SAXSdb — 9wyd

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1. Structure Basics

entry_id	9wyd
deposition_date	2025-09-26
last_revision	2026-02-11
title	Crystal structure of HAstV8 spike and FcRn
keywords	Human astrovirus (HAstV), spike protein, FcRn, VIRAL PROTEIN; VIRAL PROTEIN
method	X-RAY DIFFRACTION

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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	28.33 Å
rg_electron	27.27 Å
i0	67435600.00
molecular_weight	64331.0 kDa
excluded_volume	80467 Å³
envelope_volume	104380 Å³
shell_volume	31740 Å³
envelope_diameter	92.9 Å
shell_rg	34.71 Å
envelope_rg	26.98 Å
shape_rg	27.24 Å
total_rg	28.12 Å
total_atoms	4549
n_residues	568
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	88.8 Å
rg_real	28.21 Å
rg_real_error	0.64 Å
i0_real	6.7440e+07
i0_real_error	1.1010e+06
rg_reciprocal	28.25 Å
i0_reciprocal	67440000.0000
total_estimate	0.9090
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	36.5 Å
skewness	0.163
kurtosis	-0.539
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	11320000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.966

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	IgG receptor FcRn large subunit p51
formula_weight	30408.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4581

AESHLSLLYHLTAVSSPAPGTPAFWVSGWLGPQQYLSYNSLRGEAEPCGAWVWENQVSWYWEKETTDLRIKEKLFLEAFKALGGKGPYTLQGLLGCELGPDNTSVPTAKFALNGEEFMNFDLKQGTWGGDWPEALAISQRWQQQDKAANKELTFLLFSCPHRLREHLERGRGNLEWKEPPSMRLKARPSSPGFSVLTCSAFSFYPPELQLRFLRNGLAAGTGQGDFGPNSDGSFHASSSLTVKSGDEHHYCCIVQHAGLAQPLRVELESPAKSS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Baculovirus expression vector pFastBac1-HM

Entity 2 polymer

description	Beta-2-microglobulin
formula_weight	11748.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Baculovirus expression vector pFastBac1-HM

Entity 3 polymer

description	Spike protein VP27
formula_weight	26148.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

GATPMTFGRSIPEPGEQFRVLLTVGPPMAPNTANSQNWVNKTIVPPENQYTVKIGIDLEHYTTMQGFTPVESVSWYTADFQPSDEPSPIPGLYARVNNTKKADVYGVQQFKSSHTNNRHQITSVFLVRVTTSFQVINYTSYFIRGAESGSNVSNLKIRDQTYHTPLQFTQGKWYLLTSTVMHDGPTSSGWVWMNQELTNNIAYRVDPGMMYLITPPPAASQLYFELHTVLPQ

Source

organism	Human astrovirus-8
ncbi_taxonomy_id	43358
host_organism	Escherichia coli

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	26

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6. Citations (1)

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length_a	173.120 Å
length_b	84.429 Å
length_c	53.953 Å
angle_alpha	90.00 °
angle_beta	97.42 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.650 Å
resolution_low	37.880 Å
r_factor	0.1893
r_work	0.1869
r_free	0.2323

fit	/app/data/saxs_computation/wy/9wyd/9wyd.fit
pddf	/app/data/pr_computation/wy/9wyd/9wyd.pr.out
profile	/app/data/saxs_computation/wy/9wyd/9wyd.dat

Crystal structure of HAstV8 spike and FcRn

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

Refinement

Diffraction

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)