNNVNETFRPGGGDMRDNWRSELYKYKVVEIEPLGVAPTRCKRRVVE

Source

organism	Human immunodeficiency virus
ncbi_taxonomy_id	12721
host_organism	Homo sapiens

Entity 4 polymer

description	Envelope gp41 ectodomain
formula_weight	17205.7 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	c,e,g

AVGIGAVRRGFLGAAGSTMGAASITLTVQARQLLSGIVQPQNNLLRAPEAQQHLLKLGVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNKSLDEIWNNMTWLQWDKEIGNYTQLIYRLIEESQNQQEKNEKELLALD

Source

organism	Human immunodeficiency virus
ncbi_taxonomy_id	12721
host_organism	Homo sapiens

Entity 5 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	28

Entity 6 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	4

Entity 7 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 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	1

Entity 9 branched

description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	1235.1 kDa
src_method	man
entity_count	1

Entity 10 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	32

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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	2.900 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

fit	/app/data/saxs_computation/zr/9zry/9zry.fit
pddf	/app/data/pr_computation/zr/9zry/9zry.pr.out
profile	/app/data/saxs_computation/zr/9zry/9zry.dat

Cryo-EM structure of SHIV-elicited CN81-2029 Fab in complex with HIV Env trimer Q23-SCT27

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 (10)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 branched

Entity 6 branched

Entity 7 branched

Entity 8 branched

Entity 9 branched

Entity 10 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)