4ms8

42F3 TCR pCPB9/H-2Ld Complex

Method: X-RAY DIFFRACTION D_max: 99.6 Å Quality: GOOD

▼

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

H-2 class I histocompatibility antigen, L-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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 25–203	Mutation：F8Y, V12T, P15R, I23T, N30D, A49V, K131R	42F3 alpha × 1 42F3 beta × 1 pCPB9 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；20% PEG 4000, 100mM TRIS pH8, 200mM sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.92 Å R-free 0.219

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 4MS8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1LD9 THE THREE-DIMENSIONAL STRUCTURE OF AN H-2LD PEPTIDE COMPLEX EXPLAINS THE UNIQUE INTERACTION OF LD WITH BETA2M AND PEPTIDE Deposited 1997-04-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 25–292（268 aa） Fragment：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 0.279
1LD9 THE THREE-DIMENSIONAL STRUCTURE OF AN H-2LD PEPTIDE COMPLEX EXPLAINS THE UNIQUE INTERACTION OF LD WITH BETA2M AND PEPTIDE Deposited 1997-04-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 25–292（268 aa） Fragment：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 0.279
1LDP CRYSTAL STRUCTURE OF MURINE MHC CLASS I H-2LD WITH A MIXTURE OF BOUND PEPTIDES Deposited 1998-03-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 25–296（272 aa） Fragment：CHAIN H IS THE HEAVY CHAIN, PEPTIDE BINDING DOMAIN, CHAIN L IS THE LIGHT CHAIN OR BETA-2-MICROGLOBULIN	Mutation：HEAVY CHAIN TRUNCATED AFTER RESIDUE 274, B2M, LIGHT CHAIN TRUNCATED AFTER RESIDUE 99	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 100MM SODIUM CACODYLATE, 0.2M AMMONIUM SULFATE, 0.5M SODIUM BROMIDE, 30% PEG 8000, PH 6.5.	Resolution 3.10 Å R-free 0.371
2E7L Structure of a high-affinity mutant of the 2C TCR in complex with Ld/QL9 Deposited 2007-01-11	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 25–205（181 aa） Fragment：alpha 1,2 domains (UNP RESIDUES 25-205)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2M ammonium phosphate, 20% PEG 3350, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.50 Å R-free 0.246
2E7L Structure of a high-affinity mutant of the 2C TCR in complex with Ld/QL9 Deposited 2007-01-11	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 25–205（181 aa） Fragment：alpha 1,2 domains (UNP RESIDUES 25-205)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2M ammonium phosphate, 20% PEG 3350, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.50 Å R-free 0.246
2OI9 Structure of the 2C/Ld/QL9 allogeneic complex Deposited 2007-01-10	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 25–203（179 aa） Fragment：alpha 1,2 domains	Mutation：F9Y, V12T, I23T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；0.9M sodium dihydrogen phosphate, 0.01M di-potassium hydrogen phosphate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.35 Å R-free 0.226
3E2H Structure of the m67 high-affinity mutant of the 2C TCR in complex with Ld/QL9 Deposited 2008-08-05	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 25–199（175 aa）	Mutation：F8Y, V12T, P15R, I23T, N30D, A49V, I66V, R97W, K131R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；2M ammonium tartrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.80 Å R-free 0.276
3E3Q Structure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9 Deposited 2008-08-07	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 25–199（175 aa） Fragment：UNP residues 25-199	Mutation：F8Y, V12T, P15R, I23T, N30D, A49V, I66V, W97R, K131R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M ammonium citrate, 20% PEG 3350, 3% trimethyl amine N-oxide dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.95 Å R-free 0.275
3E3Q Structure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9 Deposited 2008-08-07	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 25–199（175 aa） Fragment：UNP residues 25-199	Mutation：F8Y, V12T, P15R, I23T, N30D, A49V, I66V, W97R, K131R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M ammonium citrate, 20% PEG 3350, 3% trimethyl amine N-oxide dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.95 Å R-free 0.275
