5dmk

Crystal Structure of IAg7 in complex with RLGL-WE14

Method: X-RAY DIFFRACTION D_max: 129.4 Å Quality: EXCELLENT

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

H-2 class II histocompatibility antigen, A-D alpha chain

Mus musculus

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 26–198	Not recorded	beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein × 1 （Q31135） FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；1M Ammonium Citrate	Resolution 2.45 Å R-free 0.260
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 26–198	Not recorded	beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein × 1 （Q31135）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；1M Ammonium Citrate	Resolution 2.45 Å R-free 0.260
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 26–198	Not recorded	beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein × 1 （Q31135） FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；1M Ammonium Citrate	Resolution 2.45 Å R-free 0.260
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 26–198	Not recorded	beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein × 1 （Q31135）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；1M Ammonium Citrate	Resolution 2.45 Å R-free 0.260

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 5DMK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ES0 CRYSTAL STRUCTURE OF THE MURINE CLASS II ALLELE I-A(G7) COMPLEXED WITH THE GLUTAMIC ACID DECARBOXYLASE (GAD65) PEPTIDE 207-220 Deposited 2000-04-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 24–205（182 aa） Fragment：ALPHA CHAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16-18% PEG 4000, 0.2 M LICL (PH 6.6), 1% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.60 Å R-free 0.258
1F3J HISTOCOMPATIBILITY ANTIGEN I-AG7 Deposited 2000-06-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 27–208（182 aa） Fragment：A-D ALPHA CHAIN Chain D 27–208（182 aa） Fragment：A-D ALPHA CHAIN	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.4；pH 4.4	Resolution 3.10 Å R-free 0.299
1IAO CLASS II MHC I-AD IN COMPLEX WITH OVALBUMIN PEPTIDE 323-339 Deposited 1998-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–209（186 aa） Chain B 28–216（189 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；32% PEG 600, 0.1 IMIDAZOLE MALATE, PH 5.5	Resolution 2.60 Å R-free 0.320
1IAO CLASS II MHC I-AD IN COMPLEX WITH OVALBUMIN PEPTIDE 323-339 Deposited 1998-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 24–209（186 aa） Chain B 28–216（189 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；32% PEG 600, 0.1 IMIDAZOLE MALATE, PH 5.5	Resolution 2.60 Å R-free 0.320
2IAD CLASS II MHC I-AD IN COMPLEX WITH AN INFLUENZA HEMAGGLUTININ PEPTIDE 126-138 Deposited 1998-03-13	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 24–209（186 aa） Fragment：RESIDUES 126P - 138P OF CHAIN B ARE COVALENTLY LINKED INFLUENZA HEMAGGLUTININ PEPTIDE	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；19% PEG 8000 0.2 M TRIS, PH 7.4	Resolution 2.40 Å R-free 0.308
2IAD CLASS II MHC I-AD IN COMPLEX WITH AN INFLUENZA HEMAGGLUTININ PEPTIDE 126-138 Deposited 1998-03-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 24–209（186 aa） Fragment：RESIDUES 126P - 138P OF CHAIN B ARE COVALENTLY LINKED INFLUENZA HEMAGGLUTININ PEPTIDE	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；19% PEG 8000 0.2 M TRIS, PH 7.4	Resolution 2.40 Å R-free 0.308
3CUP Crystal structure of the MHC class II molecule I-Ag7 in complex with the peptide GAD221-235 Deposited 2008-04-16	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 24–205（182 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；295 K；0.1M Hepes pH 7.5, 28% PEG 8000, 2% Jeffamine 900, VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 7.50	Resolution 3.09 Å R-free 0.286
