8rlu

TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 S3N peptide

Method: X-RAY DIFFRACTION Dmax: 166.7 Å Quality: GOOD

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

HLA class I histocompatibility antigen, alpha chain E

Homo sapiens

UniProt P13747

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 22–297 Not recorded Beta-2-microglobulin × 1 (P61769) Large envelope protein × 1 (Q67953) T cell receptor alpha variable 12-2,T cell receptor alpha chain MC.7.G5 × 1 (A0A075B6T6,P0DTU3) T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5 × 1 (A0A0K0K1A5,P0DTU4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;20% (w/v) PEG 3350, 100 mM BIS-TRIS propane pH 8.5, 200 mM sodium sulfate Resolution 2.35 Å R-free 0.261
2 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain F; UniProt 22–297 Not recorded Beta-2-microglobulin × 1 (P61769) Large envelope protein × 1 (Q67953) T cell receptor alpha variable 12-2,T cell receptor alpha chain MC.7.G5 × 1 (A0A075B6T6,P0DTU3) T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5 × 1 (A0A0K0K1A5,P0DTU4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;20% (w/v) PEG 3350, 100 mM BIS-TRIS propane pH 8.5, 200 mM sodium sulfate Resolution 2.35 Å R-free 0.261

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.

28 other PDB entries and 56 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HLAE_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–276; UniProt 22–297 Author chain F; PDBConstruct 1–276; UniProt 22–297

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 Insufficient information 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, alpha chain E × 1 (P13747) Large envelope protein × 1 (Q67953) T cell receptor alpha variable 12-2,T cell receptor alpha chain MC.7.G5 × 1 (A0A075B6T6,P0DTU3) T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5 × 1 (A0A0K0K1A5,P0DTU4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;20% (w/v) PEG 3350, 100 mM BIS-TRIS propane pH 8.5, 200 mM sodium sulfate Resolution 2.35 Å R-free 0.261
2 Insufficient information 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, alpha chain E × 1 (P13747) Large envelope protein × 1 (Q67953) T cell receptor alpha variable 12-2,T cell receptor alpha chain MC.7.G5 × 1 (A0A075B6T6,P0DTU3) T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5 × 1 (A0A0K0K1A5,P0DTU4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;20% (w/v) PEG 3350, 100 mM BIS-TRIS propane pH 8.5, 200 mM sodium sulfate Resolution 2.35 Å R-free 0.261

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

Large envelope protein

OrganismNot specified

UniProt Q67953

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 427–435 Not recorded HLA class I histocompatibility antigen, alpha chain E × 1 (P13747) Beta-2-microglobulin × 1 (P61769) T cell receptor alpha variable 12-2,T cell receptor alpha chain MC.7.G5 × 1 (A0A075B6T6,P0DTU3) T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5 × 1 (A0A0K0K1A5,P0DTU4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;20% (w/v) PEG 3350, 100 mM BIS-TRIS propane pH 8.5, 200 mM sodium sulfate Resolution 2.35 Å R-free 0.261
2 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain H; UniProt 427–435 Not recorded HLA class I histocompatibility antigen, alpha chain E × 1 (P13747) Beta-2-microglobulin × 1 (P61769) T cell receptor alpha variable 12-2,T cell receptor alpha chain MC.7.G5 × 1 (A0A075B6T6,P0DTU3) T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5 × 1 (A0A0K0K1A5,P0DTU4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;20% (w/v) PEG 3350, 100 mM BIS-TRIS propane pH 8.5, 200 mM sodium sulfate Resolution 2.35 Å R-free 0.261

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 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q67953_HBV
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 427–435 Author chain H; PDBConstruct 1–9; UniProt 427–435

T cell receptor alpha variable 12-2,T cell receptor alpha chain MC.7.G5

Homo sapiens

UniProt A0A075B6T6

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain D; UniProt 23–112 Not recorded HLA class I histocompatibility antigen, alpha chain E × 1 (P13747) Beta-2-microglobulin × 1 (P61769) Large envelope protein × 1 (Q67953) T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5 × 1 (A0A0K0K1A5,P0DTU4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;20% (w/v) PEG 3350, 100 mM BIS-TRIS propane pH 8.5, 200 mM sodium sulfate Resolution 2.35 Å R-free 0.261
2 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain I; UniProt 23–112 Not recorded HLA class I histocompatibility antigen, alpha chain E × 1 (P13747) Beta-2-microglobulin × 1 (P61769) Large envelope protein × 1 (Q67953) T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5 × 1 (A0A0K0K1A5,P0DTU4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;20% (w/v) PEG 3350, 100 mM BIS-TRIS propane pH 8.5, 200 mM sodium sulfate Resolution 2.35 Å R-free 0.261

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.

