SAXSdb — 9wyt

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1. Structure Basics

entry_id	9wyt
deposition_date	2025-09-27
title	Cryo-EM structure of the IgY-FcRY complex
keywords	Immunoglobulin Y, IMMUNE SYSTEM; 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	39.14 Å
rg_electron	38.44 Å
i0	651161000.00
molecular_weight	206130.0 kDa
excluded_volume	256350 Å³
envelope_volume	333910 Å³
shell_volume	70136 Å³
envelope_diameter	127.8 Å
shell_rg	46.07 Å
envelope_rg	38.07 Å
shape_rg	38.40 Å
total_rg	38.99 Å
total_atoms	14522
n_residues	1758
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	124.6 Å
rg_real	38.96 Å
rg_real_error	0.64 Å
i0_real	6.5120e+08
i0_real_error	1.1000e+07
rg_reciprocal	39.07 Å
i0_reciprocal	651200000.0000
total_estimate	0.8872
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	46.7 Å
skewness	0.236
kurtosis	-0.407
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	78810000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.850

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Ig-like domain-containing protein
formula_weight	35320.7 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	14525

EVQVLHASSCTPSQSESVELLCLVTGFSPASAEVEWLVDGVGGLLVASQSPAVRSGSTYSLSSRVNVSGTDWREGKSYSCRVRHPATNTVVEDHVKGCPDGAQSCSPIQLYAIPPSPGELYISLDAKLRCLVVNLPSDSSLSVTWTREKSGNLRPDPMVLQEHFNGTYSASSAVPVSTQDWLSGERFTCTVQHEELPLPLSKSVYRNTGPTTPPLIYPFAPHPEELSLSRVTLSCLVRGFRPRDIEIRWLRDHRAVPATEFVTTAVLPEERTANGAGGDGDTFFVYSKMSVETAKWNGGTVFACMAVHEALPMRFSQRTLQKQA

Entity 2 polymer

description	yolk sac IgY receptor precursor
formula_weight	168748.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	J

MLGVLLLACCLLLGGRSLPRGDAALSRDELPSLRNKGIFIIQSSGSNLCIKADTAGLVLEDCSQISKHMLWKWVSNRRLFNIGRSSCLGLNISRPEQPLTMLECDSNRYSLWWNCDGRALVGVSEYRLAVENSKRIVAKKKSDYQWIQYMSYDEDLCEHPFQETYTLLGNSFGFPCVFPFKYNNKWYYECTRDGKEFEWCATTSYYEQDEKWGFCPGVEHGCGTFWKENPATHVCYQFNPSAVLSWHEARAACQAQGGDLLSITSPEEQSYLSNLSRQLNTTDAVLWTGLNRLEEGAGWQWSDGAPLVFVNWKADVSEDHSSENHCAVMSSKLKYGWKSYLCESGLPFVCKKYLNKIEQETLDTWKYYATRCDAGWYPYNRYCYRLHKEAKSWNDALISCQSDSSGLISISSMADAELLHNLLQRENITETWIGLYNSNISVVFEWSDGTPVKFSYWHSQEPNTFQRAGQLCVSAQGPEGHWKVKKCEDKNFYICKKAGEFNSVSSDAESSCPEGWERHGGYCYKIDSTPRSFEHASSGYFCPSALVSVTNRFEQAFITSMIRSVVKSERTYFWIGLQDLNNTGEYVWLTKDGKNHSVSYTNWNKHQPRHSGGCVAMRGQDPVGYWEVKSCKNFKAMSLCKQKISSYEEPELTFQRHLSSCYFGWESEGNLLNCYKIFHREKILMKRTWSEAETLCQDFGAHLASFSHVYEETFLNNLLYTIFDRTEERQFWIGFNRRNPFSGGTWQWSDRTPVVASFLESKYVEDDSRNCGVFKVNRTIFPAHCNEKREWICKIPKGVKPKNPDWYIAELPWSYYQGAEYLFHVNPTDWDTYEFICVWLRSEMATIHSADEQAFIENKIKKLSDSDVHWWIGLHAESISNEFRWKDGSQITYQNWNEGRDRYLRKPGKRCGFISSQTGRWDDENCTVSLPCICKRKSAWKIEKEIPKDQNPQGTCPKGWLHFGYKCFLIQIPKDPEHLRSWYSAQTFCSRYDGSLASLEDELEQAFITMNLFGRKTSVWIAFQGDDYEKWMNENPPRYSNWSPIEAVHRPRYNGVYVEEQVPLCTLVSNNPNFYFTGKWYLENCEKNYGFVCQKGQDTSRHIVNASEMYPVPDTLQYANRTYTLIRGNFTWSAALKACMANGAELVSIADQYHQSFLTIIVNRLGYNHWIGLFTADNGLNFEWSDGTRSLFTFWEDDESQALGSCVYMDTSGRWKSTSCERLLPGAVCHVPPKKKLTEYKGLCSESNVPWIKFKNSCYSFNTVLQGTSFDTAYEVCRNQGSNLLTIKDEDENAFILEELHSFGYSVKMVWLNILQVTDNETVSWFDGSPLNYSNWGIREPEFDHLKGNFCISLRTADGVWQISPCREIKGFVCKKDADLDAAEPSKKQSYPGLAALAVFVTLVMLAAISFFLWCLYKQNNRFFHRILWVRNAYFPQINSDAPALEESILISDFERDDN

Source

organism	Gallus gallus
common_name	chicken
ncbi_taxonomy_id	9031
host_organism	Homo sapiens

Entity 3 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	570.5 kDa
src_method	man
entity_count	1

Entity 4 non-polymer

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

Entity 5 non-polymer

description	beta-D-mannopyranose
formula_weight	180.2 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	alpha-D-mannopyranose
formula_weight	180.2 kDa
src_method	syn
entity_count	10

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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	3.060 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.06 Å
resolution_method	—
num_particles	127853

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

Cryo-EM structure of the IgY-FcRY complex

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

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Source

Entity 3 branched

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)