3ecb

Crystal structure of mouse H-2Dd in complex with peptide P18-I10 derived from human immunodeficiency virus envelope glycoprotein 120

Method: X-RAY DIFFRACTION D_max: 72.2 Å Quality: EXCELLENT

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

H-2 class I histocompatibility antigen, D-D alpha chain

Mus musculus

UniProt P01900

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 26–301	Fragment：UNP residues 26 to 298	Beta-2 microglobulin × 1 （Q91XJ8） Peptide P18-I10 from HIV gp160 × 1 （P19551） EDO 1,2-ETHANEDIOL × 6 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；16% PEG 3350, 0.2M Magnesium formate, , pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.70 Å R-free 0.227

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 3ECB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BII THE CRYSTAL STRUCTURE OF H-2DD MHC CLASS I IN COMPLEX WITH THE HIV-1 DERIVED PEPTIDE P18-110 Deposited 1998-06-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–365（365 aa） Fragment：HEAVY CHAIN, EXTRACELLULAR DOMAINS	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.40 Å R-free 0.323
1DDH MHC CLASS I H-2DD HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND AN IMMUNODOMINANT PEPTIDE P18-I10 FROM THE HUMAN IMMUNODEFICIENCY VIRUS ENVELOPE GLYCOPROTEIN 120 Deposited 1998-06-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–298（273 aa） Fragment：EXTRACELLULAR DOMAINS	Mutation：G1M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 3.10 Å R-free 0.337
1QO3 Complex between NK cell receptor Ly49A and its MHC class I ligand H-2Dd Deposited 1999-11-01	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 26–301（276 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.30 Å R-free 0.238
1QO3 Complex between NK cell receptor Ly49A and its MHC class I ligand H-2Dd Deposited 1999-11-01	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 A 26–301（276 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.30 Å R-free 0.238
3DMM Crystal structure of the CD8 alpha beta/H-2Dd complex Deposited 2008-07-01	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 26–299（274 aa） Fragment：Alpha-1,2,3 regions: Residues 26-299	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；291 K；12% PEG 3000, 0.05M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.60 Å R-free 0.292
3E6F MHC CLASS I H-2Dd Heavy chain complexed with Beta-2 Microglobulin and a variant peptide, PA9, from the Human immunodeficiency virus (BaL) envelope glycoprotein 120 Deposited 2008-08-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–298（273 aa） Fragment：UNP residues 26 to 298	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；12% PEG 20000, 0.1M MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.41 Å R-free 0.271
3E6H MHC CLASS I H-2Dd heavy chain complexed with Beta-2 Microglobulin and a variant peptide, PI10, from the human immunodeficiency virus (BaL) envelope glycoprotein 120 Deposited 2008-08-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–299（274 aa） Fragment：EXTRACELLULAR DOMAINS	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；11% PEG20000,0.1M MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.10 Å R-free 0.250
5IVX Crystal Structure of B4.2.3 T-Cell Receptor and H2-Dd P18-I10 Complex Deposited 2016-03-21	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 26–301（276 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；15% PEG 3350, 0.1M HEPES, 0.15M Magnesium Chloride	Resolution 2.10 Å R-free 0.220
5KD4 Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a Variant of Peptide (PVI10) of HIV gp120 MN Isolate (IGPGRAFYVI) Deposited 2016-06-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–301（276 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；15% PEG 20000, 0.1M Sodium Cacodylate	Resolution 3.05 Å R-free 0.224
5KD4 Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a Variant of Peptide (PVI10) of HIV gp120 MN Isolate (IGPGRAFYVI) Deposited 2016-06-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 26–301（276 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；15% PEG 20000, 0.1M Sodium Cacodylate	Resolution 3.05 Å R-free 0.224