3E3Q Structure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9 Deposited 2008-08-07	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain c 25–199（175 aa） Fragment：UNP residues 25-199	Mutation：F8Y, V12T, P15R, I23T, N30D, A49V, I66V, W97R, K131R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M ammonium citrate, 20% PEG 3350, 3% trimethyl amine N-oxide dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.95 Å R-free 0.275
3E3Q Structure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9 Deposited 2008-08-07	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 25–199（175 aa） Fragment：UNP residues 25-199	Mutation：F8Y, V12T, P15R, I23T, N30D, A49V, I66V, W97R, K131R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M ammonium citrate, 20% PEG 3350, 3% trimethyl amine N-oxide dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.95 Å R-free 0.275
3E3Q Structure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9 Deposited 2008-08-07	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain L 25–199（175 aa） Fragment：UNP residues 25-199	Mutation：F8Y, V12T, P15R, I23T, N30D, A49V, I66V, W97R, K131R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M ammonium citrate, 20% PEG 3350, 3% trimethyl amine N-oxide dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.95 Å R-free 0.275
3E3Q Structure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9 Deposited 2008-08-07	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain P 25–199（175 aa） Fragment：UNP residues 25-199	Mutation：F8Y, V12T, P15R, I23T, N30D, A49V, I66V, W97R, K131R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M ammonium citrate, 20% PEG 3350, 3% trimethyl amine N-oxide dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.95 Å R-free 0.275
3E3Q Structure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9 Deposited 2008-08-07	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain U 25–199（175 aa） Fragment：UNP residues 25-199	Mutation：F8Y, V12T, P15R, I23T, N30D, A49V, I66V, W97R, K131R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M ammonium citrate, 20% PEG 3350, 3% trimethyl amine N-oxide dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.95 Å R-free 0.275
3E3Q Structure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9 Deposited 2008-08-07	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain Y 25–199（175 aa） Fragment：UNP residues 25-199	Mutation：F8Y, V12T, P15R, I23T, N30D, A49V, I66V, W97R, K131R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M ammonium citrate, 20% PEG 3350, 3% trimethyl amine N-oxide dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.95 Å R-free 0.275
3UO1 Structure of a monoclonal antibody complexed with its MHC-I antigen Deposited 2011-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 70–78（9 aa） Fragment：H-2L(d) PEPTIDE SEGMENT 46-54	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；antibody at 6.8 mg/ml mixed with equimolar peptide and then 1:1 with 0.1 M LiSO4, 0.1 M TRIS, 30% w/v PEG 3000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 1.64 Å R-free 0.206
3UYR Structure of a monoclonal antibody complexed with its MHC-I antigen Deposited 2011-12-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 70–77（8 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1M LiSO4, 0.1M Tris pH 8.5, 30% (w/v) PEG 3000, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.70 Å R-free 0.226
3V4U Structure of a monoclonal antibody complexed with its MHC-I antigen Deposited 2011-12-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 70–78（9 aa） Fragment：H-2L(d) PEPTIDE SEGMENT 46-54	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1M LiSO4, 0.1M Tris, 30%(w/v)PEG 3000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.64 Å R-free 0.251
3V52 Structure of a monoclonal antibody complexed with its MHC-I antigen Deposited 2011-12-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 70–77（8 aa） Fragment：H-2Ld peptide p46-53	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1M LiSO4, 0.1M Tris, 30% (w/v/) PEG 3000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.70 Å R-free 0.227
3VJ6 Structure of the MHC class Ib molecule Qa-1b Deposited 2011-10-12	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 P 3–11（9 aa）	Not recorded	NI NICKEL (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；6% PEG 4000, 10mM NiCl2, 0.1M sodium acetate, pH 6.3. , VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.242
