8vcy

Human TCR A2.13 in complex with DQ8-InsC8-15NPY

Method: X-RAY DIFFRACTION D_max: 129.1 Å Quality: GOOD

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

MHC class II HLA-DQ-alpha chain

Homo sapiens

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 1–184	Mutation：I75C	MHC class II HLA-DQ-beta-1 × 1 （O19707） Hybrid insulin peptide (HIP; InsC8-15-NPY68-74) × 1 T-CELL-RECEPTOR, TCR A2.13 alpha × 1 T-CELL-RECEPTOR, TCR A2.13 beta × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 5 PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；0.2 M Potassium sodium tartrate, 14% PEG 20,000 with seeding C8 silver bullet (Hampton Research)	Resolution 2.60 Å R-free 0.225

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 8VCY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4Z7U S13 complex Deposited 2015-04-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–184（184 aa） Fragment：UNP residues 1-184	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；140 mM Na-acetate, 0.1 M Bis-Tris-Propane pH 7.5, 15% PEG8000	Resolution 2.70 Å R-free 0.220
4Z7U S13 complex Deposited 2015-04-08	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 C 1–184（184 aa） Fragment：UNP residues 1-184	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；140 mM Na-acetate, 0.1 M Bis-Tris-Propane pH 7.5, 15% PEG8000	Resolution 2.70 Å R-free 0.220
4Z7V L3-12 complex Deposited 2015-04-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–184（184 aa） Fragment：UNP residues 1-184	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；80 mM Na-acetate, 0.1 M Bis-Tris-Propane pH 6.5, 16% PEG8000	Resolution 2.65 Å R-free 0.226
4Z7V L3-12 complex Deposited 2015-04-08	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 C 1–184（184 aa） Fragment：UNP residues 1-184	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；80 mM Na-acetate, 0.1 M Bis-Tris-Propane pH 6.5, 16% PEG8000	Resolution 2.65 Å R-free 0.226
4Z7W T316 complex Deposited 2015-04-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–184（184 aa） Fragment：UNP residues 1-184	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；0.32 M (NH4)2SO4, 0.1 M HEPES pH 7.8, 20% PEG3350	Resolution 2.89 Å R-free 0.247
4Z7W T316 complex Deposited 2015-04-08	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 C 1–184（184 aa） Fragment：UNP residues 1-184	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.32 M (NH4)2SO4, 0.1 M HEPES pH 7.8, 20% PEG3350	Resolution 2.89 Å R-free 0.247
6DFX human diabetogenic TCR T1D3 in complex with DQ8-p8E9E peptide Deposited 2018-05-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 3–184（182 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；10% PEG 8000, 100mM cacodylate pH6.2, 400mM NaCl	Resolution 2.03 Å R-free 0.217
6DFX human diabetogenic TCR T1D3 in complex with DQ8-p8E9E peptide Deposited 2018-05-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 3–184（182 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；10% PEG 8000, 100mM cacodylate pH6.2, 400mM NaCl	Resolution 2.03 Å R-free 0.217
6XC9 Immune receptor complex Deposited 2020-06-08	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–184（184 aa）	Mutation：I72C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；13% PEG 8000, 0.2 M Potassium dihydrogen phosphate	Resolution 2.40 Å R-free 0.219
6XC9 Immune receptor complex Deposited 2020-06-08	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 1–184（184 aa）	Mutation：I72C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；13% PEG 8000, 0.2 M Potassium dihydrogen phosphate	Resolution 2.40 Å R-free 0.219
6XCO Immune receptor complex Deposited 2020-06-08	Different mutation/modification 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 1–184（184 aa）	Mutation：I72C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 6 CAC CACODYLATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293.15 K；0.1 M calcium acetate, 0.1 M sodium cacodylate pH 5.5, 13% polyethylene glycol (PEG) 20,000	Resolution 2.90 Å R-free 0.247
6XCP Immune receptor complex Deposited 2020-06-08	Different mutation/modification 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 1–184（184 aa）	Mutation：I72C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；13% PEG 8000, 0.2M Potassium dihydrogen phosphate	Resolution 3.30 Å R-free 0.268
8VCX Human TCR A2.13 in complex with DQ8-InsCpep Deposited 2023-12-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–185（185 aa）	Mutation：C75I	PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；0.2 M Potassium sodium tartrate, 24% PEG 3350	Resolution 2.59 Å R-free 0.238
8VD0 Human TCR ET650-4 in complex with DQ8-InsC8-15-IAPP2 Deposited 2023-12-14	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 A 1–185（185 aa）	Mutation：I75C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 4 PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；0.2 M K Na tartrate, 15% w/v PEG 20,000 with seeding and additive C8 silver bullet	Resolution 2.40 Å R-free 0.220
8VD0 Human TCR ET650-4 in complex with DQ8-InsC8-15-IAPP2 Deposited 2023-12-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 1–185（185 aa）	Mutation：I75C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 8 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；0.2 M K Na tartrate, 15% w/v PEG 20,000 with seeding and additive C8 silver bullet	Resolution 2.40 Å R-free 0.220
8VD2 Human TCR ET650-4 in complex with DQ8-InsC8-15-IAPP1 Deposited 2023-12-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–185（185 aa）	Mutation：I75C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；0.2 M potassium dihydrogen phosphate (KH2PO4), 15% w/v PEG 20,000 with seeding and additive 30 mM MnCl2	Resolution 2.90 Å R-free 0.259
8VDD Crystal structure of Proinsulin C-peptide bound to HLA-DQ8 Deposited 2023-12-14	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 1–184（184 aa）	Mutation：I75C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；0.2 M K Na tartrate, 14% w/v PEG 20,000 with seeding and additive C8 silver bullet	Resolution 2.60 Å R-free 0.280
8VDU Crystal structure of hybrid insulin peptide (InsC8-15-IAPP74-80) bound to HLA-DQ8 Deposited 2023-12-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–184（184 aa） Chain D 1–184（184 aa） Chain G 1–184（184 aa） Chain J 1–184（184 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；0.2 M Monopotassium phosphate, 17% PEG 8K	Resolution 3.50 Å R-free 0.246

