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4d8p

Structural and functional studies of the trans-encoded HLA-DQ2.3 (DQA1*03:01/DQB1*02:01) molecule

Method: X-RAY DIFFRACTION Dmax: 93.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

HLA-DQA1 protein

Homo sapiens

UniProt L8E864

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 24–217 Fragment：UNP residues 24-217 Peptide from Gamma-gliadin,HLA class II histocompatibility antigen, DQ beta 1 chain × 1 （Q94G94,Q5Y7D3） GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2M Li2So4, 0.1M Tris, 30% PEG 4000, 8% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 3.05 Å R-free 0.283
2 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 24–217 Fragment：UNP residues 24-217 Peptide from Gamma-gliadin,HLA class II histocompatibility antigen, DQ beta 1 chain × 1 （Q94G94,Q5Y7D3） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2M Li2So4, 0.1M Tris, 30% PEG 4000, 8% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 3.05 Å R-free 0.283

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name L8E864_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–194； UniProt 24–217 Author chain C； PDBConstruct 1–194； UniProt 24–217

Peptide from Gamma-gliadin,HLA class II histocompatibility antigen, DQ beta 1 chain

Homo sapiens

UniProt Q5Y7D3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 33–230 Mutation：Q26E, Q23E HLA-DQA1 protein × 1 （L8E864） GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2M Li2So4, 0.1M Tris, 30% PEG 4000, 8% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 3.05 Å R-free 0.283
2 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 33–230 Mutation：Q26E, Q23E HLA-DQA1 protein × 1 （L8E864） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2M Li2So4, 0.1M Tris, 30% PEG 4000, 8% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 3.05 Å R-free 0.283

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 4D8P Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4OZF JR5.1 protein complex Deposited 2014-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 33–224（192 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Mother liquor: 0.15 - 0.25M CaOAc, 0.1M Tris/HCl, 12-18% PEG3350, Additives:2-3 mM reduced and oxidised Glutathione
Resolution 2.70 Å R-free 0.238
4OZG D2 protein complex Deposited 2014-02-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 33–224（192 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Mother liquor: 0.15- 0.25M CaOAc, 0.1 M Tris/HCl, 12-18% PEG3350, Additives: 2-3 mM reduced and oxidised Glutathione
Resolution 3.00 Å R-free 0.241
4OZG D2 protein complex Deposited 2014-02-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 33–224（192 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Mother liquor: 0.15- 0.25M CaOAc, 0.1 M Tris/HCl, 12-18% PEG3350, Additives: 2-3 mM reduced and oxidised Glutathione
Resolution 3.00 Å R-free 0.241
4OZH S16 protein complex Deposited 2014-02-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 33–224（192 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Mother liquor: 0.15- 0.25M CaOAc, 0.1 M Tris/HCl, 12-18% PEG3350, Additives: 2-3 mM reduced and oxidised Glutathione
Resolution 2.80 Å R-free 0.243
4OZH S16 protein complex Deposited 2014-02-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 33–224（192 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Mother liquor: 0.15- 0.25M CaOAc, 0.1 M Tris/HCl, 12-18% PEG3350, Additives: 2-3 mM reduced and oxidised Glutathione
Resolution 2.80 Å R-free 0.243
4OZI S2 protein complex Deposited 2014-02-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 33–224（192 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Mother liquor: 0.15- 0.25M CaOAc, 0.1 M Tris/HCl, 12-18% PEG3350, Additives: 2-3 mM reduced and oxidised Glutathione
Resolution 3.20 Å R-free 0.243
4OZI S2 protein complex Deposited 2014-02-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 33–224（192 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Mother liquor: 0.15- 0.25M CaOAc, 0.1 M Tris/HCl, 12-18% PEG3350, Additives: 2-3 mM reduced and oxidised Glutathione
Resolution 3.20 Å R-free 0.243

4 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q5Y7D3_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 34–231； UniProt 33–230 Author chain D； PDBConstruct 34–231； UniProt 33–230

Peptide from Gamma-gliadin,HLA class II histocompatibility antigen, DQ beta 1 chain

Homo sapiens

UniProt Q94G94

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 68–81 Mutation：Q26E, Q23E HLA-DQA1 protein × 1 （L8E864） GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2M Li2So4, 0.1M Tris, 30% PEG 4000, 8% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 3.05 Å R-free 0.283
2 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 68–81 Mutation：Q26E, Q23E HLA-DQA1 protein × 1 （L8E864） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2M Li2So4, 0.1M Tris, 30% PEG 4000, 8% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 3.05 Å R-free 0.283

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name Q94G94_WHEAT
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 5–18； UniProt 68–81 Author chain D； PDBConstruct 5–18； UniProt 68–81

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.

SAXS scattering curve SAXS Profile

SAXS profile for 4d8p

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4d8p
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4d8p
Deposition date deposition_date2012-01-11
Structure title titleStructural and functional studies of the trans-encoded HLA-DQ2.3 (DQA1*03:01/DQB1*02:01) molecule
Keywords keywordsclass II MHC, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier29.56 Å
Radius of gyration Rg (electron density) rg_electron28.43 Å
Forward intensity I(0) i0120046000.00
Molecular weight molecular_weight86430.0 kDa
Excluded volume excluded_volume108090 ų
Envelope volume envelope_volume140920 ų
Hydration-shell volume shell_volume40258 ų
Envelope diameter envelope_diameter99.5 Å
Shell Rg shell_rg36.79 Å
Envelope Rg envelope_rg27.89 Å
Shape Rg shape_rg28.44 Å
Total Rg total_rg29.26 Å
Total atoms total_atoms6114
Residues n_residues749
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax93.1 Å
Rg (real space) rg_real29.37 Å
Rg uncertainty (real space) rg_real_error0.58 Å
I(0) (real space) i0_real1.2000e+08
I(0) uncertainty (real space) i0_real_error1.5780e+06
Rg (reciprocal space) rg_reciprocal29.45 Å
I(0) (reciprocal space) i0_reciprocal120100000.0000
Solution quality estimate total_estimate0.8967
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.6 Å
Skewness Skewness skewness0.067
Kurtosis Kurtosis kurtosis-0.498
Angular range angular_range— – 0.2700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15660000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.992
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id4d8pA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id4d8pA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4d8pB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id4d8pB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4d8pC01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id4d8pC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4d8pD01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id4d8pD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)