SAXSdb — 9wyt

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ig-like domain-containing protein

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 1	yolk sac IgY receptor precursor × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 beta-D-mannopyranose × 2 alpha-D-mannopyranose × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8V0XHB9_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–324； UniProt 240–563 Author chain B； PDBConstruct 1–324； UniProt 240–563

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9wyt
Deposition date deposition_date	2025-09-27
Structure title title	Cryo-EM structure of the IgY-FcRY complex
Keywords keywords	Immunoglobulin Y, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9wyt__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9wyt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9wyt__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	39.14 Å
Rg (electron density)	38.44 Å
Total Rg	38.99 Å
Atom count	14522
Residues	1758
Excluded volume	256350 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9wyt__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Ig-like domain-containing protein
Molecular weight formula_weight	35320.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	14525

EVQVLHASSCTPSQSESVELLCLVTGFSPASAEVEWLVDGVGGLLVASQSPAVRSGSTYSLSSRVNVSGTDWREGKSYSCRVRHPATNTVVEDHVKGCPDGAQSCSPIQLYAIPPSPGELYISLDAKLRCLVVNLPSDSSLSVTWTREKSGNLRPDPMVLQEHFNGTYSASSAVPVSTQDWLSGERFTCTVQHEELPLPLSKSVYRNTGPTTPPLIYPFAPHPEELSLSRVTLSCLVRGFRPRDIEIRWLRDHRAVPATEFVTTAVLPEERTANGAGGDGDTFFVYSKMSVETAKWNGGTVFACMAVHEALPMRFSQRTLQKQA

Entity 2 Entity 2 polymer

Description description	yolk sac IgY receptor precursor
Molecular weight formula_weight	168748.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MLGVLLLACCLLLGGRSLPRGDAALSRDELPSLRNKGIFIIQSSGSNLCIKADTAGLVLEDCSQISKHMLWKWVSNRRLFNIGRSSCLGLNISRPEQPLTMLECDSNRYSLWWNCDGRALVGVSEYRLAVENSKRIVAKKKSDYQWIQYMSYDEDLCEHPFQETYTLLGNSFGFPCVFPFKYNNKWYYECTRDGKEFEWCATTSYYEQDEKWGFCPGVEHGCGTFWKENPATHVCYQFNPSAVLSWHEARAACQAQGGDLLSITSPEEQSYLSNLSRQLNTTDAVLWTGLNRLEEGAGWQWSDGAPLVFVNWKADVSEDHSSENHCAVMSSKLKYGWKSYLCESGLPFVCKKYLNKIEQETLDTWKYYATRCDAGWYPYNRYCYRLHKEAKSWNDALISCQSDSSGLISISSMADAELLHNLLQRENITETWIGLYNSNISVVFEWSDGTPVKFSYWHSQEPNTFQRAGQLCVSAQGPEGHWKVKKCEDKNFYICKKAGEFNSVSSDAESSCPEGWERHGGYCYKIDSTPRSFEHASSGYFCPSALVSVTNRFEQAFITSMIRSVVKSERTYFWIGLQDLNNTGEYVWLTKDGKNHSVSYTNWNKHQPRHSGGCVAMRGQDPVGYWEVKSCKNFKAMSLCKQKISSYEEPELTFQRHLSSCYFGWESEGNLLNCYKIFHREKILMKRTWSEAETLCQDFGAHLASFSHVYEETFLNNLLYTIFDRTEERQFWIGFNRRNPFSGGTWQWSDRTPVVASFLESKYVEDDSRNCGVFKVNRTIFPAHCNEKREWICKIPKGVKPKNPDWYIAELPWSYYQGAEYLFHVNPTDWDTYEFICVWLRSEMATIHSADEQAFIENKIKKLSDSDVHWWIGLHAESISNEFRWKDGSQITYQNWNEGRDRYLRKPGKRCGFISSQTGRWDDENCTVSLPCICKRKSAWKIEKEIPKDQNPQGTCPKGWLHFGYKCFLIQIPKDPEHLRSWYSAQTFCSRYDGSLASLEDELEQAFITMNLFGRKTSVWIAFQGDDYEKWMNENPPRYSNWSPIEAVHRPRYNGVYVEEQVPLCTLVSNNPNFYFTGKWYLENCEKNYGFVCQKGQDTSRHIVNASEMYPVPDTLQYANRTYTLIRGNFTWSAALKACMANGAELVSIADQYHQSFLTIIVNRLGYNHWIGLFTADNGLNFEWSDGTRSLFTFWEDDESQALGSCVYMDTSGRWKSTSCERLLPGAVCHVPPKKKLTEYKGLCSESNVPWIKFKNSCYSFNTVLQGTSFDTAYEVCRNQGSNLLTIKDEDENAFILEELHSFGYSVKMVWLNILQVTDNETVSWFDGSPLNYSNWGIREPEFDHLKGNFCISLRTADGVWQISPCREIKGFVCKKDADLDAAEPSKKQSYPGLAALAVFVTLVMLAAISFFLWCLYKQNNRFFHRILWVRNAYFPQINSDAPALEESILISDFERDDN

Source Source

Source organism organism	Gallus gallus
Common name common_name	chicken
NCBI taxonomy ID ncbi_taxonomy_id	9031
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	570.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 5 Entity 5 non-polymer

Description description	beta-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	alpha-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	syn
Copy count entity_count	10

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.060 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.06 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	127853

Cryo-EM structure of the IgY-FcRY complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ig-like domain-containing protein

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9wyt__assembly_1__model_1

9wyt__assembly_1__model_1 | I(q)

9wyt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

7. Citations (1)

Cryo-EM structure of the IgY-FcRY complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ig-like domain-containing protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9wyt__assembly_1__model_1

9wyt__assembly_1__model_1 | I(q)

9wyt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

7. Citations (1)