12 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q30069_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–184； UniProt 1–184

MHC class II HLA-DQ-beta-1

Homo sapiens

UniProt O19707

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain B； UniProt 1–192	Not recorded	MHC class II HLA-DQ-alpha chain × 1 （Q30069） Hybrid insulin peptide (HIP; InsC8-15-NPY68-74) × 1 T-CELL-RECEPTOR, TCR A2.13 alpha × 1 T-CELL-RECEPTOR, TCR A2.13 beta × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 5 PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；0.2 M Potassium sodium tartrate, 14% PEG 20,000 with seeding C8 silver bullet (Hampton Research)	Resolution 2.60 Å R-free 0.225

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8VCY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4Z7U S13 complex Deposited 2015-04-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–192（192 aa） Fragment：UNP residues 1-192	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；140 mM Na-acetate, 0.1 M Bis-Tris-Propane pH 7.5, 15% PEG8000	Resolution 2.70 Å R-free 0.220
4Z7U S13 complex Deposited 2015-04-08	Different construct 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 1–192（192 aa） Fragment：UNP residues 1-192	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；140 mM Na-acetate, 0.1 M Bis-Tris-Propane pH 7.5, 15% PEG8000	Resolution 2.70 Å R-free 0.220
4Z7V L3-12 complex Deposited 2015-04-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–192（192 aa） Fragment：UNP residues 1-192	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；80 mM Na-acetate, 0.1 M Bis-Tris-Propane pH 6.5, 16% PEG8000	Resolution 2.65 Å R-free 0.226
4Z7V L3-12 complex Deposited 2015-04-08	Different construct 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 1–192（192 aa） Fragment：UNP residues 1-192	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；80 mM Na-acetate, 0.1 M Bis-Tris-Propane pH 6.5, 16% PEG8000	Resolution 2.65 Å R-free 0.226
4Z7W T316 complex Deposited 2015-04-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–192（192 aa） Fragment：UNP residues 1-192	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；0.32 M (NH4)2SO4, 0.1 M HEPES pH 7.8, 20% PEG3350	Resolution 2.89 Å R-free 0.247
4Z7W T316 complex Deposited 2015-04-08	Different construct 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 1–192（192 aa） Fragment：UNP residues 1-192	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.32 M (NH4)2SO4, 0.1 M HEPES pH 7.8, 20% PEG3350	Resolution 2.89 Å R-free 0.247
5KSA Bel602-DQ8.5-glia-gamma1 complex Deposited 2016-07-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–192（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；0.1 M Ca-Acetate, 21 % PEG3350, Tris pH 8.0	Resolution 2.00 Å R-free 0.206
5KSB T15-DQ8.5-glia-gamma1 complex Deposited 2016-07-08	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–192（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；8% Tacsimate pH 7.5, 20% PEG3350	Resolution 2.90 Å R-free 0.254
5KSB T15-DQ8.5-glia-gamma1 complex Deposited 2016-07-08	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 1–192（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；8% Tacsimate pH 7.5, 20% PEG3350	Resolution 2.90 Å R-free 0.254