5KD7 Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a Variant of Peptide (PV9) of HIV gp120 MN Isolate (IGPGRAFYV) Deposited 2016-06-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–300（275 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；12% PEG 20000, 0.1M MES buffer	Resolution 2.35 Å R-free 0.249
5KD7 Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a Variant of Peptide (PV9) of HIV gp120 MN Isolate (IGPGRAFYV) Deposited 2016-06-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 26–300（275 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；12% PEG 20000, 0.1M MES buffer	Resolution 2.35 Å R-free 0.249
5KD7 Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a Variant of Peptide (PV9) of HIV gp120 MN Isolate (IGPGRAFYV) Deposited 2016-06-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 26–300（275 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；12% PEG 20000, 0.1M MES buffer	Resolution 2.35 Å R-free 0.249
5KD7 Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a Variant of Peptide (PV9) of HIV gp120 MN Isolate (IGPGRAFYV) Deposited 2016-06-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 26–300（275 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；12% PEG 20000, 0.1M MES buffer	Resolution 2.35 Å R-free 0.249
5T7G Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a Variant of Peptide (PT9) of HIV gp120 MN Isolate (IGPGRAFYT) Deposited 2016-09-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–300（275 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；12% PEG 10000, 0.1M MES buffer	Resolution 1.96 Å R-free 0.238
5T7G Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a Variant of Peptide (PT9) of HIV gp120 MN Isolate (IGPGRAFYT) Deposited 2016-09-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 26–300（275 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；12% PEG 10000, 0.1M MES buffer	Resolution 1.96 Å R-free 0.238
5WER Crystal Structure of TAPBPR and H2-Dd complex Deposited 2017-07-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–301（276 aa） Fragment：residues 26-301	Mutation：S73C	EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；291 K；1.0 M ammonium sulfate, 0.1 M TRIS pH 8.8, 0.2 M NaCl, 0.15-0.20 M sodium citrate, 2%-5% PEG 400	Resolution 3.41 Å R-free 0.269
5WER Crystal Structure of TAPBPR and H2-Dd complex Deposited 2017-07-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 26–301（276 aa） Fragment：residues 26-301	Mutation：S73C	EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；291 K；1.0 M ammonium sulfate, 0.1 M TRIS pH 8.8, 0.2 M NaCl, 0.15-0.20 M sodium citrate, 2%-5% PEG 400	Resolution 3.41 Å R-free 0.269
5WER Crystal Structure of TAPBPR and H2-Dd complex Deposited 2017-07-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 26–301（276 aa） Fragment：residues 26-301	Mutation：S73C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；291 K；1.0 M ammonium sulfate, 0.1 M TRIS pH 8.8, 0.2 M NaCl, 0.15-0.20 M sodium citrate, 2%-5% PEG 400	Resolution 3.41 Å R-free 0.269
5WER Crystal Structure of TAPBPR and H2-Dd complex Deposited 2017-07-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 26–301（276 aa） Fragment：residues 26-301	Mutation：S73C	GOL GLYCEROL × 1 1PE PENTAETHYLENE GLYCOL × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；291 K；1.0 M ammonium sulfate, 0.1 M TRIS pH 8.8, 0.2 M NaCl, 0.15-0.20 M sodium citrate, 2%-5% PEG 400	Resolution 3.41 Å R-free 0.269
5WES Crystal Structure H2-Dd with disulfide-linked 5mer peptide Deposited 2017-07-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–301（276 aa） Fragment：residues 26-301	Mutation：S73C	GLY GLYCINE × 1 LEU LEUCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；10-15% PEG 20000, 0.1M MES	Resolution 2.71 Å R-free 0.246
5WET Crystal Structure of H2-Dd with disulfide-linked 6mer peptide Deposited 2017-07-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–301（276 aa） Fragment：residues 26-301	Mutation：S73C	GLY GLYCINE × 1 LEU LEUCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；10-15% PEG 20000, 0.1M MES	Resolution 2.64 Å R-free 0.243
5WEU Crystal Structure of H2-Dd with disulfide-linked 10mer peptide Deposited 2017-07-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–301（276 aa） Fragment：residues 26-301	Mutation：S73C	EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；10% PEG 10K, 0.1M Cacodylate	Resolution 1.58 Å R-free 0.216