3MBE TCR 21.30 in complex with MHC class II I-Ag7HEL(11-27) Deposited 2010-03-25	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 A 24–205（182 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；20% PEG4000, 0.2M K formate, 0.1M Na Cacodylate., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.89 Å R-free 0.281
3MBE TCR 21.30 in complex with MHC class II I-Ag7HEL(11-27) Deposited 2010-03-25	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 E 24–205（182 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；20% PEG4000, 0.2M K formate, 0.1M Na Cacodylate., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.89 Å R-free 0.281
6BLQ Crystal Structure of IAg7 in complex with insulin mimotope p8E9E Deposited 2017-11-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 24–208（185 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 IPA ISOPROPYL ALCOHOL × 4 EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；20% PEG3350, 100mM sodium citrate at pH5.0, 5% isopropanol	Resolution 1.80 Å R-free 0.203
6BLR Crystal Structure of IAg7 in complex with insulin mimotope p8E9E6SS Deposited 2017-11-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–208（183 aa）	Mutation：N64C	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；15% PEG4000, 10mM sodium citrate at pH5.0, 100 mM MgCl2	Resolution 1.96 Å R-free 0.228
6BLX Crystal structure of IAg7 in complex with insulin mimotope p8G9E Deposited 2017-11-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–208（183 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 4 FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；18% PEG20000, 100mM sodium citrate at pH5.0	Resolution 2.32 Å R-free 0.220
6DFS mouse TCR I.29 in complex with IAg7-p8E9E6ss Deposited 2018-05-15	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 C 26–208（183 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；12% PEG 20000, 100mM bicine pH9.0, 20% ethylene glycol	Resolution 3.10 Å R-free 0.285
6DFW TCR 8F10 in complex with IAg7-p8G9E Deposited 2018-05-15	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 26–208（183 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；11% PEG 3350, 100mM formate pH7.0	Resolution 3.20 Å R-free 0.297
6DFW TCR 8F10 in complex with IAg7-p8G9E Deposited 2018-05-15	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 26–208（183 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；11% PEG 3350, 100mM formate pH7.0	Resolution 3.20 Å R-free 0.297
7QHP Structure of I-Ag7 with a bound hybrid insulin peptide Deposited 2021-12-13	Different construct Different mutation/modification 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 24–218（195 aa）	Mutation：I91C	GOL GLYCEROL × 2 SO4 SULFATE ION × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.17 M ammonium sulfate, 25% w/v PEG 4000, 15% glycerol	Resolution 1.82 Å R-free 0.219
7RDV TFH TCR bound to MHC Class II IAd presenting aggrecan epitope Deposited 2021-07-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 28–205（178 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293.15 K；0.1M Sodium Cacodylate pH6.0 15% w/v PEG4000	Resolution 2.90 Å R-free 0.265
7Z50 Structure of the highly diabetogenic 4.1-T cell receptor targeting a hybrid insulin peptide bound to I-Ag7. Deposited 2022-03-06	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 A 24–218（195 aa）	Mutation：I91C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1 M MgCl2, 0.1 M Na HEPES pH 7.0, 15% w/v PEG 4000	Resolution 2.65 Å R-free 0.261
7Z50 Structure of the highly diabetogenic 4.1-T cell receptor targeting a hybrid insulin peptide bound to I-Ag7. Deposited 2022-03-06	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 C 24–218（195 aa）	Mutation：I91C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 EDO 1,2-ETHANEDIOL × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1 M MgCl2, 0.1 M Na HEPES pH 7.0, 15% w/v PEG 4000	Resolution 2.65 Å R-free 0.261

