5bs0

MAGE-A3 Reactive TCR in complex with Titin Epitope in HLA-A1

Method: X-RAY DIFFRACTION Dmax: 133.2 Å Quality: GOOD

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

HLA class I histocompatibility antigen, A-1 alpha chain

Homo sapiens

UniProt P30443

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 25–298 Not recorded Beta-2-microglobulin × 1 (P61769) Titin × 1 (Q8WZ42) Protein TRAV21,T-cell receptor alpha chain C region × 1 (A0A0B4J279,P01848) Protein TRBV5-1,Human nkt tcr beta chain × 1 (A0A578,K7N5M4) GOL GLYCEROL × 1 SO4 SULFATE ION × 11 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;291 K;0.2M Ammonium Chloride, 0.1M MES, 20% PEG 4000 Resolution 2.40 Å R-free 0.262

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.

7 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1A01_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–274; UniProt 25–298

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 Not recorded HLA class I histocompatibility antigen, A-1 alpha chain × 1 (P30443) Titin × 1 (Q8WZ42) Protein TRAV21,T-cell receptor alpha chain C region × 1 (A0A0B4J279,P01848) Protein TRBV5-1,Human nkt tcr beta chain × 1 (A0A578,K7N5M4) GOL GLYCEROL × 1 SO4 SULFATE ION × 11 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;291 K;0.2M Ammonium Chloride, 0.1M MES, 20% PEG 4000 Resolution 2.40 Å R-free 0.262

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 2–100; UniProt 21–119

Titin

OrganismNot specified

UniProt Q8WZ42

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 24337–24345 Fragment:UNP residues 24337-24345 HLA class I histocompatibility antigen, A-1 alpha chain × 1 (P30443) Beta-2-microglobulin × 1 (P61769) Protein TRAV21,T-cell receptor alpha chain C region × 1 (A0A0B4J279,P01848) Protein TRBV5-1,Human nkt tcr beta chain × 1 (A0A578,K7N5M4) GOL GLYCEROL × 1 SO4 SULFATE ION × 11 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;291 K;0.2M Ammonium Chloride, 0.1M MES, 20% PEG 4000 Resolution 2.40 Å R-free 0.262

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.

54 other PDB entries and 123 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TITIN_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 24337–24345

Protein TRAV21,T-cell receptor alpha chain C region

Homo sapiens

UniProt A0A0B4J279

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 21–112 Not recorded HLA class I histocompatibility antigen, A-1 alpha chain × 1 (P30443) Beta-2-microglobulin × 1 (P61769) Titin × 1 (Q8WZ42) Protein TRBV5-1,Human nkt tcr beta chain × 1 (A0A578,K7N5M4) GOL GLYCEROL × 1 SO4 SULFATE ION × 11 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;291 K;0.2M Ammonium Chloride, 0.1M MES, 20% PEG 4000 Resolution 2.40 Å R-free 0.262

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 A0A0B4J279_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 2–93; UniProt 21–112

Protein TRAV21,T-cell receptor alpha chain C region

Homo sapiens

UniProt P01848

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 3–84 Not recorded HLA class I histocompatibility antigen, A-1 alpha chain × 1 (P30443) Beta-2-microglobulin × 1 (P61769) Titin × 1 (Q8WZ42) Protein TRBV5-1,Human nkt tcr beta chain × 1 (A0A578,K7N5M4) GOL GLYCEROL × 1 SO4 SULFATE ION × 11 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;291 K;0.2M Ammonium Chloride, 0.1M MES, 20% PEG 4000 Resolution 2.40 Å R-free 0.262

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.

34 other PDB entries and 51 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TCA_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 116–197; UniProt 3–84

Protein TRBV5-1,Human nkt tcr beta chain

Homo sapiens

UniProt A0A578

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 21–113 Not recorded HLA class I histocompatibility antigen, A-1 alpha chain × 1 (P30443) Beta-2-microglobulin × 1 (P61769) Titin × 1 (Q8WZ42) Protein TRAV21,T-cell receptor alpha chain C region × 1 (A0A0B4J279,P01848) GOL GLYCEROL × 1 SO4 SULFATE ION × 11 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;291 K;0.2M Ammonium Chloride, 0.1M MES, 20% PEG 4000 Resolution 2.40 Å R-free 0.262

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 A0A578_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain E; PDBConstruct 1–93; UniProt 21–113

Protein TRBV5-1,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 E; UniProt 108–249 Not recorded HLA class I histocompatibility antigen, A-1 alpha chain × 1 (P30443) Beta-2-microglobulin × 1 (P61769) Titin × 1 (Q8WZ42) Protein TRAV21,T-cell receptor alpha chain C region × 1 (A0A0B4J279,P01848) GOL GLYCEROL × 1 SO4 SULFATE ION × 11 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;291 K;0.2M Ammonium Chloride, 0.1M MES, 20% PEG 4000 Resolution 2.40 Å R-free 0.262

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 E; PDBConstruct 100–241; UniProt 108–249

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 5bs0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5bs0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5bs0
Deposition date deposition_date2015-06-01
Structure title titleMAGE-A3 Reactive TCR in complex with Titin Epitope in HLA-A1
Keywords keywordsImmuno pMHC TCR Titin, 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_guinier37.53
Radius of gyration Rg (electron density) rg_electron38.05
Forward intensity I(0) i0151807000.00
Molecular weight molecular_weight94229.0 kDa
Excluded volume excluded_volume115630 ų
Envelope volume envelope_volume157360 ų
Hydration-shell volume shell_volume37922 ų
Envelope diameter envelope_diameter144.0
Shell Rg shell_rg39.33
Envelope Rg envelope_rg38.41
Shape Rg shape_rg38.07
Total Rg total_rg38.08
Total atoms total_atoms6625
Residues n_residues822
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 dmax133.2
Rg (real space) rg_real38.16
Rg uncertainty (real space) rg_real_error1.31
I(0) (real space) i0_real1.5180e+08
I(0) uncertainty (real space) i0_real_error2.5720e+06
Rg (reciprocal space) rg_reciprocal37.77
I(0) (reciprocal space) i0_reciprocal151700000.0000
Solution quality estimate total_estimate0.7773
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.7
Skewness Skewness skewness0.675
Kurtosis Kurtosis kurtosis-0.130
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18000000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.608; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.687; Smooth: 0.590

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id5bs0A01
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_id5bs0A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5bs0B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5bs0D01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5bs0D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5bs0E01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5bs0E02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)