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9u35

Helical Reconstruction of DENV2 THSTI/TRC/01 tubular particles bound with D14.F25.S02 fab

Method: ELECTRON MICROSCOPY D_max: 152.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u35
deposition_date	2025-03-18
title	Helical Reconstruction of DENV2 THSTI/TRC/01 tubular particles bound with D14.F25.S02 fab
keywords	;Dengue virus, neutralizing antibody binding, fab-virus complex, E-protein, helical, flavivirus, VIRUS, 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	45.16 Å
rg_electron	46.08 Å
i0	195568000.00
molecular_weight	112850.0 kDa
excluded_volume	140880 Å³
envelope_volume	205750 Å³
shell_volume	41635 Å³
envelope_diameter	163.1 Å
shell_rg	43.65 Å
envelope_rg	45.47 Å
shape_rg	46.07 Å
total_rg	46.00 Å
total_atoms	9646
n_residues	1027
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	152.0 Å
rg_real	45.83 Å
rg_real_error	1.93 Å
i0_real	1.9560e+08
i0_real_error	3.8940e+06
rg_reciprocal	45.16 Å
i0_reciprocal	195400000.0000
total_estimate	0.7577
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	39.1 Å
skewness	0.581
kurtosis	-0.433
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	13980000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.703; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.555; Smooth: 0.183

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Envelope Glycoprotein
formula_weight	54262.6 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	9646

MRCIGISNRDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDFELIKTEAKQPATLRKYCIEAKLTNTTTASRCPTQGEPSLNEEQDKRFVCKHSMVDRGWGNGCGLFGKGGIVTCAMFTCKKNMEGKIVQPENLEYTIVITPHSGEENAVGNDTGKHGKEVKVTPQSSITEAELTGYGTVTMECSPRTGLDFNEMVLLQMENKAWLVHRQWFLDLPLPWLPGADTQGSNWIQKETLVTFKNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSGNLLFTGHLKCRLRMDKLQLKGMSYSMCTGKFKVVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTEKDSPVNIEAEPPFGDSYIIIGVEPGQLKLSWFKKGSSIGQMFETTMRGAKRMAILGDTAWDFGSLGGVFTSIGKALHQVFGAIYGAAFSGVSWTMKILIGVVITWIGMNSRSTSLSVSLVLVGVVTLYLGVMVQA

Entity 2 polymer

description	D14.F25.S02 light chain
formula_weight	11679.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	M

QSALTQPRSVSGSPGQSVTISCTGTSSDVGGYKYVSWYQQHPGKAPKLMIYDVTKRPSGVPDRFSGSKSGNTASLTISGLQADDEADYYCCSYAGSYTHVVFGGGTKLTVL

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 3 polymer

description	D14.F25.S02 heavy chain
formula_weight	13980.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	K

QVQLVQSGAEVKKPGSSAKVSCKASGGTFSSYAISWVRQAPGQGLEWMGSIMPIFGTVNYAQKFQGRVTITADESTSTAYMELSRLRSEDTAVYFCARGWGGNYRSADLWIYFDLWGQGTLVTVSSRS

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

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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	—

resolution	17.37 Å
resolution_method	—
num_particles	1358

fit	/app/data/saxs_computation/u3/9u35/9u35.fit
pddf	/app/data/pr_computation/u3/9u35/9u35.pr.out
profile	/app/data/saxs_computation/u3/9u35/9u35.dat

Helical Reconstruction of DENV2 THSTI/TRC/01 tubular particles bound with D14.F25.S02 fab

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

EM 3D

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)