5UJT Crystal structure of human HLA-DQ8 in complex with insulin mimotope binding in register 3 Deposited 2017-01-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 3–191（189 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；278 K；15% PEG3350, 100mM Tacsimate	Resolution 1.94 Å R-free 0.238
5UJT Crystal structure of human HLA-DQ8 in complex with insulin mimotope binding in register 3 Deposited 2017-01-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 3–191（189 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；278 K；15% PEG3350, 100mM Tacsimate	Resolution 1.94 Å R-free 0.238
5UJT Crystal structure of human HLA-DQ8 in complex with insulin mimotope binding in register 3 Deposited 2017-01-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 3–191（189 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；278 K；15% PEG3350, 100mM Tacsimate	Resolution 1.94 Å R-free 0.238
6XCO Immune receptor complex Deposited 2020-06-08	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 1–192（192 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 6 CAC CACODYLATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293.15 K；0.1 M calcium acetate, 0.1 M sodium cacodylate pH 5.5, 13% polyethylene glycol (PEG) 20,000	Resolution 2.90 Å R-free 0.247
6XCP Immune receptor complex Deposited 2020-06-08	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–192（192 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；13% PEG 8000, 0.2M Potassium dihydrogen phosphate	Resolution 3.30 Å R-free 0.268
8VCX Human TCR A2.13 in complex with DQ8-InsCpep Deposited 2023-12-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–192（192 aa）	Not recorded	PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；0.2 M Potassium sodium tartrate, 24% PEG 3350	Resolution 2.59 Å R-free 0.238
8VD0 Human TCR ET650-4 in complex with DQ8-InsC8-15-IAPP2 Deposited 2023-12-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–192（192 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 4 PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；0.2 M K Na tartrate, 15% w/v PEG 20,000 with seeding and additive C8 silver bullet	Resolution 2.40 Å R-free 0.220
8VD0 Human TCR ET650-4 in complex with DQ8-InsC8-15-IAPP2 Deposited 2023-12-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 1–192（192 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 8 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；0.2 M K Na tartrate, 15% w/v PEG 20,000 with seeding and additive C8 silver bullet	Resolution 2.40 Å R-free 0.220
8VD2 Human TCR ET650-4 in complex with DQ8-InsC8-15-IAPP1 Deposited 2023-12-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–192（192 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；0.2 M potassium dihydrogen phosphate (KH2PO4), 15% w/v PEG 20,000 with seeding and additive 30 mM MnCl2	Resolution 2.90 Å R-free 0.259
8VDD Crystal structure of Proinsulin C-peptide bound to HLA-DQ8 Deposited 2023-12-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–192（192 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；0.2 M K Na tartrate, 14% w/v PEG 20,000 with seeding and additive C8 silver bullet	Resolution 2.60 Å R-free 0.280
8VDU Crystal structure of hybrid insulin peptide (InsC8-15-IAPP74-80) bound to HLA-DQ8 Deposited 2023-12-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 1–192（192 aa） Chain E 1–192（192 aa） Chain H 1–192（192 aa） Chain K 1–192（192 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；0.2 M Monopotassium phosphate, 17% PEG 8K	Resolution 3.50 Å R-free 0.246

