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9u34

Helical Reconstruction of DENV2 US/BID-V594/2006 tubular particles bound with D14.F25.S02 fab

Method: ELECTRON MICROSCOPY D_max: 161.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u34
deposition_date	2025-03-18
title	Helical Reconstruction of DENV2 US/BID-V594/2006 tubular particles bound with D14.F25.S02 fab
keywords	dengue virus, neutralizing antibody, fab-virus complex, E-protein, helical, 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	46.34 Å
rg_electron	46.47 Å
i0	455349000.00
molecular_weight	176320.0 kDa
excluded_volume	221120 Å³
envelope_volume	324990 Å³
shell_volume	61202 Å³
envelope_diameter	163.4 Å
shell_rg	47.67 Å
envelope_rg	45.74 Å
shape_rg	46.47 Å
total_rg	46.53 Å
total_atoms	24677
n_residues	1618
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	161.1 Å
rg_real	46.66 Å
rg_real_error	2.05 Å
i0_real	4.5530e+08
i0_real_error	9.3870e+06
rg_reciprocal	46.35 Å
i0_reciprocal	455200000.0000
total_estimate	0.8505
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	42.6 Å
skewness	0.453
kurtosis	-0.435
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	58590000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.792; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.949; Smooth: 0.728

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Envelope Glycoprotein E
formula_weight	54413.8 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,A
atom_count	24677

MRCIGISNRDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDFELIKTEAKQPATLRKYCIEAKLTNTTTESRCPTQGEPSLNEEQDKRFICKHSMVDRGWGNGCGLFGKGGIVTCAMFTCKKNMEGKVVLPENLEYTIVITPHSGEEHAVGNDTGKHGKEIKITPQSSITEAELTGYGTVTMECSPRTGLDFNEMVLLQMEDKAWLVHRQWFLDLPLPWLPGADTQGSNWIQKETLVTFKNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSGNLLFTGHLKCRLRMDKLQLKGMSYSMCTGKFKIVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTEKDSPVNIEAEPPFGDSYIIIGVEPGQLKLNWFKKGSSIGQMFETTMRGAKRMAILGDTAWDFGSLGGVFTSIGKALHQVFGAIYGAAFSGVSWTMKILIGVIITWIGMNSRSTSLSVSLVLVGVVTLYLGVMVQA

Entity 2 polymer

description	D14.F25.S02 Light chain
formula_weight	11679.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	L,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	2

Polymer

type	polypeptide(L)
strand_id	H,K

QVQLVQSGAEVKKPGSSAKVSCKASGGTFSSYAISWVRQAPGQGLEWMGSIMPIFGTVNYAQKFQGRVTITADESTSTAYMELSRLRSEDTAVYFCARGWGGNYRSADLWIYFDLWGQGTLVTVSSRS

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 4 polymer

description	Membrane Glycoprotein
formula_weight	8373.8 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

SVALVPHVGMGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILAYTIGTTHFQRALIFILLTAVAPSMT

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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	14.70 Å
resolution_method	—
num_particles	405

fit	/app/data/saxs_computation/u3/9u34/9u34.fit
pddf	/app/data/pr_computation/u3/9u34/9u34.pr.out
profile	/app/data/saxs_computation/u3/9u34/9u34.dat

Helical Reconstruction of DENV2 US/BID-V594/2006 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 (4)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)