6NPR Crystal structure of H-2Dd with C84-C139 disulfide in complex with gp120 derived peptide P18-I10 Deposited 2019-01-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–301（276 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M Ammonium acetate, 0.1M Bis-Tris (5.5) and 25%PEG 3350	Resolution 2.37 Å R-free 0.251
6NPR Crystal structure of H-2Dd with C84-C139 disulfide in complex with gp120 derived peptide P18-I10 Deposited 2019-01-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 26–301（276 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M Ammonium acetate, 0.1M Bis-Tris (5.5) and 25%PEG 3350	Resolution 2.37 Å R-free 0.251
8D5E The complex of Gtf2b Peptide TGAASFDEF Presented by H2-Dd Deposited 2022-06-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–299（274 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；309.15 K；15% w/v PEG1500	Resolution 2.46 Å R-free 0.242
8D5F The complex of Gtf2b neoantigen TGAARFDEF Presented by H2-Dd Deposited 2022-06-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–299（274 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；309.15 K；20% PEG3350, 200 nM sodium tartrate dibasic dihydrate	Resolution 2.31 Å R-free 0.199
8FHL Structure of pyruvate dehydrogenase phosphatase regulatory subunit neoepitope presented by H2-Dd Deposited 2022-12-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–301（276 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2 M sodium isothiocyanate, 20% PEG4000	Resolution 2.19 Å R-free 0.248
8FHU Structure of Pyruvate dehydrogenase phosphatase regulatory subunit epitope presented by H2-Dd Deposited 2022-12-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–301（276 aa）	Not recorded	K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298.15 K；0.2M Potassium thiocyanate and 20% PEG 3350	Resolution 1.80 Å R-free 0.249
8FHU Structure of Pyruvate dehydrogenase phosphatase regulatory subunit epitope presented by H2-Dd Deposited 2022-12-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 26–301（276 aa）	Not recorded	K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298.15 K；0.2M Potassium thiocyanate and 20% PEG 3350	Resolution 1.80 Å R-free 0.249
8TQ4 Crystal structure of Fab M142 in complex with MHC-I (H2-Dd) Deposited 2023-08-06	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 A 26–298（273 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；10% PEG4000, 0.2 M sodium acetate, 0.1 M sodium citrate, pH 5.5	Resolution 3.59 Å R-free 0.270
8TQ4 Crystal structure of Fab M142 in complex with MHC-I (H2-Dd) Deposited 2023-08-06	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 E 26–298（273 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；10% PEG4000, 0.2 M sodium acetate, 0.1 M sodium citrate, pH 5.5	Resolution 3.59 Å R-free 0.270
8TQ7 Crystal structure of Fab.34.2.12 in complex with MHC-I (H2-Dd) Deposited 2023-08-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 26–298（273 aa） Chain C 26–298（273 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；12% PEG8000, 0.1 M MES, pH 6.5	Resolution 2.80 Å R-free 0.271
8TQ8 Crystal structure of Fab.34.5.8 in complex with MHC-I (H2-Dd) Deposited 2023-08-06	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 A 26–298（273 aa）	Not recorded	GOL GLYCEROL × 3 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；18% PEG4000, 0.1 M MES, pH 6.0, 0.12 M calcium acetate	Resolution 2.69 Å R-free 0.242
8TQ8 Crystal structure of Fab.34.5.8 in complex with MHC-I (H2-Dd) Deposited 2023-08-06	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 C 26–298（273 aa）	Not recorded	GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；18% PEG4000, 0.1 M MES, pH 6.0, 0.12 M calcium acetate	Resolution 2.69 Å R-free 0.242
8TQ9 Crystal structure of Fab.S19.8 in complex with MHC-I (H2-Dd) Deposited 2023-08-06	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 A 26–298（273 aa）	Not recorded	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；0.5 M ammonium sulfate, 0.1 M sodium citrate, pH 5.6, 1.0 M lithium sulfate	Resolution 2.90 Å R-free 0.240
9D72 CryoEM structure of anti-MHC-I Fab M1/42 complex with H2-Dd Deposited 2024-08-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 26–298（273 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.67 Å