6 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TVAL2_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 3–92; UniProt 23–112 Author chain I; PDBConstruct 3–92; UniProt 23–112

T cell receptor alpha variable 12-2,T cell receptor alpha chain MC.7.G5

Homo sapiens

UniProt P0DTU3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain D; UniProt 132–220 Not recorded HLA class I histocompatibility antigen, alpha chain E × 1 (P13747) Beta-2-microglobulin × 1 (P61769) Large envelope protein × 1 (Q67953) T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5 × 1 (A0A0K0K1A5,P0DTU4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;20% (w/v) PEG 3350, 100 mM BIS-TRIS propane pH 8.5, 200 mM sodium sulfate Resolution 2.35 Å R-free 0.261
2 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain I; UniProt 132–220 Not recorded HLA class I histocompatibility antigen, alpha chain E × 1 (P13747) Beta-2-microglobulin × 1 (P61769) Large envelope protein × 1 (Q67953) T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5 × 1 (A0A0K0K1A5,P0DTU4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;20% (w/v) PEG 3350, 100 mM BIS-TRIS propane pH 8.5, 200 mM sodium sulfate Resolution 2.35 Å R-free 0.261

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 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRAR2_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 111–199; UniProt 132–220 Author chain I; PDBConstruct 111–199; UniProt 132–220

T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5

Homo sapiens

UniProt A0A0K0K1A5

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain E; UniProt 20–112 Not recorded HLA class I histocompatibility antigen, alpha chain E × 1 (P13747) Beta-2-microglobulin × 1 (P61769) Large envelope protein × 1 (Q67953) T cell receptor alpha variable 12-2,T cell receptor alpha chain MC.7.G5 × 1 (A0A075B6T6,P0DTU3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;20% (w/v) PEG 3350, 100 mM BIS-TRIS propane pH 8.5, 200 mM sodium sulfate Resolution 2.35 Å R-free 0.261
2 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain J; UniProt 20–112 Not recorded HLA class I histocompatibility antigen, alpha chain E × 1 (P13747) Beta-2-microglobulin × 1 (P61769) Large envelope protein × 1 (Q67953) T cell receptor alpha variable 12-2,T cell receptor alpha chain MC.7.G5 × 1 (A0A075B6T6,P0DTU3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;20% (w/v) PEG 3350, 100 mM BIS-TRIS propane pH 8.5, 200 mM sodium sulfate Resolution 2.35 Å R-free 0.261

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.

11 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TVB65_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain E; PDBConstruct 2–94; UniProt 20–112 Author chain J; PDBConstruct 2–94; UniProt 20–112

T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5

Homo sapiens

UniProt P0DTU4

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain E; UniProt 127–266 Not recorded HLA class I histocompatibility antigen, alpha chain E × 1 (P13747) Beta-2-microglobulin × 1 (P61769) Large envelope protein × 1 (Q67953) T cell receptor alpha variable 12-2,T cell receptor alpha chain MC.7.G5 × 1 (A0A075B6T6,P0DTU3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;20% (w/v) PEG 3350, 100 mM BIS-TRIS propane pH 8.5, 200 mM sodium sulfate Resolution 2.35 Å R-free 0.261
2 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain J; UniProt 127–266 Not recorded HLA class I histocompatibility antigen, alpha chain E × 1 (P13747) Beta-2-microglobulin × 1 (P61769) Large envelope protein × 1 (Q67953) T cell receptor alpha variable 12-2,T cell receptor alpha chain MC.7.G5 × 1 (A0A075B6T6,P0DTU3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;20% (w/v) PEG 3350, 100 mM BIS-TRIS propane pH 8.5, 200 mM sodium sulfate Resolution 2.35 Å R-free 0.261

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.

6 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRBR2_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain E; PDBConstruct 104–243; UniProt 127–266 Author chain J; PDBConstruct 104–243; UniProt 127–266

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 8rlu

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8rlu
Deposition date deposition_date2024-01-03
Structure title titleTCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 S3N peptide
Keywords keywordsTCR-MHC, TCR, HLA-E, HBV, affinity matured, pHLA, 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_guinier48.36
Radius of gyration Rg (electron density) rg_electron48.32
Forward intensity I(0) i0518268000.00
Molecular weight molecular_weight182540.0 kDa
Excluded volume excluded_volume225630 ų
Envelope volume envelope_volume324090 ų
Hydration-shell volume shell_volume57138 ų
Envelope diameter envelope_diameter172.2
Shell Rg shell_rg50.55
Envelope Rg envelope_rg48.06
Shape Rg shape_rg48.29
Total Rg total_rg48.49
Total atoms total_atoms25121
Residues n_residues1605
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 dmax166.7
Rg (real space) rg_real48.56
Rg uncertainty (real space) rg_real_error1.78
I(0) (real space) i0_real5.1830e+08
I(0) uncertainty (real space) i0_real_error1.0100e+07
Rg (reciprocal space) rg_reciprocal48.36
I(0) (reciprocal space) i0_reciprocal518100000.0000
Solution quality estimate total_estimate0.8652
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary60.6
Skewness Skewness skewness0.340
Kurtosis Kurtosis kurtosis-0.426
Angular range angular_range— – 0.1650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha32310000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.946; Smooth: 0.675

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)