9eb5

Chicken YF1.7*1 presenting myristoylated peptide derived from tegument protein MDV023

Method: X-RAY DIFFRACTION

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

MHC Rfp-Y class I alpha chain

Gallus gallus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Beta-2-microglobulin × 1 （P21611） 5mer derived from a tegument protein in MDV × 1 DI(HYDROXYETHYL)ETHER × 1 SODIUM ION × 1 CHLORIDE ION × 2 MAGNESIUM ION × 1 MYRISTIC ACID × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9BCW3_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–270； UniProt 22–291

Beta-2-microglobulin

Gallus gallus

UniProt P21611

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	MHC Rfp-Y class I alpha chain × 1 （Q9BCW3） 5mer derived from a tegument protein in MDV × 1 DI(HYDROXYETHYL)ETHER × 1 SODIUM ION × 1 CHLORIDE ION × 2 MAGNESIUM ION × 1 MYRISTIC ACID × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B2MG_CHICK
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–98； UniProt 22–119

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	9eb5
Deposition date deposition_date	2024-11-11
Last revision last_revision	2025-07-23
Structure title title	Chicken YF1.7*1 presenting myristoylated peptide derived from tegument protein MDV023
Keywords keywords	;Chicken, Antigen presentation, lipopeptide, MHC-like, Marek's disease virus, MDV, tegument, IMMUNE SYSTEM ;; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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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.

9eb5__assembly_1__model_1

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

Download this curve (.dat)

9eb5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9eb5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.39 Å
Rg (electron density)	22.48 Å
Total Rg	23.36 Å
Atom count	2914
Residues	373
Excluded volume	51355 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9eb5__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 (9)

Entity 1 Entity 1 polymer

Description description	MHC Rfp-Y class I alpha chain
Molecular weight formula_weight	31036.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3206

GSHSLRYFLTGMTDPGPGMPRFVIVGYVDDKIFGTYNSKSRTAQPIVEMLPQEDQEHWDTQTQKAQGGERDFDWNLNRLPERYNKSKGSHTMQMMFGCDILEDGSIRGYDQYAFDGRDFLAFDMDTMTFTAADPVAEITKRRWETEGTYAERWKHELGTVCVQNLRRYLEHGKAALKRRVQPEVRVWGKEADGILTLSCHAHGFYPRPITISWMKDGMVRDQETRWGGIVPNSDGTYHASAAIDVLPEDGDKYWCRVEHASLPQPGLFSW

Source Source

Source organism organism	Gallus gallus
Common name common_name	chicken
NCBI taxonomy ID ncbi_taxonomy_id	9031
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Beta-2-microglobulin
Molecular weight formula_weight	11062.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DLTPKVQVYSRFPASAGTKNVLNCFAAGFHPPKISITLMKDGVPMEGAQYSDMSFNDDWTFQRLVHADFTPSSGSTYACKVEHETLKEPQVYKWDPEF

Source Source

Source organism organism	Gallus gallus
Common name common_name	chicken
NCBI taxonomy ID ncbi_taxonomy_id	9031
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	5mer derived from a tegument protein in MDV
Molecular weight formula_weight	460.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GQAVS

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	MYRISTIC ACID
Molecular weight formula_weight	228.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	244

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Unit-cell length a length_a	57.116 Å
Unit-cell length b length_b	55.429 Å
Unit-cell length c length_c	133.412 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.43 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	I 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	2.080 Å
Low-resolution limit resolution_low	48.130 Å
R factor r_factor	0.1890
R_work r_work	0.1862
R_free r_free	0.2427

Chicken YF1.7*1 presenting myristoylated peptide derived from tegument protein MDV023

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

MHC Rfp-Y class I alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Beta-2-microglobulin

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

9eb5__assembly_1__model_1

9eb5__assembly_1__model_1 | I(q)

9eb5__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (1)

Chicken YF1.7*1 presenting myristoylated peptide derived from tegument protein MDV023

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

MHC Rfp-Y class I alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Beta-2-microglobulin

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

9eb5__assembly_1__model_1

9eb5__assembly_1__model_1 | I(q)

9eb5__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (1)