24 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HA12_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–277； UniProt 26–301

Beta-2 microglobulin

Mus musculus

UniProt Q91XJ8

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 21–119	Fragment：UNP residues 21 to 119	H-2 class I histocompatibility antigen, D-D alpha chain × 1 （P01900） Peptide P18-I10 from HIV gp160 × 1 （P19551） EDO 1,2-ETHANEDIOL × 6 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；16% PEG 3350, 0.2M Magnesium formate, , pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.70 Å R-free 0.227

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3ECB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2QRI Crystal structure of a single chain trimer composed of the MHC I heavy chain H-2Kb WT, beta-2microglobulin, and ovalbumin-derived peptide. Deposited 2007-07-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–119（99 aa） Fragment：;Fusion protein of ovalbumin-derived peptide, linker, Beta-2 microglobulin, linker, and H-2 class I histocompatibility antigen K-B alpha chain extracellular domain ;	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；298 K；13% PEG 10000, 100 mM MES, pH 6.2, vapor diffusion, hanging drop, temperature 298K	Resolution 2.00 Å R-free 0.253
2QRI Crystal structure of a single chain trimer composed of the MHC I heavy chain H-2Kb WT, beta-2microglobulin, and ovalbumin-derived peptide. Deposited 2007-07-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 21–119（99 aa） Fragment：;Fusion protein of ovalbumin-derived peptide, linker, Beta-2 microglobulin, linker, and H-2 class I histocompatibility antigen K-B alpha chain extracellular domain ;	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；298 K；13% PEG 10000, 100 mM MES, pH 6.2, vapor diffusion, hanging drop, temperature 298K	Resolution 2.00 Å R-free 0.253
2QRS Crystal Structure of a single chain trimer composed of the MHC I heavy chain H-2Kb Y84A, beta-2microglobulin, and ovalbumin-derived peptide. Deposited 2007-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–119（99 aa） Fragment：;Fusion protein of ovalbumin-derived peptide, linker, Beta-2 microglobulin, linker, and H-2 class I histocompatibility antigen K-B alpha chain extracellular domain ;	Mutation：Y105A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；14% PEG 6000, 100 mM MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.252
2QRS Crystal Structure of a single chain trimer composed of the MHC I heavy chain H-2Kb Y84A, beta-2microglobulin, and ovalbumin-derived peptide. Deposited 2007-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 21–119（99 aa） Fragment：;Fusion protein of ovalbumin-derived peptide, linker, Beta-2 microglobulin, linker, and H-2 class I histocompatibility antigen K-B alpha chain extracellular domain ;	Mutation：Y105A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；14% PEG 6000, 100 mM MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.252
2QRT Crystal Structure of a disulfide trapped single chain trimer composed of the MHC I heavy chain H-2Kb Y84C, beta-2microglobulin, and ovalbumin-derived peptide. Deposited 2007-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–119（99 aa） Fragment：;Fusion protein of ovalbumin-derived peptide, linker, Beta-2 microglobulin, linker, and H-2 class I histocompatibility antigen K-B alpha chain extracellular domain ;	Mutation：Y105C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；298 K；13% PEG 6000, 100 mM MES, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.239
2QRT Crystal Structure of a disulfide trapped single chain trimer composed of the MHC I heavy chain H-2Kb Y84C, beta-2microglobulin, and ovalbumin-derived peptide. Deposited 2007-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 21–119（99 aa） Fragment：;Fusion protein of ovalbumin-derived peptide, linker, Beta-2 microglobulin, linker, and H-2 class I histocompatibility antigen K-B alpha chain extracellular domain ;	Mutation：Y105C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；298 K；13% PEG 6000, 100 mM MES, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.239
3C8K The crystal structure of Ly49C bound to H-2Kb Deposited 2008-02-12	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 21–119（99 aa） Fragment：UNP residues 21-119	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；2.0 M ammonium sulfate, 2% (volume/volume) PEG 400 and 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.90 Å R-free 0.263
3DMM Crystal structure of the CD8 alpha beta/H-2Dd complex Deposited 2008-07-01	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 21–119（99 aa） Fragment：Residues 21-119	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；291 K；12% PEG 3000, 0.05M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.60 Å R-free 0.292