13 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	O19707_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–192； UniProt 1–192

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8vcy
Deposition date deposition_date	2023-12-14
Structure title title	Human TCR A2.13 in complex with DQ8-InsC8-15NPY
Keywords keywords	Immune receptor complex, 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	36.15 Å
Radius of gyration Rg (electron density) rg_electron	36.55 Å
Forward intensity I(0) i0	133021000.00
Molecular weight molecular_weight	90489.0 kDa
Excluded volume excluded_volume	112140 Å³
Envelope volume envelope_volume	148500 Å³
Hydration-shell volume shell_volume	36951 Å³
Envelope diameter envelope_diameter	137.5 Å
Shell Rg shell_rg	38.75 Å
Envelope Rg envelope_rg	36.98 Å
Shape Rg shape_rg	36.55 Å
Total Rg total_rg	36.71 Å
Total atoms total_atoms	6374
Residues n_residues	802
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	129.1 Å
Rg (real space) rg_real	36.67 Å
Rg uncertainty (real space) rg_real_error	1.64 Å
I(0) (real space) i0_real	1.3300e+08
I(0) uncertainty (real space) i0_real_error	2.4880e+06
Rg (reciprocal space) rg_reciprocal	36.35 Å
I(0) (reciprocal space) i0_reciprocal	133000000.0000
Solution quality estimate total_estimate	0.7704
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.3 Å
Skewness Skewness skewness	0.682
Kurtosis Kurtosis kurtosis	-0.017
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16350000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.632; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.588; Smooth: 0.529

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	MHC class II HLA-DQ-alpha chain
Molecular weight formula_weight	21124.5 kDa
Mutation mutation	I75C
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	6519

EDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNCVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHWEPES

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	MHC class II HLA-DQ-beta-1
Molecular weight formula_weight	22605.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

RDSPEDFVYQFKGMCYFTNGTERVRLVTRYIYNREEYARFDSDVGVYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQNPIIVEWRAQS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	Hybrid insulin peptide (HIP; InsC8-15-NPY68-74)
Molecular weight formula_weight	1433.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GQVELGGGSSPETCI

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Trichoplusia ni

Entity 4 Entity 4 polymer

Description description	T-CELL-RECEPTOR, TCR A2.13 alpha
Molecular weight formula_weight	22633.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MKTTQPPSMDCAEGRAANLPCNHSTISGNEYVYWYRQIHSQGPQYIIHGLKNNETNEMASLIITEDRKSSTLILPHATLRDTAVYYCIVSHNAGNMLTFGGGTRLMVKPHIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	T-CELL-RECEPTOR, TCR A2.13 beta
Molecular weight formula_weight	27076.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

GVTQTPRYLIKTRGQQVTLSCSPISGHRSVSWYQQTPGQGLQFLFEYFSETQRNKGNFPGRFSGRQFSNSRSEMNVSTLELGDSALYLCASSLERETQYFGPGTRLLVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 8 Entity 8 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	145

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8. Citations (1)

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Unit-cell length a length_a	67.803 Å
Unit-cell length b length_b	106.695 Å
Unit-cell length c length_c	132.962 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	4

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

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	49.510 Å
R factor r_factor	0.1865
R_work r_work	0.1845
R_free r_free	0.2250

fit	/app/data/saxs_computation/vc/8vcy/8vcy.fit
pddf	/app/data/pr_computation/vc/8vcy/8vcy.pr.out
profile	/app/data/saxs_computation/vc/8vcy/8vcy.dat

Human TCR A2.13 in complex with DQ8-InsC8-15NPY

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

MHC class II HLA-DQ-alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

MHC class II HLA-DQ-beta-1

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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)