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9u36

Cryo-EM structure of Dengue virus serotype2 THSTI/TRC/01 strain bound with D14.F25.SO2 fab

Method: ELECTRON MICROSCOPY D_max: 187.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u36
deposition_date	2025-03-18
title	Cryo-EM structure of Dengue virus serotype2 THSTI/TRC/01 strain bound with D14.F25.SO2 fab
keywords	Antibody binding, fab-virus complex, E-protein, Neutralization, VIRUS; VIRUS
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	51.54 Å
rg_electron	51.69 Å
i0	1002070000.00
molecular_weight	263080.0 kDa
excluded_volume	329630 Å³
envelope_volume	509500 Å³
shell_volume	84865 Å³
envelope_diameter	201.1 Å
shell_rg	52.99 Å
envelope_rg	50.59 Å
shape_rg	51.68 Å
total_rg	51.79 Å
total_atoms	23633
n_residues	2427
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	187.6 Å
rg_real	51.73 Å
rg_real_error	1.74 Å
i0_real	1.0020e+09
i0_real_error	1.9860e+07
rg_reciprocal	51.39 Å
i0_reciprocal	1002000000.0000
total_estimate	0.8379
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	60.5 Å
skewness	0.541
kurtosis	0.112
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	73210000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.693; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.944; Smooth: 0.866

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Envelope Glycoprotein
formula_weight	54262.6 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,E
atom_count	23633

MRCIGISNRDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDFELIKTEAKQPATLRKYCIEAKLTNTTTASRCPTQGEPSLNEEQDKRFVCKHSMVDRGWGNGCGLFGKGGIVTCAMFTCKKNMEGKIVQPENLEYTIVITPHSGEENAVGNDTGKHGKEVKVTPQSSITEAELTGYGTVTMECSPRTGLDFNEMVLLQMENKAWLVHRQWFLDLPLPWLPGADTQGSNWIQKETLVTFKNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSGNLLFTGHLKCRLRMDKLQLKGMSYSMCTGKFKVVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTEKDSPVNIEAEPPFGDSYIIIGVEPGQLKLSWFKKGSSIGQMFETTMRGAKRMAILGDTAWDFGSLGGVFTSIGKALHQVFGAIYGAAFSGVSWTMKILIGVVITWIGMNSRSTSLSVSLVLVGVVTLYLGVMVQA

Entity 2 polymer

description	Membrane glycoprotein
formula_weight	8398.8 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	C,D,F

SVALVPHVGMGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTYFQRVLIFILLTAVAPSMT

Entity 3 polymer

description	D14.F25.S02 Heavy chain variable region
formula_weight	13980.6 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	H,K,N

QVQLVQSGAEVKKPGSSAKVSCKASGGTFSSYAISWVRQAPGQGLEWMGSIMPIFGTVNYAQKFQGRVTITADESTSTAYMELSRLRSEDTAVYFCARGWGGNYRSADLWIYFDLWGQGTLVTVSSRS

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 4 polymer

description	D14.F25.S02 Light chain variable region
formula_weight	11679.9 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	L,M,O

QSALTQPRSVSGSPGQSVTISCTGTSSDVGGYKYVSWYQQHPGKAPKLMIYDVTKRPSGVPDRFSGSKSGNTASLTISGLQADDEADYYCCSYAGSYTHVVFGGGTKLTVL

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	19.08 Å
resolution_method	—
num_particles	4715

fit	/app/data/saxs_computation/u3/9u36/9u36.fit
pddf	/app/data/pr_computation/u3/9u36/9u36.pr.out
profile	/app/data/saxs_computation/u3/9u36/9u36.dat

Cryo-EM structure of Dengue virus serotype2 THSTI/TRC/01 strain bound with D14.F25.SO2 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

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)