14 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HA2D_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–173； UniProt 26–198 Author chain C； PDBConstruct 1–173； UniProt 26–198 Author chain E； PDBConstruct 1–173； UniProt 26–198 Author chain G； PDBConstruct 1–173； UniProt 26–198

beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein

Mus musculus

UniProt Q31135

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 31–215	Fragment：UNP residues 31-215	H-2 class II histocompatibility antigen, A-D alpha chain × 1 （P04228） FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；1M Ammonium Citrate	Resolution 2.45 Å R-free 0.260
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 31–215	Fragment：UNP residues 31-215	H-2 class II histocompatibility antigen, A-D alpha chain × 1 （P04228）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；1M Ammonium Citrate	Resolution 2.45 Å R-free 0.260
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 31–215	Fragment：UNP residues 31-215	H-2 class II histocompatibility antigen, A-D alpha chain × 1 （P04228） FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；1M Ammonium Citrate	Resolution 2.45 Å R-free 0.260
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 31–215	Fragment：UNP residues 31-215	H-2 class II histocompatibility antigen, A-D alpha chain × 1 （P04228）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；1M Ammonium Citrate	Resolution 2.45 Å R-free 0.260

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5DMK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1F3J HISTOCOMPATIBILITY ANTIGEN I-AG7 Deposited 2000-06-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 31–217（187 aa） Fragment：BETA CHAIN Chain E 31–217（187 aa） Fragment：BETA CHAIN	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.4；pH 4.4	Resolution 3.10 Å R-free 0.299
3CUP Crystal structure of the MHC class II molecule I-Ag7 in complex with the peptide GAD221-235 Deposited 2008-04-16	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 B 28–214（187 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；295 K；0.1M Hepes pH 7.5, 28% PEG 8000, 2% Jeffamine 900, VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 7.50	Resolution 3.09 Å R-free 0.286
3MBE TCR 21.30 in complex with MHC class II I-Ag7HEL(11-27) Deposited 2010-03-25	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 28–214（187 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；20% PEG4000, 0.2M K formate, 0.1M Na Cacodylate., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.89 Å R-free 0.281
3MBE TCR 21.30 in complex with MHC class II I-Ag7HEL(11-27) Deposited 2010-03-25	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 F 28–214（187 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；20% PEG4000, 0.2M K formate, 0.1M Na Cacodylate., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.89 Å R-free 0.281
6BLQ Crystal Structure of IAg7 in complex with insulin mimotope p8E9E Deposited 2017-11-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 30–217（188 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 IPA ISOPROPYL ALCOHOL × 4 EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；20% PEG3350, 100mM sodium citrate at pH5.0, 5% isopropanol	Resolution 1.80 Å R-free 0.203
6BLR Crystal Structure of IAg7 in complex with insulin mimotope p8E9E6SS Deposited 2017-11-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 30–217（188 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；15% PEG4000, 10mM sodium citrate at pH5.0, 100 mM MgCl2	Resolution 1.96 Å R-free 0.228
6BLX Crystal structure of IAg7 in complex with insulin mimotope p8G9E Deposited 2017-11-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 30–217（188 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 4 FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；18% PEG20000, 100mM sodium citrate at pH5.0	Resolution 2.32 Å R-free 0.220
6DFS mouse TCR I.29 in complex with IAg7-p8E9E6ss Deposited 2018-05-15	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 D 30–217（188 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；12% PEG 20000, 100mM bicine pH9.0, 20% ethylene glycol	Resolution 3.10 Å R-free 0.285
6DFW TCR 8F10 in complex with IAg7-p8G9E Deposited 2018-05-15	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 30–217（188 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；11% PEG 3350, 100mM formate pH7.0	Resolution 3.20 Å R-free 0.297
6DFW TCR 8F10 in complex with IAg7-p8G9E Deposited 2018-05-15	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 30–217（188 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；11% PEG 3350, 100mM formate pH7.0	Resolution 3.20 Å R-free 0.297
7Z50 Structure of the highly diabetogenic 4.1-T cell receptor targeting a hybrid insulin peptide bound to I-Ag7. Deposited 2022-03-06	Different construct 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 28–224（197 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1 M MgCl2, 0.1 M Na HEPES pH 7.0, 15% w/v PEG 4000	Resolution 2.65 Å R-free 0.261
7Z50 Structure of the highly diabetogenic 4.1-T cell receptor targeting a hybrid insulin peptide bound to I-Ag7. Deposited 2022-03-06	Different construct 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 28–224（197 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 EDO 1,2-ETHANEDIOL × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1 M MgCl2, 0.1 M Na HEPES pH 7.0, 15% w/v PEG 4000	Resolution 2.65 Å R-free 0.261

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

View Construct and Data Evidence

UniProt name	Q31135_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 28–212； UniProt 31–215 Author chain D； PDBConstruct 28–212； UniProt 31–215 Author chain F； PDBConstruct 28–212； UniProt 31–215 Author chain H； PDBConstruct 28–212； UniProt 31–215

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.

