3jvg

Crystal Structure of chicken CD1-1

Method: X-RAY DIFFRACTION

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

T-cell surface glycoprotein CD1A1 antigen

Gallus gallus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Beta-2-microglobulin × 1 （P21611） UNKNOWN LIGAND × 2 CHLORIDE ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Beta-2-microglobulin × 1 （P21611） UNKNOWN LIGAND × 2 CHLORIDE ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A5HUM9_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–275； UniProt 18–292 Author chain B； PDBConstruct 1–275； UniProt 18–292

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 2	T-cell surface glycoprotein CD1A1 antigen × 1 （A5HUM9） UNKNOWN LIGAND × 2 CHLORIDE ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	T-cell surface glycoprotein CD1A1 antigen × 1 （A5HUM9） UNKNOWN LIGAND × 2 CHLORIDE ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 2	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 C； PDBConstruct 1–98； UniProt 22–119 Author chain D； 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	3jvg
Deposition date deposition_date	2009-09-16
Structure title title	Crystal Structure of chicken CD1-1
Keywords keywords	;cd1, T-Cell, lipid, antigen, Transmembrane, Disulfide bond, Immune response, Immunoglobulin domain, MHC I, Polymorphism, Secreted, 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.

3jvg__assembly_1__model_1

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

Download this curve (.dat)

3jvg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3jvg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.02 Å
Rg (electron density)	23.07 Å
Total Rg	23.98 Å
Atom count	2954
Residues	362
Excluded volume	52696 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3jvg__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3jvg__assembly_2__model_1`	dimeric （2）	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	T-cell surface glycoprotein CD1A1 antigen
Molecular weight formula_weight	31582.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6274

EPEGSHMLKLLHFATFQNSTSVLVGGLGLLGDVKMGSLDSRTGNIRYYRPWLRPSLPKGDWDVIESSIKSYVRDFSRLVQMYTTVPYPFVFQSSIGCELQSNGTIRTFFDIAYEGQNFLRFNLDAGTWDQMQHNQLSAKAEHLMANASTLNEVIQVLLNDTCVDILRLFIQAGKADLERQVPPMAVVFARTAGQAQLLLVCRVTSFYPRPIAVTWLRDGREVPPSPALSTGTVLPNADLTYQLRSTLLVSPQDGHGYACRVQHCSLGDRSLLVPWHHHHHH

Source Source

Source organism organism	Gallus gallus
Common name common_name	bantam,chickens
NCBI taxonomy ID ncbi_taxonomy_id	9031
Host organism host_organism	Spodoptera frugiperda

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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

DLTPKVQVYSRFPASAGTKNVLNCFAAGFHPPKISITLMKDGVPMEGAQYSDMSFNDDWTFQRLVHADFTPSSGSTYACKVEHETLKEPQVYKWDPEF

Source Source

Source organism organism	Gallus gallus
Common name common_name	bantam,chickens
NCBI taxonomy ID ncbi_taxonomy_id	9031
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 non-polymer

Description description	UNKNOWN LIGAND
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	6

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	328

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3jvga1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
Family Family family	d.19.1.0 — automated matches

Domain ID domain_id	d3jvga2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d3jvga3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3jvgb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
Family Family family	d.19.1.0 — automated matches

Domain ID domain_id	d3jvgb2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d3jvgb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3jvgc_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d3jvgd_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	3jvgA01
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	3jvgA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3jvgB01
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	3jvgB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3jvgC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3jvgD00
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	40.839 Å
Unit-cell length b length_b	112.124 Å
Unit-cell length c length_c	201.773 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	43.060 Å
R factor r_factor	0.2176
R_work r_work	0.2157
R_free r_free	0.2520

Crystal Structure of chicken CD1-1

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

T-cell surface glycoprotein CD1A1 antigen

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

3jvg__assembly_1__model_1

3jvg__assembly_1__model_1 | I(q)

3jvg__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal Structure of chicken CD1-1

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

T-cell surface glycoprotein CD1A1 antigen

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

3jvg__assembly_1__model_1

3jvg__assembly_1__model_1 | I(q)

3jvg__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)

7. Citations (1)