SAXSdb — 6t3y

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

MHC class II 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 2	MHC class II beta chain 2 × 1 （B5BSA0） GLYCEROL × 3 ACETATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q4U5Z6_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–183； UniProt 27–207

MHC class II beta chain 2

Gallus gallus

UniProt B5BSA0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	MHC class II alpha chain × 1 （Q4U5Z6） GLYCEROL × 3 ACETATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B5BSA0_CHICK
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 39–224； UniProt 30–215

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	6t3y
Deposition date deposition_date	2019-10-11
Structure title title	Improved High Resolution Structure of MHC Class II complex
Keywords keywords	MHC II, Immune Synapse, 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.

6t3y__assembly_1__model_1

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

Download this curve (.dat)

6t3y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6t3y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.23 Å
Rg (electron density)	23.12 Å
Total Rg	24.05 Å
Atom count	3076
Residues	379
Excluded volume	53692 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6t3y__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	MHC class II alpha chain
Molecular weight formula_weight	21033.5 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	3393

ARHVLLQAEFYQRSEGPDKAWAQFGFHFDADELFHVELDAAQTVWRLPEFGRFASFEAQGALQNMAVGKQNLEVMISNSNRSQQDFVTPELALFPAEAVSLEEPNVLICYADKFWPPVATMEWRRNGAVVSEGVYDSVYYGRPDLLFRKFSYLPFVPQRGDVYSCAVRHWGAEGPVQRMWEPE

Source Source

Source organism organism	Gallus gallus
Common name common_name	Chicken
NCBI taxonomy ID ncbi_taxonomy_id	9031
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	MHC class II beta chain 2
Molecular weight formula_weight	24879.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ADRPQIESLSLNGVPNIFLSTKAGGGGSGGGGSGGGGSSAFFFCGAIFECHYLNGTERVRYLQRYIYNRQQLVHFDSDVGKFVADTPLGEPQAEYWNSNAELLENIMNIADGSCRHNYGILESFTVQRSVEPKVRVSALQSGSLPETDRLACYVTGFYPPEIEVKWFLNGREETERVVSTDVMQNGDWTYQVLVVLETVPRRGDSYVCRVEHASLRQPISQAWE

Source Source

Source organism organism	Gallus gallus
Common name common_name	Chicken
NCBI taxonomy ID ncbi_taxonomy_id	9031
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	317

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d6t3ya1
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	d6t3ya2
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	d6t3ya3
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

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Unit-cell length a length_a	154.153 Å
Unit-cell length b length_b	60.002 Å
Unit-cell length c length_c	51.713 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.75 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	26.850 Å
R factor r_factor	0.1747
R_work r_work	0.1715
R_free r_free	0.2021

Improved High Resolution Structure of MHC Class II complex

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

MHC class II alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

MHC class II beta chain 2

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

6t3y__assembly_1__model_1

6t3y__assembly_1__model_1 | I(q)

6t3y__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

7. Citations (1)

Improved High Resolution Structure of MHC Class II complex

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

MHC class II 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

MHC class II beta chain 2

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

6t3y__assembly_1__model_1

6t3y__assembly_1__model_1 | I(q)

6t3y__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

7. Citations (1)