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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 27–207	Not recorded	MHC class II beta chain 2 × 1 （B5BSA0） GOL GLYCEROL × 3 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2 M Na Acetate 0.1 M TRIS 30 %w/v PEG 4K	Resolution 1.70 Å R-free 0.202

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6T3Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6KVM Crystal structure of Chicken MHC Class II for 1.9 angstrom Deposited 2019-09-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 24–217（194 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；30% PEG 4000, 100mM Tris base/Hydrochloric acid pH 8.5, 200mM Lithium sulfate	Resolution 1.90 Å R-free 0.227
6ZWA CLIP peptide bound to chicken MHC class II molecule (BL-2) from B19 haplotype Deposited 2020-07-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 27–207（181 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.1 M TRIS pH 8.5, 20.0% w/v PEG 4000, 200mM CaCl2	Resolution 1.68 Å R-free 0.252
7APZ CLIP peptide bound to chicken MHC class II molecule (BL-2) from B2 haplotype with a decamer mode of binding Deposited 2020-10-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 27–207（181 aa）	Not recorded	IMD IMIDAZOLE × 4 ACE ACETYL GROUP × 20 ZN ZINC ION × 20 PEG DI(HYDROXYETHYL)ETHER × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NI NICKEL (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M Zinc Acetate (Salt) 0.1 M Imidazole pH 6.5 (Buffer) 10 %w/v PEG 8000 (Precipitant)	Resolution 1.97 Å R-free 0.255
7PDY A viral peptide from Marek's disease virus bound to chicken MHC-II molecule Deposited 2021-08-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 27–214（188 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 3 ACT ACETATE ION × 3 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；PEG 4000, sodium acetate	Resolution 2.54 Å R-free 0.252
7PDY A viral peptide from Marek's disease virus bound to chicken MHC-II molecule Deposited 2021-08-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 27–214（188 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 1 ACT ACETATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；PEG 4000, sodium acetate	Resolution 2.54 Å R-free 0.252
7PDY A viral peptide from Marek's disease virus bound to chicken MHC-II molecule Deposited 2021-08-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 27–214（188 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；PEG 4000, sodium acetate	Resolution 2.54 Å R-free 0.252

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 30–215	Not recorded	MHC class II alpha chain × 1 （Q4U5Z6） GOL GLYCEROL × 3 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2 M Na Acetate 0.1 M TRIS 30 %w/v PEG 4K	Resolution 1.70 Å R-free 0.202

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6T3Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7APZ CLIP peptide bound to chicken MHC class II molecule (BL-2) from B2 haplotype with a decamer mode of binding Deposited 2020-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 30–224（195 aa）	Not recorded	IMD IMIDAZOLE × 4 ACE ACETYL GROUP × 20 ZN ZINC ION × 20 PEG DI(HYDROXYETHYL)ETHER × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NI NICKEL (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M Zinc Acetate (Salt) 0.1 M Imidazole pH 6.5 (Buffer) 10 %w/v PEG 8000 (Precipitant)	Resolution 1.97 Å R-free 0.255

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.23 Å
Radius of gyration Rg (electron density) rg_electron	23.12 Å
Forward intensity I(0) i0	31750500.00
Molecular weight molecular_weight	43100.0 kDa
Excluded volume excluded_volume	53692 Å³
Envelope volume envelope_volume	65132 Å³
Hydration-shell volume shell_volume	23752 Å³
Envelope diameter envelope_diameter	83.4 Å
Shell Rg shell_rg	29.98 Å
Envelope Rg envelope_rg	23.49 Å
Shape Rg shape_rg	23.09 Å
Total Rg total_rg	24.05 Å
Total atoms total_atoms	3076
Residues n_residues	379
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	78.5 Å
Rg (real space) rg_real	24.23 Å
Rg uncertainty (real space) rg_real_error	0.74 Å
I(0) (real space) i0_real	3.1750e+07
I(0) uncertainty (real space) i0_real_error	4.9120e+05
Rg (reciprocal space) rg_reciprocal	24.23 Å
I(0) (reciprocal space) i0_reciprocal	31750000.0000
Solution quality estimate total_estimate	0.8073
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	27.0 Å
Skewness Skewness skewness	0.343
Kurtosis Kurtosis kurtosis	-0.363
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8677000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.861; Stabil: 0.975; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

来源 Source

来源生物 organism	Gallus gallus
通用名 common_name	Chicken
NCBI Class编号 ncbi_taxonomy_id	9031
宿主生物 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

来源 Source

来源生物 organism	Gallus gallus
通用名 common_name	Chicken
NCBI Class编号 ncbi_taxonomy_id	9031
宿主生物 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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7. 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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8. Citations (1)

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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

fit	/app/data/saxs_computation/t3/6t3y/6t3y.fit
pddf	/app/data/pr_computation/t3/6t3y/6t3y.pr.out
profile	/app/data/saxs_computation/t3/6t3y/6t3y.dat

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)