4MVB 42F3 pCPB7/H-2Ld Complex Deposited 2013-09-23	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 25–203（179 aa） Fragment：UNP residues 25-203	Mutation：F8Y, V12T, P15R, I23T, N30D, A49V, K131R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；25% PEG 3350, 100mM BIS-TRIS pH 5.5 and 200mM ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.09 Å R-free 0.279
4MXQ 42F3 TCR pCPC5/H-2Ld Complex Deposited 2013-09-26	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 25–203（179 aa） Fragment：UNP residues 25-203	Mutation：F8Y, V12T, P15R, I23T, N30D, A49V, K131R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；14% PEG 3350, 100mM BIS-TRIS, pH 7.0 and 200mM magnesium nitrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.60 Å R-free 0.240
4N0C 42F3 TCR pCPE3/H-2Ld complex Deposited 2013-10-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 25–203（179 aa） Fragment：UNP residues 25-203	Mutation：F8Y, V12T, P15R, I23T, N30D, A49V, K131R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；17% PEG 3350 and 100mM BiS-TRIS, pH 6.6 and 200mM magnesium nitrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.90 Å R-free 0.247
4N0C 42F3 TCR pCPE3/H-2Ld complex Deposited 2013-10-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 25–203（179 aa） Fragment：UNP residues 25-203	Mutation：F8Y, V12T, P15R, I23T, N30D, A49V, K131R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；17% PEG 3350 and 100mM BiS-TRIS, pH 6.6 and 200mM magnesium nitrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.90 Å R-free 0.247
4N5E 42F3 TCR pCPA12/H-2Ld complex Deposited 2013-10-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 25–203（179 aa） Fragment：UNP residues 25-203	Mutation：F8Y, V12T, P15R, I23T, N30D, A49V, K131R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；16% PEG 3350, 100mM TRIS, pH 7.5 and 200mM magnesium nitrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.06 Å R-free 0.227
4NHU The M33 TCR p3M33l/H-2 Ld Complex Deposited 2013-11-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 25–204（180 aa）	Mutation：N30D, A49V, I66V, W97R, K131R, W167A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；Crystals grown in 20% PEG 3350 and 200mM Ammonium Nitrate and micro seeded into 20% PEG 3350 and 200mM Ammonium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.90 Å R-free 0.260
4NHU The M33 TCR p3M33l/H-2 Ld Complex Deposited 2013-11-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 25–204（180 aa）	Mutation：N30D, A49V, I66V, W97R, K131R, W167A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；Crystals grown in 20% PEG 3350 and 200mM Ammonium Nitrate and micro seeded into 20% PEG 3350 and 200mM Ammonium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.90 Å R-free 0.260
5VCL Structure of the Qdm peptide bound to Qa-1a Deposited 2017-03-31	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 P 3–11（9 aa） Fragment：UNP residues 3-11	Not recorded	GOL GLYCEROL × 4 NA SODIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；5% polyethylene glycol 1000, 40% ethylene glycol, 100 mM HEPES pH 6.5	Resolution 2.05 Å R-free 0.246
8D5N Crystal structure of Ld-HF10 Deposited 2022-06-05	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 C 25–298（274 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PG4 TETRAETHYLENE GLYCOL × 1 PPI PROPANOIC ACID × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；20% w/v PEG10K, 0.1M Sodium citrate tribasic dihydrate pH5.5, and 1M Lithium sulfate monohydrate	Resolution 1.80 Å R-free 0.219
8D5N Crystal structure of Ld-HF10 Deposited 2022-06-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 25–298（274 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；20% w/v PEG10K, 0.1M Sodium citrate tribasic dihydrate pH5.5, and 1M Lithium sulfate monohydrate	Resolution 1.80 Å R-free 0.219
8D5Q TCR TG6 in complex with Ld-HF10 Deposited 2022-06-05	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 25–203（179 aa）	Not recorded	SO4 SULFATE ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；11 % w/v PEG 8000, 0.1 M MES 6.0, 0.24 M Ammonium sulfate	Resolution 2.50 Å R-free 0.222
8UMO Murine CD94-NKG2A receptor in complex with Qa-1b presenting AMAPRTLLL Deposited 2023-10-18	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 P 3–11（9 aa） Fragment：UNP residues 3-11	Not recorded	BR BROMIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；23% PEG3350 and 0.2M NaBr	Resolution 2.60 Å R-free 0.251

