5c08

1E6 TCR in Complex with HLA-A0e carrying RQWGPDPAAV

Method: X-RAY DIFFRACTION Dmax: 231.0 Å Quality: REASONABLE

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:UNP residues 25-300 Beta-2-microglobulin × 1 (P61769) Marker peptide × 1 1E6 TCR Alpha Chain × 1 1E6 TCR Beta Chain × 1 EDO 1,2-ETHANEDIOL × 12 GOL GLYCEROL × 3 SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.2M sodium cholride, 0.1M MES pH6, 20% PEG 6000 Resolution 2.33 Å R-free 0.272
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain F; UniProt 25–300 Fragment:UNP residues 25-300 Beta-2-microglobulin × 1 (P61769) Marker peptide × 1 1E6 TCR Alpha Chain × 1 1E6 TCR Beta Chain × 1 EDO 1,2-ETHANEDIOL × 13 SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.2M sodium cholride, 0.1M MES pH6, 20% PEG 6000 Resolution 2.33 Å R-free 0.272

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 464 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 Author chain F; 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:UNP residues 21-119 HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Marker peptide × 1 1E6 TCR Alpha Chain × 1 1E6 TCR Beta Chain × 1 EDO 1,2-ETHANEDIOL × 12 GOL GLYCEROL × 3 SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.2M sodium cholride, 0.1M MES pH6, 20% PEG 6000 Resolution 2.33 Å R-free 0.272
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain G; UniProt 21–119 Fragment:UNP residues 21-119 HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Marker peptide × 1 1E6 TCR Alpha Chain × 1 1E6 TCR Beta Chain × 1 EDO 1,2-ETHANEDIOL × 13 SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.2M sodium cholride, 0.1M MES pH6, 20% PEG 6000 Resolution 2.33 Å R-free 0.272

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 1997 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

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 5c08

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5c08
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5c08
Deposition date deposition_date2015-06-12
Structure title title1E6 TCR in Complex with HLA-A0e carrying RQWGPDPAAV
Keywords keywordsIMMUNO, HLA-A02, 1E6-TCR, Cross-reactivity, 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_guinier68.56
Radius of gyration Rg (electron density) rg_electron70.04
Forward intensity I(0) i0563610000.00
Molecular weight molecular_weight190470.0 kDa
Excluded volume excluded_volume235000 ų
Envelope volume envelope_volume354420 ų
Hydration-shell volume shell_volume52509 ų
Envelope diameter envelope_diameter248.8
Shell Rg shell_rg48.13
Envelope Rg envelope_rg71.10
Shape Rg shape_rg70.00
Total Rg total_rg69.58
Total atoms total_atoms13407
Residues n_residues1641
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 dmax231.0
Rg (real space) rg_real69.55
Rg uncertainty (real space) rg_real_error2.95
I(0) (real space) i0_real5.6350e+08
I(0) uncertainty (real space) i0_real_error1.2790e+07
Rg (reciprocal space) rg_reciprocal64.96
I(0) (reciprocal space) i0_reciprocal558900000.0000
Solution quality estimate total_estimate0.6084
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary40.2
Skewness Skewness skewness0.665
Kurtosis Kurtosis kurtosis-0.448
Angular range angular_range— – 0.1150 −1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha12730000.0000
Real-space data points n_real_points24
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.201; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.086; Smooth: 0.225

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

7. Fold Classification (SCOP + CATH) 14 domains

CATH v4.4 (14 domains)

Domain ID domain_id5c08A01
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_id5c08A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5c08B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5c08D01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5c08D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5c08E01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5c08E02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5c08F01
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_id5c08F02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5c08G00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5c08I01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5c08I02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5c08J01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5c08J02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)