8sbl

Structure of HLA-A*24:02 in complex with peptide, LYLPVRVLI

Method: X-RAY DIFFRACTION Dmax: 159.0 Å Quality: GOOD

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

MHC class I antigen

Homo sapiens

UniProt A0A411J078

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 25–304 Not recorded Beta-2-microglobulin × 1 (P61769) LEU-TYR-LEU-PRO-VAL-ARG-VAL-LEU-ILE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;294 K;0.05M MES monohydrate pH 6.5, 22.5% Polyethylene Glycol w/v 3350 Resolution 3.00 Å R-free 0.270
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 25–304 Not recorded Beta-2-microglobulin × 1 (P61769) LEU-TYR-LEU-PRO-VAL-ARG-VAL-LEU-ILE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;294 K;0.05M MES monohydrate pH 6.5, 22.5% Polyethylene Glycol w/v 3350 Resolution 3.00 Å R-free 0.270
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain G; UniProt 25–304 Not recorded Beta-2-microglobulin × 1 (P61769) LEU-TYR-LEU-PRO-VAL-ARG-VAL-LEU-ILE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;294 K;0.05M MES monohydrate pH 6.5, 22.5% Polyethylene Glycol w/v 3350 Resolution 3.00 Å R-free 0.270
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain J; UniProt 25–304 Not recorded Beta-2-microglobulin × 1 (P61769) LEU-TYR-LEU-PRO-VAL-ARG-VAL-LEU-ILE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;294 K;0.05M MES monohydrate pH 6.5, 22.5% Polyethylene Glycol w/v 3350 Resolution 3.00 Å R-free 0.270

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.

24 other PDB entries and 40 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A411J078_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–283; UniProt 25–304 Author chain D; PDBConstruct 4–283; UniProt 25–304 Author chain G; PDBConstruct 4–283; UniProt 25–304 Author chain J; PDBConstruct 4–283; UniProt 25–304

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 Fragment:UNP residues 21-119 MHC class I antigen × 1 (A0A411J078) LEU-TYR-LEU-PRO-VAL-ARG-VAL-LEU-ILE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;294 K;0.05M MES monohydrate pH 6.5, 22.5% Polyethylene Glycol w/v 3350 Resolution 3.00 Å R-free 0.270
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 21–119 Fragment:UNP residues 21-119 MHC class I antigen × 1 (A0A411J078) LEU-TYR-LEU-PRO-VAL-ARG-VAL-LEU-ILE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;294 K;0.05M MES monohydrate pH 6.5, 22.5% Polyethylene Glycol w/v 3350 Resolution 3.00 Å R-free 0.270
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain H; UniProt 21–119 Fragment:UNP residues 21-119 MHC class I antigen × 1 (A0A411J078) LEU-TYR-LEU-PRO-VAL-ARG-VAL-LEU-ILE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;294 K;0.05M MES monohydrate pH 6.5, 22.5% Polyethylene Glycol w/v 3350 Resolution 3.00 Å R-free 0.270
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain K; UniProt 21–119 Fragment:UNP residues 21-119 MHC class I antigen × 1 (A0A411J078) LEU-TYR-LEU-PRO-VAL-ARG-VAL-LEU-ILE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;294 K;0.05M MES monohydrate pH 6.5, 22.5% Polyethylene Glycol w/v 3350 Resolution 3.00 Å R-free 0.270

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 1995 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 Author chain E; PDBConstruct 2–100; UniProt 21–119 Author chain H; PDBConstruct 2–100; UniProt 21–119 Author chain K; PDBConstruct 2–100; UniProt 21–119

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 8sbl

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8sbl
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8sbl
Deposition date deposition_date2023-04-03
Structure title titleStructure of HLA-A*24:02 in complex with peptide, LYLPVRVLI
Keywords keywordsMajor Histocompatibility Complex (MHC), 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_guinier45.61
Radius of gyration Rg (electron density) rg_electron45.65
Forward intensity I(0) i0507551000.00
Molecular weight molecular_weight178620.0 kDa
Excluded volume excluded_volume220580 ų
Envelope volume envelope_volume313900 ų
Hydration-shell volume shell_volume60348 ų
Envelope diameter envelope_diameter166.9
Shell Rg shell_rg47.27
Envelope Rg envelope_rg44.53
Shape Rg shape_rg45.63
Total Rg total_rg45.80
Total atoms total_atoms12604
Residues n_residues1540
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 dmax159.0
Rg (real space) rg_real45.82
Rg uncertainty (real space) rg_real_error1.73
I(0) (real space) i0_real5.0760e+08
I(0) uncertainty (real space) i0_real_error9.5790e+06
Rg (reciprocal space) rg_reciprocal45.61
I(0) (reciprocal space) i0_reciprocal507400000.0000
Solution quality estimate total_estimate0.8518
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary54.5
Skewness Skewness skewness0.477
Kurtosis Kurtosis kurtosis-0.054
Angular range angular_range— – 0.1750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha33580000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.806; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.940; Smooth: 0.712

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (2)

9. Files and Curves (10)