2p5e

Crystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC Reveal Native Diagonal Binding Geometry

Method: X-RAY DIFFRACTION Dmax: 131.1 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 Fragment:EXTRACELLULAR DOMAINS ALPHA 1, ALPHA2 AND ALPHA3, RESIDUES 25-299 Beta-2-microglobulin × 1 (P61769) Cancer/testis antigen 1B × 1 (P78358) T-Cell Receptor, Alpha Chain × 1 (A2NVQ1) Hypothetical protein × 1 (Q2YDB4) GOL GLYCEROL × 8 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 5 IPA ISOPROPYL ALCOHOL × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;293 K;85 mM HEPES, 8.5% Isopropanol, 17% PEG 4000, 15% Glycerol, pH 7.5, VAPOR DIFFUSION, temperature 293K, pH 7.50 Resolution 1.89 Å R-free 0.236

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 465 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 1–276; 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 Fragment:BETA-2 MICROGLOBULIN, RESIDUES 21-119 HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Cancer/testis antigen 1B × 1 (P78358) T-Cell Receptor, Alpha Chain × 1 (A2NVQ1) Hypothetical protein × 1 (Q2YDB4) GOL GLYCEROL × 8 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 5 IPA ISOPROPYL ALCOHOL × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;293 K;85 mM HEPES, 8.5% Isopropanol, 17% PEG 4000, 15% Glycerol, pH 7.5, VAPOR DIFFUSION, temperature 293K, pH 7.50 Resolution 1.89 Å R-free 0.236

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 3–100; UniProt 21–119

Cancer/testis antigen 1B

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 157–165 Fragment:RESIDUES 157-165 HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) T-Cell Receptor, Alpha Chain × 1 (A2NVQ1) Hypothetical protein × 1 (Q2YDB4) GOL GLYCEROL × 8 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 5 IPA ISOPROPYL ALCOHOL × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;293 K;85 mM HEPES, 8.5% Isopropanol, 17% PEG 4000, 15% Glycerol, pH 7.5, VAPOR DIFFUSION, temperature 293K, pH 7.50 Resolution 1.89 Å R-free 0.236

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 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 157–165

T-Cell Receptor, Alpha Chain

Homo sapiens

UniProt A2NVQ1

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 D; UniProt 20–111 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Cancer/testis antigen 1B × 1 (P78358) Hypothetical protein × 1 (Q2YDB4) GOL GLYCEROL × 8 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 5 IPA ISOPROPYL ALCOHOL × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;293 K;85 mM HEPES, 8.5% Isopropanol, 17% PEG 4000, 15% Glycerol, pH 7.5, VAPOR DIFFUSION, temperature 293K, pH 7.50 Resolution 1.89 Å R-free 0.236

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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A2NVQ1_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 2–93; UniProt 20–111

Hypothetical protein

Homo sapiens

UniProt Q2YDB4

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 E; UniProt 22–263 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Cancer/testis antigen 1B × 1 (P78358) T-Cell Receptor, Alpha Chain × 1 (A2NVQ1) GOL GLYCEROL × 8 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 5 IPA ISOPROPYL ALCOHOL × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;293 K;85 mM HEPES, 8.5% Isopropanol, 17% PEG 4000, 15% Glycerol, pH 7.5, VAPOR DIFFUSION, temperature 293K, pH 7.50 Resolution 1.89 Å R-free 0.236

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.

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q2YDB4_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain E; PDBConstruct 1–241; UniProt 22–263

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 2p5e

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2p5e
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2p5e
Deposition date deposition_date2007-03-15
Structure title titleCrystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC Reveal Native Diagonal Binding Geometry
Keywords keywordsT-CELL RECEPTOR, CDR3, PHAGE DISPLAY, MUTANT, HIGH AFFINITY, NY-ESO-1, 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_guinier37.19
Radius of gyration Rg (electron density) rg_electron37.31
Forward intensity I(0) i0149071000.00
Molecular weight molecular_weight94728.0 kDa
Excluded volume excluded_volume116790 ų
Envelope volume envelope_volume153710 ų
Hydration-shell volume shell_volume37504 ų
Envelope diameter envelope_diameter138.3
Shell Rg shell_rg39.19
Envelope Rg envelope_rg37.88
Shape Rg shape_rg37.31
Total Rg total_rg37.44
Total atoms total_atoms6661
Residues n_residues820
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 dmax131.1
Rg (real space) rg_real37.79
Rg uncertainty (real space) rg_real_error1.37
I(0) (real space) i0_real1.4910e+08
I(0) uncertainty (real space) i0_real_error2.6500e+06
Rg (reciprocal space) rg_reciprocal37.42
I(0) (reciprocal space) i0_reciprocal149000000.0000
Solution quality estimate total_estimate0.7677
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary33.5
Skewness Skewness skewness0.670
Kurtosis Kurtosis kurtosis-0.128
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16340000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.631; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.502; Smooth: 0.582

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (11)

7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2p5ea1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd2p5ea2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd2p5eb2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd2p5eb3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (7 domains)

Domain ID domain_id2p5eA01
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_id2p5eA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2p5eB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2p5eD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2p5eD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2p5eE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2p5eE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)