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	5dmk
Deposition date deposition_date	2015-09-08
Structure title title	Crystal Structure of IAg7 in complex with RLGL-WE14
Keywords keywords	Chromogranin A, Type I Diabetes, T cell, fusion protein, 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	41.10 Å
Radius of gyration Rg (electron density) rg_electron	40.42 Å
Forward intensity I(0) i0	423352000.00
Molecular weight molecular_weight	167750.0 kDa
Excluded volume excluded_volume	209320 Å³
Envelope volume envelope_volume	282880 Å³
Hydration-shell volume shell_volume	58706 Å³
Envelope diameter envelope_diameter	131.5 Å
Shell Rg shell_rg	45.88 Å
Envelope Rg envelope_rg	39.67 Å
Shape Rg shape_rg	40.42 Å
Total Rg total_rg	40.70 Å
Total atoms total_atoms	11867
Residues n_residues	1445
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	129.4 Å
Rg (real space) rg_real	40.97 Å
Rg uncertainty (real space) rg_real_error	0.93 Å
I(0) (real space) i0_real	4.2340e+08
I(0) uncertainty (real space) i0_real_error	7.0350e+06
Rg (reciprocal space) rg_reciprocal	41.10 Å
I(0) (reciprocal space) i0_reciprocal	423400000.0000
Solution quality estimate total_estimate	0.9048
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	54.5 Å
Skewness Skewness skewness	0.105
Kurtosis Kurtosis kurtosis	-0.657
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	34890000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.957; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.890

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5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	H-2 class II histocompatibility antigen, A-D alpha chain
Molecular weight formula_weight	19659.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	12200

DIEADHVGFYGTTVYQSPGDIGQYTHEFDGDELFYVDLDKKKTVWRLPEFGQLILFEPQGGLQNIAAEKHNLGILTKRSNFTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVTDGVYETSFLVNRDHSFHKLSYLTFIPSDDDIYDCKVEHWGLE

来源 Source

来源生物 organism	Mus musculus
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein
Molecular weight formula_weight	24925.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

SRLGLWSRMDQLAKELTAELVPRGSGSERHFVHQFKGECYFTNGTQRIRLVTRYIYNREEYLRFDSDVGEYRAVTELGRHSAEYYNKQYLERTRAELDTACRHNYEETEVPTSLRRLEQPNVAISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPHQGEVYTCHVEHPSLKSPITVEWR

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Trichoplusia ni

Entity 3 Entity 3 non-polymer

Description description	CITRATE ANION
Molecular weight formula_weight	189.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	333

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7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d5dmka1
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.19.1.1 — MHC antigen-recognition domain

Domain ID domain_id	d5dmka2
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.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d5dmkc1
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.19.1.1 — MHC antigen-recognition domain

Domain ID domain_id	d5dmkc2
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.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d5dmke1
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.19.1.1 — MHC antigen-recognition domain

Domain ID domain_id	d5dmke2
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.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d5dmkg1
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.19.1.1 — MHC antigen-recognition domain

Domain ID domain_id	d5dmkg2
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.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (16 domains)

Domain ID domain_id	5dmkA01
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	5dmkA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5dmkB01
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	5dmkB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5dmkC01
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	5dmkC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5dmkD01
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	5dmkD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5dmkE01
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	5dmkE02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5dmkF01
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	5dmkF02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5dmkG01
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	5dmkG02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5dmkH01
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	5dmkH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

8. Citations (1)

▶

Unit-cell length a length_a	161.765 Å
Unit-cell length b length_b	161.765 Å
Unit-cell length c length_c	204.162 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	32

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	44.866 Å
R factor r_factor	0.2138
R_work r_work	0.2113
R_free r_free	0.2600

fit	/app/data/saxs_computation/dm/5dmk/5dmk.fit
pddf	/app/data/pr_computation/dm/5dmk/5dmk.pr.out
profile	/app/data/saxs_computation/dm/5dmk/5dmk.dat

Crystal Structure of IAg7 in complex with RLGL-WE14

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

H-2 class II histocompatibility antigen, A-D alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein

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 (4)

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 water

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

CATH v4.4 (16 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)