SAXSdb — 9q5m

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1. Structure Basics

entry_id	9q5m
deposition_date	2025-08-20
title	Structure of the Measles virus Fusion glycoprotein ectodomain in complex with neutralizing antibody Y10F
keywords	;VIRAL PROTEIN, glycoprotein, immune system, measles, high-resolution, ectodomain, fusion, antibody, complex, 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	39.50 Å
rg_electron	38.77 Å
i0	462516000.00
molecular_weight	175800.0 kDa
excluded_volume	220810 Å³
envelope_volume	296990 Å³
shell_volume	64644 Å³
envelope_diameter	145.4 Å
shell_rg	44.22 Å
envelope_rg	38.11 Å
shape_rg	38.77 Å
total_rg	39.08 Å
total_atoms	12331
n_residues	1585
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	136.1 Å
rg_real	39.45 Å
rg_real_error	1.40 Å
i0_real	4.6250e+08
i0_real_error	8.1910e+06
rg_reciprocal	39.48 Å
i0_reciprocal	462500000.0000
total_estimate	0.8624
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	47.6 Å
skewness	0.371
kurtosis	-0.102
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	56680000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.759; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.931

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Fusion glycoprotein F0
formula_weight	57379.5 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	12394

MGLKVNVSAIFMAVLLTLQTPTGQIHWGNLSKIGVVGIGSASYKVMTRSSHQSLVIKLMPNITLLNNCTRVEIAEYRRLLRTVLEPIRDALNAMTQNIRPVQSVASSRRHKRFAGVVLAGAALGVATAAQITAGIALHQSMLNSQAIDNLRASLETTNQAIEAIRQAGQGMILAVQGVQDYINNELIPSMNQLSCDLIGQKLGLKLLRYYTEILSLFGPSLRDPISAEISIQALSYALGGDINKVLEKLGYSGGDLLGILESRGIKARITHVDTESYFIVLSIAYPTLSEIKGVIVHRLEGVSYNIGSQEWYTTVPKYVATQGYLISNFDESSCTFMPEGTVCSQNALYPMSPLLQECLRGSTKSCARTLVSGSFGNRFILSQGNLIANCASILCKCYTTGTIINQDPDKILTYIAADHCPVVEVNGVTIQVGSRRYPDAVYLHRIDLGPPISLGRLDVGTNLGNAIAKLEDAKELLESSDQILRSMKGLSSTSIGVDDDDKAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK

Source

organism	Measles morbillivirus
ncbi_taxonomy_id	11234
host_organism	Drosophila melanogaster

Entity 2 polymer

description	Y10F light chain
formula_weight	25209.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MGWSCIILFLVATATGVHSQIVLSQSPAILSASPGEKVTMTCRATSSVVYMHWYQQKPGSSPKPWIYATSNLASGVPTRFSGSGSGTSYSLTISRVEAEDAATYYCQQWNSNPYTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Cricetulus griseus

Entity 3 polymer

description	Y10F heavy chain
formula_weight	52295.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

MGWSCIILFLVATATGVHSQVQLQQSGAELMKPGASVKISCKAAGYTFSNYWIEWVKQRPGHGLEWIGEILPGNSYTNYNEKFRGKATITADTSSNTAYMQLSSLTSEDSAVYYCASPLSGNYVRFAYWGQGTLVTVSTASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQGPTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Cricetulus griseus

Entity 4 branched

description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	586.5 kDa
src_method	man
entity_count	1

Entity 5 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	4

Entity 6 branched

description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	910.8 kDa
src_method	man
entity_count	2

Entity 7 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	63

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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	triclinic

resolution	2.59 Å
resolution_method	—
num_particles	130000

fit	/app/data/saxs_computation/q5/9q5m/9q5m.fit
pddf	/app/data/pr_computation/q5/9q5m/9q5m.pr.out
profile	/app/data/saxs_computation/q5/9q5m/9q5m.dat

Structure of the Measles virus Fusion glycoprotein ectodomain in complex with neutralizing antibody Y10F

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 (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 branched

Entity 5 branched

Entity 6 branched

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)