20 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HA1L_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 2–180； UniProt 25–203

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4ms8
Deposition date deposition_date	2013-09-18
Structure title title	42F3 TCR pCPB9/H-2Ld Complex
Keywords keywords	Ig, TCR MHC, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	30.15 Å
Radius of gyration Rg (electron density) rg_electron	29.46 Å
Forward intensity I(0) i0	77986700.00
Molecular weight molecular_weight	68144.0 kDa
Excluded volume excluded_volume	84469 Å³
Envelope volume envelope_volume	108860 Å³
Hydration-shell volume shell_volume	31924 Å³
Envelope diameter envelope_diameter	100.8 Å
Shell Rg shell_rg	35.68 Å
Envelope Rg envelope_rg	29.36 Å
Shape Rg shape_rg	29.45 Å
Total Rg total_rg	30.08 Å
Total atoms total_atoms	4813
Residues n_residues	606
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

▼

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

Maximum dimension Dmax dmax	99.6 Å
Rg (real space) rg_real	30.28 Å
Rg uncertainty (real space) rg_real_error	0.60 Å
I(0) (real space) i0_real	7.7990e+07
I(0) uncertainty (real space) i0_real_error	1.0810e+06
Rg (reciprocal space) rg_reciprocal	30.23 Å
I(0) (reciprocal space) i0_reciprocal	77980000.0000
Solution quality estimate total_estimate	0.8767
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	0
Primary peak position r_peak_primary	— Å
Skewness Skewness skewness	0.430
Kurtosis Kurtosis kurtosis	-0.476
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	15750000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.851; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.920; Smooth: 0.920

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	42F3 alpha
Molecular weight formula_weight	23383.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	5275

GSHMAQSVTQPDARVTVSEGASLQLRCKYSYSATPYLFWYVQYPRQGLQMLLKYYSGDPVVQGVNGFEAEFSKSDSSFHLRKASVHWSDSAVYFCAVSAKGTGSKLSFGKGAKLTVSPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS

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	42F3 beta
Molecular weight formula_weight	27248.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MGEAAVTQSPRNKVTVTGGNVTLSCRQTNSHNYMYWYRQDTGHGLRLIHYSYGAGNLQIGDVPDGYKATRTTQEDFFLLLELASPSQTSLYFCASSDAPGQLYFGEGSKLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

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	H-2 class I histocompatibility antigen, L-D alpha chain
Molecular weight formula_weight	21115.3 kDa
Mutation mutation	F8Y, V12T, P15R, I23T, N30D, A49V, K131R
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MGPHSMRYYETATSRRGLGEPRYTSVGYVDDKEFVRFDSDAENPRYEPQVPWMEQEGPEYWERITQIAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQWMYGCDVGSDGRLLRGYEQFAYDGCDYIALNEDLRTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNGNATL

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 4 Entity 4 polymer

Description description	pCPB9
Molecular weight formula_weight	938.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SPAEAGFFL

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	456

▼

7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4ms8a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
Family Family family	d.19.1.0 — automated matches

Domain ID domain_id	d4ms8a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4ms8c1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d4ms8c2
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	d4ms8d1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d4ms8d2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

CATH v4.4 (5 domains)

Domain ID domain_id	4ms8A00
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	4ms8C01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ms8C02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ms8D01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ms8D02
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	175.260 Å
Unit-cell length b length_b	60.620 Å
Unit-cell length c length_c	70.100 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.06 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.922 Å
Low-resolution limit resolution_low	34.854 Å
R factor r_factor	0.1825
R_work r_work	0.1805
R_free r_free	0.2189

fit	/app/data/saxs_computation/ms/4ms8/4ms8.fit
pddf	/app/data/pr_computation/ms/4ms8/4ms8.pr.out
profile	/app/data/saxs_computation/ms/4ms8/4ms8.dat

42F3 TCR pCPB9/H-2Ld Complex

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

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

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)