3E6F MHC CLASS I H-2Dd Heavy chain complexed with Beta-2 Microglobulin and a variant peptide, PA9, from the Human immunodeficiency virus (BaL) envelope glycoprotein 120 Deposited 2008-08-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 21–119（99 aa） Fragment：UNP residues 21 to 119	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；12% PEG 20000, 0.1M MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.41 Å R-free 0.271
3E6H MHC CLASS I H-2Dd heavy chain complexed with Beta-2 Microglobulin and a variant peptide, PI10, from the human immunodeficiency virus (BaL) envelope glycoprotein 120 Deposited 2008-08-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 21–119（99 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；11% PEG20000,0.1M MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.10 Å R-free 0.250
3G08 Crystal structure of the alpha-galactosylceramide analog OCH in complex with mouse CD1d Deposited 2009-01-27	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 20–118（99 aa） Fragment：UNP residues 21-119	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 FEE N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyoctyl}tetracosanamide × 1 PLM PALMITIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；16% polyethylene glycol 3350, 100mM Tris pH8.5, 2% tacsimate pH8.0 , VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.60 Å R-free 0.226
3GML Structure of mouse CD1d in complex with C6Ph Deposited 2009-03-14	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 21–119（99 aa） Fragment：UNP residues 21-119	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 C6Q N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}-6-phenylhexanamide × 1 PLM PALMITIC ACID × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.70 Å R-free 0.216
3GMM Structure of mouse CD1d in complex with C8Ph Deposited 2009-03-14	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 21–119（99 aa） Fragment：UNP residues 21-119	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 C8P N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}-8-phenyloctanamide × 1 PLM PALMITIC ACID × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.80 Å R-free 0.219
3GMN Structure of mouse CD1d in complex with C10Ph Deposited 2009-03-14	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 21–119（99 aa） Fragment：UNP residues 21-119	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 C1Q N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}-10-phenyldecanamide × 1 PLM PALMITIC ACID × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.70 Å R-free 0.218
3GMO Structure of mouse CD1d in complex with C8PhF Deposited 2009-03-14	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 21–119（99 aa） Fragment：UNP residues 21-119	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 C8F 8-(4-fluorophenyl)-N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}octanamide × 1 PLM PALMITIC ACID × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.60 Å R-free 0.216
3GMP Structure of mouse CD1d in complex with PBS-25 Deposited 2009-03-14	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 21–119（99 aa） Fragment：UNP residues 21-119	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PBS (2S,3S,4R)-N-OCTANOYL-1-[(ALPHA-D-GALACTOPYRANOSYL)OXY]-2-AMINO-OCTADECANE-3,4-DIOL × 1 PLM PALMITIC ACID × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.70 Å R-free 0.216
3GMQ Structure of mouse CD1d expressed in SF9 cells, no ligand added Deposited 2009-03-14	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 21–119（99 aa） Fragment：UNP residues 21-119	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PLM PALMITIC ACID × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.80 Å R-free 0.231
3GMR Structure of mouse CD1d in complex with C8Ph, different space group Deposited 2009-03-14	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 21–119（99 aa） Fragment：UNP residues 21-119	Not recorded	C8P N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}-8-phenyloctanamide × 1 PLM PALMITIC ACID × 1 EDO 1,2-ETHANEDIOL × 4 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.90 Å R-free 0.230
3ILP Structure of mCD1d with bound glycolipid BbGL-2f from Borrelia burgdorferi Deposited 2009-08-07	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 21–119（99 aa） Fragment：UNP residues 21-119	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 1L2 (2S)-3-(alpha-D-galactopyranosyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl (9Z,12Z)-octadeca-9,12-dienoate × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；20% polyethylene glycol 4000, 100mM sodium citrate, 10% n-propanol, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.85 Å R-free 0.233
3ILQ Structure of mCD1d with bound glycolipid BbGL-2c from Borrelia burgdorferi Deposited 2009-08-07	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 D 21–119（99 aa） Fragment：UNP residues 21-119	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 1O2 (2S)-3-(alpha-D-galactopyranosyloxy)-2-(hexadecanoyloxy)propyl (9Z)-octadec-9-enoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；17% polyethylene glycol 3350, 150mM di-ammonium hydrogen citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.05 Å R-free 0.251
