SAXSdb — 6kvm

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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 3	MHC class II beta chain 2 × 1 （Q4U600） peptide from 60S ribosomal protein L30 × 1 （P67883） GLYCEROL × 1 water × 3	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 1–194； UniProt 24–217

MHC class II beta chain 2

Gallus gallus

UniProt Q4U600

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	MHC class II alpha chain × 1 （Q4U5Z6） peptide from 60S ribosomal protein L30 × 1 （P67883） GLYCEROL × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q4U600_CHICK
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 17–214； UniProt 27–224

peptide from 60S ribosomal protein L30

Gallus gallus

UniProt P67883

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	MHC class II alpha chain × 1 （Q4U5Z6） MHC class II beta chain 2 × 1 （Q4U600） GLYCEROL × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL30_CHICK
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–17； UniProt 99–115

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	6kvm
Deposition date deposition_date	2019-09-04
Structure title title	Crystal structure of Chicken MHC Class II for 1.9 angstrom
Keywords keywords	Complex crystal structure MHC class II chicken evolution, 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.

6kvm__assembly_1__model_1

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

Download this curve (.dat)

6kvm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6kvm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.55 Å
Rg (electron density)	23.49 Å
Total Rg	24.41 Å
Atom count	3107
Residues	380
Excluded volume	54575 Å³
Maximum q	0.500 Å⁻¹

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

Entity 1 Entity 1 polymer

Description description	MHC class II alpha chain
Molecular weight formula_weight	22125.7 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	3317

LKPHVLLQAEFYQRSEGPDKAWAQFGFHFDADELFHVELDAAQTVWRLPEFGRFASFEAQGALQNMAVGKQNLEVMISNSNRSQQDFVTPELALFPAEAVSLEEPNVLICYADKFWPPVATMEWRRNGAVVSEGVYDSVYYGRPDLLFRKFSYLPFVPQRGDVYSCAVRHWGAEGPVQRMWEPEVPEPPSESSA

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	MHC class II beta chain 2
Molecular weight formula_weight	24113.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SGGGSLVPRGSGGGGSTRPSAFFFCGAISECHYLNGTERVRYLQRYIYNRQQYAHFDSDVGKFVADSPLGEPQAEYWNSNAELLENRMNEVDRFCRHNYGGVESFTVQRSVEPKVRVSALQSGSLPETDRLACYVTGFYPPEIEVKWFLNGREETERVVSTDVMQNGDWTYQVLVVLETVPRRGDSYVCRVEHASLRQPISQAWEPPADAGRSK

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	peptide from 60S ribosomal protein L30
Molecular weight formula_weight	1892.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

PGDSDIIRSMPEQTSEK

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 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	nat
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	210

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6kvma1
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	d6kvma2
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	d6kvmb1
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	d6kvmb2
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 (2 domains)

Domain ID domain_id	6kvmA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

Domain ID domain_id	6kvmA02
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	152.397 Å
Unit-cell length b length_b	57.297 Å
Unit-cell length c length_c	58.057 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.68 °
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	1.897 Å
Low-resolution limit resolution_low	54.377 Å
R factor r_factor	—
R_work r_work	0.2028
R_free r_free	0.2274

Crystal structure of Chicken MHC Class II for 1.9 angstrom

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

peptide from 60S ribosomal protein L30

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

6kvm__assembly_1__model_1

6kvm__assembly_1__model_1 | I(q)

6kvm__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Chicken MHC Class II for 1.9 angstrom

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

peptide from 60S ribosomal protein L30

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

6kvm__assembly_1__model_1

6kvm__assembly_1__model_1 | I(q)

6kvm__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)