9asg

Crystal structure of HLA-A*03:01 in complex with a mutant PIK3CA peptide analogue (Trp-6 Bta)

Method: X-RAY DIFFRACTION Dmax: 74.6 Å Quality: EXCELLENT

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

HLA class I histocompatibility antigen, A alpha chain

Homo sapiens

UniProt P04439

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 25–298 Fragment:extracellular domain Beta-2-microglobulin × 1 (P61769) Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform × 1 (P42336) GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277.15 K;15% w/v Polyethylene glycol 3,350, 150mM Cesium chloride Resolution 2.03 Å R-free 0.238

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.

53 other PDB entries and 78 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HLAA_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–274; UniProt 25–298

Beta-2-microglobulin

Homo sapiens

UniProt P61769

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 Not recorded HLA class I histocompatibility antigen, A alpha chain × 1 (P04439) Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform × 1 (P42336) GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277.15 K;15% w/v Polyethylene glycol 3,350, 150mM Cesium chloride Resolution 2.03 Å R-free 0.238

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.

1313 other PDB entries and 1998 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name B2MG_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 2–100; UniProt 21–119

Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform

OrganismNot specified

UniProt P42336

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 C; UniProt 1046–1054 Fragment:residues 1046-1054 (Uniprot numbering) Mutation:H2L, W6Bta Non-standard monomer:Yes (specific site not provided by mmCIF) HLA class I histocompatibility antigen, A alpha chain × 1 (P04439) Beta-2-microglobulin × 1 (P61769) GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277.15 K;15% w/v Polyethylene glycol 3,350, 150mM Cesium chloride Resolution 2.03 Å R-free 0.238

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.

134 other PDB entries and 145 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PK3CA_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 1046–1054

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9asg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9asg
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9asg
Deposition date deposition_date2024-02-25
Structure title titleCrystal structure of HLA-A*03:01 in complex with a mutant PIK3CA peptide analogue (Trp-6 Bta)
Keywords keywordsPeptide-class I Major Histocompatibility Complex, pMHC, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.06
Radius of gyration Rg (electron density) rg_electron22.92
Forward intensity I(0) i036138700.00
Molecular weight molecular_weight44387.0 kDa
Excluded volume excluded_volume54653 ų
Envelope volume envelope_volume66903 ų
Hydration-shell volume shell_volume24511 ų
Envelope diameter envelope_diameter77.7
Shell Rg shell_rg29.56
Envelope Rg envelope_rg22.93
Shape Rg shape_rg22.90
Total Rg total_rg23.77
Total atoms total_atoms3133
Residues n_residues381
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax74.6
Rg (real space) rg_real23.98
Rg uncertainty (real space) rg_real_error0.47
I(0) (real space) i0_real3.6140e+07
I(0) uncertainty (real space) i0_real_error4.9840e+05
Rg (reciprocal space) rg_reciprocal24.00
I(0) (reciprocal space) i0_reciprocal36140000.0000
Solution quality estimate total_estimate0.9124
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.3
Skewness Skewness skewness0.224
Kurtosis Kurtosis kurtosis-0.500
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8560000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.994

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)