5ymw

Crystal structure of 8-mer peptide from Rous sarcoma virus in complex with BF2*1201

Method: X-RAY DIFFRACTION

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

Class I histocompatibility antigen, F10 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） LEU-PRO-ALA-CYS-VAL-LEU-GLU-VAL × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Beta-2-microglobulin × 1 （P21611） LEU-PRO-ALA-CYS-VAL-LEU-GLU-VAL × 1 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Beta-2-microglobulin × 1 （P21611） LEU-PRO-ALA-CYS-VAL-LEU-GLU-VAL × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Beta-2-microglobulin × 1 （P21611） LEU-PRO-ALA-CYS-VAL-LEU-GLU-VAL × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HA1F_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–271； UniProt 23–292 Author chain D； PDBConstruct 2–271； UniProt 23–292 Author chain G； PDBConstruct 2–271； UniProt 23–292 Author chain J； PDBConstruct 2–271； UniProt 23–292

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	Class I histocompatibility antigen, F10 alpha chain × 1 （P15979） LEU-PRO-ALA-CYS-VAL-LEU-GLU-VAL × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Class I histocompatibility antigen, F10 alpha chain × 1 （P15979） LEU-PRO-ALA-CYS-VAL-LEU-GLU-VAL × 1 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Class I histocompatibility antigen, F10 alpha chain × 1 （P15979） LEU-PRO-ALA-CYS-VAL-LEU-GLU-VAL × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Class I histocompatibility antigen, F10 alpha chain × 1 （P15979） LEU-PRO-ALA-CYS-VAL-LEU-GLU-VAL × 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 Author chain E； PDBConstruct 1–98； UniProt 22–119 Author chain H； PDBConstruct 1–98； UniProt 22–119 Author chain K； 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	5ymw
Deposition date deposition_date	2017-10-22
Structure title title	Crystal structure of 8-mer peptide from Rous sarcoma virus in complex with BF2*1201
Keywords keywords	MHC, chicken, Rous sarcoma virus, 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.

5ymw__assembly_1__model_1

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

Download this curve (.dat)

5ymw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ymw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.60 Å
Rg (electron density)	22.66 Å
Total Rg	23.53 Å
Atom count	3031
Residues	377
Excluded volume	53203 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ymw__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5ymw__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5ymw__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5ymw__assembly_4__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 (4)

Entity 1 Entity 1 polymer

Description description	Class I histocompatibility antigen, F10 alpha chain
Molecular weight formula_weight	31117.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J
Atom count atom_count	13228

MELHTLRYIQTAMTDPGPGQPWFVTVGYVDGELFVHYNSTARRYVPRTEWIAAKADQQYWDGQTQIGQGNEQIDRENLGILQRRYNQTGGSHTVQWMYGCDILEGGPIRGYYQMAYDGRDFTAFDKGTMTFTAAVPEAVPTKRKWEEESEPERWKNYLEETCVEWLRRYVEYGKAELGRRERPEVRVWGKEADGILTLSCRAHGFYPRPIVVSWLKDGAVRGQDAHSGGIVPNGDGTYHTWVTIDAQPGDGDKYQCRVEHASLPQPGLYSW

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

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	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,H,K

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

Entity 3 Entity 3 polymer

Description description	LEU-PRO-ALA-CYS-VAL-LEU-GLU-VAL
Molecular weight formula_weight	843.0 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,I,L

LPACVLEV

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1104

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	5ymwA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — MHC class I-like antigen recognition-like

Domain ID domain_id	5ymwA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ymwB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ymwD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — MHC class I-like antigen recognition-like

Domain ID domain_id	5ymwD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ymwE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ymwG01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — MHC class I-like antigen recognition-like

Domain ID domain_id	5ymwG02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ymwH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ymwJ01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — MHC class I-like antigen recognition-like

Domain ID domain_id	5ymwJ02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ymwK00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	86.817 Å
Unit-cell length b length_b	117.268 Å
Unit-cell length c length_c	92.507 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.21 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.997 Å
Low-resolution limit resolution_low	36.916 Å
R factor r_factor	0.1961
R_work r_work	0.1941
R_free r_free	0.2351

Crystal structure of 8-mer peptide from Rous sarcoma virus in complex with BF2*1201

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

Class I histocompatibility antigen, F10 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

5ymw__assembly_1__model_1

5ymw__assembly_1__model_1 | I(q)

5ymw__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of 8-mer peptide from Rous sarcoma virus in complex with BF2*1201

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

Class I histocompatibility antigen, F10 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

5ymw__assembly_1__model_1

5ymw__assembly_1__model_1 | I(q)

5ymw__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)