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9ua9

Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 1D6

Method: ELECTRON MICROSCOPY D_max: 135.9 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ua9
deposition_date	2025-03-31
title	Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 1D6
keywords	Henipavirus, Fusion glycoprotein, Antibody, ANTIVIRAL PROTEIN, 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	42.76 Å
rg_electron	41.92 Å
i0	731502000.00
molecular_weight	223830.0 kDa
excluded_volume	280970 Å³
envelope_volume	389540 Å³
shell_volume	76539 Å³
envelope_diameter	140.5 Å
shell_rg	48.12 Å
envelope_rg	41.26 Å
shape_rg	41.89 Å
total_rg	42.32 Å
total_atoms	15714
n_residues	2031
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	135.9 Å
rg_real	42.55 Å
rg_real_error	0.86 Å
i0_real	7.3150e+08
i0_real_error	1.2210e+07
rg_reciprocal	42.76 Å
i0_reciprocal	731700000.0000
total_estimate	0.6635
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	55.1 Å
skewness	0.131
kurtosis	-0.442
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0001
highest_alpha	75760000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 0.016; Positv: 1.000; Valcen: 0.975; Smooth: 0.914

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	1D6-VL
formula_weight	11247.2 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	F,E,D
atom_count	16357

PVLTQPPSASEAARKSVTISCSGSSSNIGSNSVSWYQQLPGTALKLLISYNDQRASGVSDRFSGSKSGTSASLAISGLQTEDEADYYCAAWDDSLSGPVFGGGTRLTVL

Source

organism	Macaca
ncbi_taxonomy_id	9539
host_organism	Homo sapiens

Entity 2 polymer

description	1D6 VH
formula_weight	13690.3 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	H,G,I

QVQLQESGPGLVKPSETLSLTCTVSGASISSYWWGWIRQPPGKGLEWIADIYPNSGSTNYNPSLKSRVTNSKDASKNQFSLKLSSVTAADTAMYYCARAPRGYSYSYVFGHRFDVWGPGVLVTVS

Source

organism	Macaca
ncbi_taxonomy_id	9539
host_organism	Homo sapiens

Entity 3 polymer

description	Fusion glycoprotein F0
formula_weight	49473.6 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,C,B

ILHYEKLSKIGLVKGVTRKYKIKSNPLTKDIVIKMIPNVSNMSQCTGSVMENYKTRLNGILTPIKGALEIYKNNTHDLVGDVRLAGVIMAGVAIGIATAAQITAGVALYEAMKNADNINKLKSSIESTNEAVVKLQETAEKTVYVLTALQDYINTNLVPTIDKISCKQTELSLDLALSKYLSDLLFVFGPNLQDPVSNSMTIQAISQAFGGNYETLLRTLGYATEDFDDLLESDSITGQIIYVDLSSYYIIVRVYFPILTEIQQAYIQELLPVSFNNDNSEWISIVPNFILVRNTLISNIEIGFCLITKRSVICNQDYATPMTNNMRECLTGSTEKCPRELVVSSHVPRFALSNGVLFANCISVTCQCQTTGRAISQSGEQTLLMIDNTTCPTAVLGNVIISLGKYLGSVNYNSEGIAIGPPVFTDKVDISSQISSMNQSLQQSKDYIKE

Source

organism	Henipavirus nipahense
ncbi_taxonomy_id	3052225
host_organism	Homo sapiens

Entity 4 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	3

Entity 5 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	9

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	553

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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	1.99 Å
resolution_method	—
num_particles	1141629

fit	/app/data/saxs_computation/ua/9ua9/9ua9.fit
pddf	/app/data/pr_computation/ua/9ua9/9ua9.pr.out
profile	/app/data/saxs_computation/ua/9ua9/9ua9.dat

Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 1D6

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

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 branched

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)