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9u38

D14.F25.S02 Fab complexed to DENV2-US/BID/V594/2006 virus-3f-2f Fab map

Method: ELECTRON MICROSCOPY D_max: 183.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u38
deposition_date	2025-03-18
title	D14.F25.S02 Fab complexed to DENV2-US/BID/V594/2006 virus-3f-2f Fab map
keywords	Dengue virus, flavivirus, broadly neutralizing antibody, 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	49.50 Å
rg_electron	49.67 Å
i0	821175000.00
molecular_weight	238820.0 kDa
excluded_volume	299740 Å³
envelope_volume	453970 Å³
shell_volume	78598 Å³
envelope_diameter	194.7 Å
shell_rg	52.10 Å
envelope_rg	48.66 Å
shape_rg	49.65 Å
total_rg	49.83 Å
total_atoms	33465
n_residues	2188
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	183.8 Å
rg_real	49.72 Å
rg_real_error	1.89 Å
i0_real	8.2120e+08
i0_real_error	1.6650e+07
rg_reciprocal	49.50 Å
i0_reciprocal	820900000.0000
total_estimate	0.6275
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	57.4 Å
skewness	0.502
kurtosis	0.127
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	61960000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.661; Stabil: 1.000; Sysdev: 0.087; Positv: 1.000; Valcen: 0.969; Smooth: 0.940

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	D14.F25.S02 Fab light chain
formula_weight	12139.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	H,D
atom_count	33465

QSALTQPRSVSGSPGQSVTISCTGTSSDVGGYKYVSWYQQHPGKAPKLMIYDVTKRPSGVPDRFSGSKSGNTASLTISGLQADDEADYYCCSYAGSYTHVVFGGGTKLTVLVVFGG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 2 polymer

description	Envelope Glycoprotein E
formula_weight	54413.8 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	B,C,A

MRCIGISNRDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDFELIKTEAKQPATLRKYCIEAKLTNTTTESRCPTQGEPSLNEEQDKRFICKHSMVDRGWGNGCGLFGKGGIVTCAMFTCKKNMEGKVVLPENLEYTIVITPHSGEEHAVGNDTGKHGKEIKITPQSSITEAELTGYGTVTMECSPRTGLDFNEMVLLQMEDKAWLVHRQWFLDLPLPWLPGADTQGSNWIQKETLVTFKNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSGNLLFTGHLKCRLRMDKLQLKGMSYSMCTGKFKIVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTEKDSPVNIEAEPPFGDSYIIIGVEPGQLKLNWFKKGSSIGQMFETTMRGAKRMAILGDTAWDFGSLGGVFTSIGKALHQVFGAIYGAAFSGVSWTMKILIGVIITWIGMNSRSTSLSVSLVLVGVVTLYLGVMVQA

Entity 3 polymer

description	D14.F25.S02 Fab heavy chain
formula_weight	14037.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	L,E

QVQLVQSGAEVKKPGSSAKVSCKASGGTFSSYAISWVRQAPGQGLEWMGSIMPIFGTVNYAQKFQGRVTITADESTSTAYMELSRLRSEDTAVYFCARGWGGNYRSADLWIYFDLWGQGTLVTVSSRSG

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	3

Polymer

type	polypeptide(L)
strand_id	P,Q,F

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	6.48 Å
resolution_method	—
num_particles	1559

fit	/app/data/saxs_computation/u3/9u38/9u38.fit
pddf	/app/data/pr_computation/u3/9u38/9u38.pr.out
profile	/app/data/saxs_computation/u3/9u38/9u38.dat

D14.F25.S02 Fab complexed to DENV2-US/BID/V594/2006 virus-3f-2f Fab map

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

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)