7ndu

Gag:02 TCR in complex with HLA-E featuring a non-natural amino acid

Method: X-RAY DIFFRACTION Dmax: 129.4 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 AAA; UniProt 22–297 Not recorded Beta-2-microglobulin × 1 (P61769) Gag6V(276-284 H4C) × 1 T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific T cell receptor alpha chain × 1 (A0A0B4J268,A0A075B6U7,P0DSE1) T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr beta chain × 1 (P04435,A0A0J9YX06,K7N5M4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;22.3% (w/v) PEG 1500, 89 mM MMT pH 9.0 Resolution 2.90 Å R-free 0.301

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 57 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 AAA; PDBConstruct 2–277; 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 BBB; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, alpha chain E × 1 (P13747) Gag6V(276-284 H4C) × 1 T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific T cell receptor alpha chain × 1 (A0A0B4J268,A0A075B6U7,P0DSE1) T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr beta chain × 1 (P04435,A0A0J9YX06,K7N5M4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;22.3% (w/v) PEG 1500, 89 mM MMT pH 9.0 Resolution 2.90 Å R-free 0.301

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 BBB; PDBConstruct 2–100; UniProt 21–119

T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific T cell receptor alpha chain

Homo sapiens

UniProt A0A075B6U7

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 DDD; UniProt 4–21 Not recorded HLA class I histocompatibility antigen, alpha chain E × 1 (P13747) Beta-2-microglobulin × 1 (P61769) Gag6V(276-284 H4C) × 1 T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr beta chain × 1 (P04435,A0A0J9YX06,K7N5M4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;22.3% (w/v) PEG 1500, 89 mM MMT pH 9.0 Resolution 2.90 Å R-free 0.301

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 A0A075B6U7_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain DDD; PDBConstruct 96–113; UniProt 4–21

T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific T cell receptor alpha chain

Homo sapiens

UniProt A0A0B4J268

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 DDD; UniProt 18–108 Not recorded HLA class I histocompatibility antigen, alpha chain E × 1 (P13747) Beta-2-microglobulin × 1 (P61769) Gag6V(276-284 H4C) × 1 T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr beta chain × 1 (P04435,A0A0J9YX06,K7N5M4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;22.3% (w/v) PEG 1500, 89 mM MMT pH 9.0 Resolution 2.90 Å R-free 0.301

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.

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TVA4_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain DDD; PDBConstruct 2–92; UniProt 18–108

T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific T cell receptor alpha chain

Homo sapiens

UniProt P0DSE1

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 DDD; UniProt 129–213 Not recorded HLA class I histocompatibility antigen, alpha chain E × 1 (P13747) Beta-2-microglobulin × 1 (P61769) Gag6V(276-284 H4C) × 1 T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr beta chain × 1 (P04435,A0A0J9YX06,K7N5M4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;22.3% (w/v) PEG 1500, 89 mM MMT pH 9.0 Resolution 2.90 Å R-free 0.301

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.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRAR1_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain DDD; PDBConstruct 115–199; UniProt 129–213

T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr beta chain

Homo sapiens

UniProt A0A0J9YX06

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 EEE; UniProt 2–15 Not recorded HLA class I histocompatibility antigen, alpha chain E × 1 (P13747) Beta-2-microglobulin × 1 (P61769) Gag6V(276-284 H4C) × 1 T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific T cell receptor alpha chain × 1 (A0A0B4J268,A0A075B6U7,P0DSE1) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;22.3% (w/v) PEG 1500, 89 mM MMT pH 9.0 Resolution 2.90 Å R-free 0.301

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 TJB12_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain EEE; PDBConstruct 101–114; UniProt 2–15

T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr beta chain

Homo sapiens

UniProt K7N5M4

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 EEE; UniProt 120–249 Not recorded HLA class I histocompatibility antigen, alpha chain E × 1 (P13747) Beta-2-microglobulin × 1 (P61769) Gag6V(276-284 H4C) × 1 T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific T cell receptor alpha chain × 1 (A0A0B4J268,A0A075B6U7,P0DSE1) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;22.3% (w/v) PEG 1500, 89 mM MMT pH 9.0 Resolution 2.90 Å R-free 0.301

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.

23 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name K7N5M4_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain EEE; PDBConstruct 115–244; UniProt 120–249

T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr beta chain

Homo sapiens

UniProt P04435

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 EEE; UniProt 20–115 Not recorded HLA class I histocompatibility antigen, alpha chain E × 1 (P13747) Beta-2-microglobulin × 1 (P61769) Gag6V(276-284 H4C) × 1 T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific T cell receptor alpha chain × 1 (A0A0B4J268,A0A075B6U7,P0DSE1) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;22.3% (w/v) PEG 1500, 89 mM MMT pH 9.0 Resolution 2.90 Å R-free 0.301

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 TVB79_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain EEE; PDBConstruct 2–97; UniProt 20–115

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 7ndu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7ndu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7ndu
Deposition date deposition_date2021-02-02
Structure title titleGag:02 TCR in complex with HLA-E featuring a non-natural amino acid
Keywords keywordsTCR-pHLA complex, non-natural amino acid, 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_guinier37.05
Radius of gyration Rg (electron density) rg_electron37.29
Forward intensity I(0) i0141951000.00
Molecular weight molecular_weight92571.0 kDa
Excluded volume excluded_volume114280 ų
Envelope volume envelope_volume157160 ų
Hydration-shell volume shell_volume38228 ų
Envelope diameter envelope_diameter138.4
Shell Rg shell_rg39.32
Envelope Rg envelope_rg37.77
Shape Rg shape_rg37.29
Total Rg total_rg37.42
Total atoms total_atoms6529
Residues n_residues809
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 dmax129.4
Rg (real space) rg_real37.62
Rg uncertainty (real space) rg_real_error1.42
I(0) (real space) i0_real1.4200e+08
I(0) uncertainty (real space) i0_real_error2.5280e+06
Rg (reciprocal space) rg_reciprocal37.27
I(0) (reciprocal space) i0_reciprocal141900000.0000
Solution quality estimate total_estimate0.7726
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.1
Skewness Skewness skewness0.670
Kurtosis Kurtosis kurtosis-0.104
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17490000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.673; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.564; Smooth: 0.456

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)