3MA7 Crystal structure of Cardiolipin bound to mouse CD1D Deposited 2010-03-23	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 D 21–119（99 aa） Fragment：UNP RESIDUES 21-119	Not recorded	CD4 (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate × 1 PLM PALMITIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions 20% POLYETHYLENE GLYCOL 4000, 300MM CALCIUM ACETATE, 6% ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K	Resolution 2.29 Å R-free 0.273
3MA7 Crystal structure of Cardiolipin bound to mouse CD1D Deposited 2010-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 21–119（99 aa） Fragment：UNP RESIDUES 21-119	Not recorded	CD4 (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate × 1 PLM PALMITIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions 20% POLYETHYLENE GLYCOL 4000, 300MM CALCIUM ACETATE, 6% ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K	Resolution 2.29 Å R-free 0.273
3NWM Crystal structure of a single chain construct composed of MHC class I H-2Kd, beta-2microglobulin and a peptide which is an autoantigen for type 1 diabetes Deposited 2010-07-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–119（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；20% PEG 8K, TrisHCl pH 8.5, Vapor diffusion, Sitting drop, temperature 298K	Resolution 2.70 Å R-free 0.284
3QUX Structure of the mouse CD1d-alpha-C-GalCer-iNKT TCR complex Deposited 2011-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 21–119（99 aa） Fragment：UNP residues 21-119	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 QUX N-[(3S,4S,5R)-4,5-dihydroxy-1-[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]nonadecan-3-yl]hexacosanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；20% polyethylene glycol 3350, 8% tacsimate, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.91 Å R-free 0.252
3QUY Structure of the mouse CD1d-BnNH-GSL-1'-iNKT TCR complex Deposited 2011-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 21–119（99 aa） Fragment：UNP residues 21-119	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 QUY (2S,3R,4S,5R,6S)-6-[(2S,3S,4R)-2-(hexacosanoylamino)-3,4-dihydroxy-octadecoxy]-3,4,5-trihydroxy-N-(phenylmethyl)oxane-2-carboxamide × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；17% polyethylene glycol 4000, 0.1 M citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.25 Å R-free 0.231
3QUZ Structure of the mouse CD1d-NU-alpha-GalCer-iNKT TCR complex Deposited 2011-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 21–119（99 aa） Fragment：UNP residues 21-119	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 QUV N-[(2S,3S,4R)-1-({6-deoxy-6-[(naphthalen-1-ylcarbamoyl)amino]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；20% polyethylene glycole, 0.2 M ammonium citrate dibasic, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.30 Å R-free 0.233
3TN0 Structure of mouse Va14Vb8.2NKT TCR-mouse CD1d-a-C-Galactosylceramide complex Deposited 2011-09-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 21–119（99 aa） Fragment：UNP residues 21-119	Not recorded	QUX N-[(3S,4S,5R)-4,5-dihydroxy-1-[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]nonadecan-3-yl]hexacosanamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；15-17% PEG 10K, 0.1M ammonium acetat, 0.1M BisTris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.20 Å R-free 0.289
3TO4 Structure of mouse Valpha14Vbeta2-mouseCD1d-alpha-Galactosylceramide Deposited 2011-09-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 21–119（99 aa） Fragment：UNP residues 21-119	Not recorded	AGH N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；17% PEG 10K, 0.1M ammonium acetate, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.10 Å R-free 0.268
4ELM Crystal structure of the mouse CD1d-lysosulfatide-Hy19.3 TCR complex Deposited 2012-04-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 21–119（99 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SGF (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl 3-O-sulfo-beta-D-galactopyranoside × 1 PLM PALMITIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；11% PEG4000, 4% tacsimate, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.48 Å R-free 0.265
4ELM Crystal structure of the mouse CD1d-lysosulfatide-Hy19.3 TCR complex Deposited 2012-04-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 21–119（99 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SGF (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl 3-O-sulfo-beta-D-galactopyranoside × 1 PLM PALMITIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；11% PEG4000, 4% tacsimate, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.48 Å R-free 0.265

