6rpb

Crystal structure of the T-cell receptor NYE_S1 bound to HLA A2*01-SLLMWITQV

Method: X-RAY DIFFRACTION Dmax: 214.0 Å Quality: GOOD

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

HLA class I histocompatibility antigen, A-2 alpha chain

Homo sapiens

UniProt P01892

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 25–300 Not recorded Beta-2-microglobulin × 1 (P61769) Heteroclitic NY-ESO-1 157-165 peptide × 1 T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Ammonium sulfate, 25 %(w/v) PEG 4000, 0.1 M tri-Sodium citrate pH 5.6 Resolution 2.50 Å R-free 0.273
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain F; UniProt 25–300 Not recorded Beta-2-microglobulin × 1 (P61769) Heteroclitic NY-ESO-1 157-165 peptide × 1 T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Ammonium sulfate, 25 %(w/v) PEG 4000, 0.1 M tri-Sodium citrate pH 5.6 Resolution 2.50 Å R-free 0.273
3 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain K; UniProt 25–300 Not recorded Beta-2-microglobulin × 1 (P61769) Heteroclitic NY-ESO-1 157-165 peptide × 1 T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Ammonium sulfate, 25 %(w/v) PEG 4000, 0.1 M tri-Sodium citrate pH 5.6 Resolution 2.50 Å R-free 0.273
4 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain P; UniProt 25–300 Not recorded Beta-2-microglobulin × 1 (P61769) Heteroclitic NY-ESO-1 157-165 peptide × 1 T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Ammonium sulfate, 25 %(w/v) PEG 4000, 0.1 M tri-Sodium citrate pH 5.6 Resolution 2.50 Å R-free 0.273

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.

271 other PDB entries and 462 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1A02_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–277; UniProt 25–300 Author chain F; PDBConstruct 2–277; UniProt 25–300 Author chain K; PDBConstruct 2–277; UniProt 25–300 Author chain P; PDBConstruct 2–277; UniProt 25–300

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Heteroclitic NY-ESO-1 157-165 peptide × 1 T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Ammonium sulfate, 25 %(w/v) PEG 4000, 0.1 M tri-Sodium citrate pH 5.6 Resolution 2.50 Å R-free 0.273
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain G; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Heteroclitic NY-ESO-1 157-165 peptide × 1 T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Ammonium sulfate, 25 %(w/v) PEG 4000, 0.1 M tri-Sodium citrate pH 5.6 Resolution 2.50 Å R-free 0.273
3 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain L; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Heteroclitic NY-ESO-1 157-165 peptide × 1 T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Ammonium sulfate, 25 %(w/v) PEG 4000, 0.1 M tri-Sodium citrate pH 5.6 Resolution 2.50 Å R-free 0.273
4 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain Q; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Heteroclitic NY-ESO-1 157-165 peptide × 1 T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Ammonium sulfate, 25 %(w/v) PEG 4000, 0.1 M tri-Sodium citrate pH 5.6 Resolution 2.50 Å R-free 0.273

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 G; PDBConstruct 2–100; UniProt 21–119 Author chain L; PDBConstruct 2–100; UniProt 21–119 Author chain Q; 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 6rpb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6rpb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6rpb
Deposition date deposition_date2019-05-14
Structure title titleCrystal structure of the T-cell receptor NYE_S1 bound to HLA A2*01-SLLMWITQV
Keywords keywordsT-cell receptor, peptide-Human leukocyte antigen complex, NY-ESO-1, cancer testis antigen, 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_guinier63.14
Radius of gyration Rg (electron density) rg_electron64.19
Forward intensity I(0) i02049880000.00
Molecular weight molecular_weight368090.0 kDa
Excluded volume excluded_volume455290 ų
Envelope volume envelope_volume708500 ų
Hydration-shell volume shell_volume100630 ų
Envelope diameter envelope_diameter243.2
Shell Rg shell_rg56.11
Envelope Rg envelope_rg63.56
Shape Rg shape_rg64.18
Total Rg total_rg64.00
Total atoms total_atoms25965
Residues n_residues3231
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 dmax214.0
Rg (real space) rg_real63.80
Rg uncertainty (real space) rg_real_error1.99
I(0) (real space) i0_real2.0480e+09
I(0) uncertainty (real space) i0_real_error3.8920e+07
Rg (reciprocal space) rg_reciprocal62.38
I(0) (reciprocal space) i0_reciprocal2044000000.0000
Solution quality estimate total_estimate0.8173
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary59.9
Skewness Skewness skewness0.639
Kurtosis Kurtosis kurtosis-0.059
Angular range angular_range— – 0.1250 −1
Current regularization parameter α current_alpha0.0065
Highest regularization parameter α highest_alpha109600000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.743; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.399

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id6rpbA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id6rpbA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6rpbB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6rpbE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6rpbF01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id6rpbF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6rpbG00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6rpbJ01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6rpbK01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id6rpbK02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6rpbL00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6rpbO01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6rpbP01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id6rpbP02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6rpbQ00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6rpbT01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)