9dl1

Crystal Structure of HLA-A*02:01/NY-ESO-1 (SLLMWITQV) and a target specific TRACeR-I

Method: X-RAY DIFFRACTION Dmax: 134.9 Å Quality: GOOD

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

MHC class I antigen, A-2 alpha chain

Homo sapiens

UniProt A0A5B8RNS7

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 × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain B; UniProt 25–299 Chain F; UniProt 25–299 Not recorded TRACeR-I × 2 Beta-2-microglobulin × 2 (P61769) Cancer/testis antigen 1 × 2 (P78358) SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Sodium Sulfate and 20% w/v PEG 3350 Resolution 2.30 Å R-free 0.265

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.

27 other PDB entries and 43 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A5B8RNS7_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 2–276; UniProt 25–299 Author chain F; PDBConstruct 2–276; UniProt 25–299

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 × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain C; UniProt 21–119 Chain G; UniProt 21–119 Fragment:UNP residues 21-119 TRACeR-I × 2 MHC class I antigen, A-2 alpha chain × 2 (A0A5B8RNS7) Cancer/testis antigen 1 × 2 (P78358) SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Sodium Sulfate and 20% w/v PEG 3350 Resolution 2.30 Å R-free 0.265

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 3
Chains and sequence ranges Author chain C; PDBConstruct 2–100; UniProt 21–119 Author chain G; PDBConstruct 2–100; UniProt 21–119

Cancer/testis antigen 1

OrganismNot specified

UniProt P78358

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 × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain E; UniProt 157–164 Chain H; UniProt 157–164 Not recorded TRACeR-I × 2 MHC class I antigen, A-2 alpha chain × 2 (A0A5B8RNS7) Beta-2-microglobulin × 2 (P61769) SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Sodium Sulfate and 20% w/v PEG 3350 Resolution 2.30 Å R-free 0.265

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.

12 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CTG1B_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain E; PDBConstruct 1–8; UniProt 157–164 Author chain H; PDBConstruct 1–8; UniProt 157–164

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 9dl1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9dl1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9dl1
Deposition date deposition_date2024-09-10
Structure title titleCrystal Structure of HLA-A*02:01/NY-ESO-1 (SLLMWITQV) and a target specific TRACeR-I
Keywords keywordsMajor Histocompatibility Complex I(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_guinier39.92
Radius of gyration Rg (electron density) rg_electron40.01
Forward intensity I(0) i0224259000.00
Molecular weight molecular_weight118680.0 kDa
Excluded volume excluded_volume147080 ų
Envelope volume envelope_volume200760 ų
Hydration-shell volume shell_volume44501 ų
Envelope diameter envelope_diameter143.1
Shell Rg shell_rg42.01
Envelope Rg envelope_rg40.75
Shape Rg shape_rg40.01
Total Rg total_rg40.12
Total atoms total_atoms8377
Residues n_residues1007
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 dmax134.9
Rg (real space) rg_real40.55
Rg uncertainty (real space) rg_real_error1.31
I(0) (real space) i0_real2.2430e+08
I(0) uncertainty (real space) i0_real_error4.1030e+06
Rg (reciprocal space) rg_reciprocal40.16
I(0) (reciprocal space) i0_reciprocal224200000.0000
Solution quality estimate total_estimate0.7775
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary33.7
Skewness Skewness skewness0.600
Kurtosis Kurtosis kurtosis-0.290
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha40440000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.712; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.731; Smooth: 0.235

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)