25 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q91XJ8_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–100； UniProt 21–119

Peptide P18-I10 from HIV gp160

OrganismNot specified

UniProt P19551

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain P； UniProt 309–318	Fragment：UNP residues 309 to 318	H-2 class I histocompatibility antigen, D-D alpha chain × 1 （P01900） Beta-2 microglobulin × 1 （Q91XJ8） EDO 1,2-ETHANEDIOL × 6 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；16% PEG 3350, 0.2M Magnesium formate, , pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.70 Å R-free 0.227

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3ECB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2PJV solution structure of hiv-1 gp41 fusion domain bound to DPC micelle Deposited 2007-04-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 510–532（23 aa） Fragment：23 N-terminal residues	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；303 K；Pressure ambient NMR sample composition 1 MM N15-PEPTIDE IN THE PRESENCE OF 200 MM D38-DPC IN 0.05% NAN3, 5 MM DTT, 20 MM D4-ACETIC ACID, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 2 MM PEPTIDE IN THE PRESENCE OF 400 MM D38-DPC IN 0.05% NAN3, 5 MM DTT, 20 MM D4-ACETIC ACID, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
9HS7 Anti-HIV-1 chimeric miniprotein mimicking the N-terminal half of gp41 NHR with an extended region targeting the MPER Deposited 2024-12-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 527–565（39 aa） Chain A 528–570（43 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1M sodium phosphate monobasic monohydrate, 0.1M potassium phosphate monobasic, 2M NaCl	Resolution 1.70 Å R-free 0.239

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ENV_HV1MF
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain P； PDBConstruct 1–10； UniProt 309–318

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	3ecb
Deposition date deposition_date	2008-08-29
Structure title title	Crystal structure of mouse H-2Dd in complex with peptide P18-I10 derived from human immunodeficiency virus envelope glycoprotein 120
Keywords keywords	;class I major histompatibility complex, MHC-I, H-2Dd, Glycoprotein, Immune response, Membrane, MHC I, Phosphoprotein, Transmembrane, Immunoglobulin domain, Secreted, AIDS, Apoptosis, Cell membrane, Cleavage on pair of basic residues, Coiled coil, Envelope protein, Fusion protein, Host-virus interaction, Lipoprotein, Palmitate, Viral immunoevasion, Virion, 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	23.50 Å
Radius of gyration Rg (electron density) rg_electron	22.53 Å
Forward intensity I(0) i0	35702300.00
Molecular weight molecular_weight	44835.0 kDa
Excluded volume excluded_volume	55533 Å³
Envelope volume envelope_volume	66842 Å³
Hydration-shell volume shell_volume	24725 Å³
Envelope diameter envelope_diameter	74.5 Å
Shell Rg shell_rg	29.44 Å
Envelope Rg envelope_rg	22.60 Å
Shape Rg shape_rg	22.51 Å
Total Rg total_rg	23.40 Å
Total atoms total_atoms	3161
Residues n_residues	382
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	72.2 Å
Rg (real space) rg_real	23.41 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	3.5700e+07
I(0) uncertainty (real space) i0_real_error	4.7190e+05
Rg (reciprocal space) rg_reciprocal	23.44 Å
I(0) (reciprocal space) i0_reciprocal	35700000.0000
Solution quality estimate total_estimate	0.9109
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.9 Å
Skewness Skewness skewness	0.222
Kurtosis Kurtosis kurtosis	-0.466
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9097000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.978

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	H-2 class I histocompatibility antigen, D-D alpha chain
Molecular weight formula_weight	32265.9 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	3476

MSHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYWERETRRAKGNEQSFRVDLRTALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDGCDYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYLEGECVEWLRRYLKNGNATLLRTDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLTWQLNGEELTQEMELVETRPAGDGTFQKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRWGKE

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	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Beta-2 microglobulin
Molecular weight formula_weight	11791.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

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	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Peptide P18-I10 from HIV gp160
Molecular weight formula_weight	1075.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

RGPGRAFVTI

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	315

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3ecbb_
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 (3 domains)

Domain ID domain_id	3ecbA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — MHC class I-like antigen recognition-like

Domain ID domain_id	3ecbA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3ecbB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	46.727 Å
Unit-cell length b length_b	89.452 Å
Unit-cell length c length_c	109.705 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	—

Resolution resolution	1.698 Å
Low-resolution limit resolution_low	28.798 Å
R factor r_factor	0.1839
R_work r_work	0.1816
R_free r_free	0.2273

fit	/app/data/saxs_computation/ec/3ecb/3ecb.fit
pddf	/app/data/pr_computation/ec/3ecb/3ecb.pr.out
profile	/app/data/saxs_computation/ec/3ecb/3ecb.dat

Crystal structure of mouse H-2Dd in complex with peptide P18-I10 derived from human immunodeficiency virus envelope glycoprotein 120

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

H-2 class I histocompatibility antigen, D-D alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Beta-2 microglobulin

State in the Current Structure

Other States of the Same Protein in the Database

Peptide P18-I10 from HIV gp160

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 (6)

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

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)