6d78

The complex between high-affinity TCR DMF5(alpha-D26Y,beta-L98W) and human Class I MHC HLA-A2 with the bound MART-1(27-35)peptide

Method: X-RAY DIFFRACTION Dmax: 132.0 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 25–299 Fragment:UNP residues 25-299 Beta-2-microglobulin × 1 (P61769) Melanoma antigen recognized by T-cells 1 × 1 (Q16655) DMF5 alpha chain,DMF5 alpha chain × 1 (K7N5M3) DMF5 beta chain,DMF5 beta chain × 1 (K7N5M4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;0.1 M Tris, 12% PEG6000, 0.2 M magnesium chloride Resolution 2.35 Å R-free 0.255

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 2–276; UniProt 25–299

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) Melanoma antigen recognized by T-cells 1 × 1 (Q16655) DMF5 alpha chain,DMF5 alpha chain × 1 (K7N5M3) DMF5 beta chain,DMF5 beta chain × 1 (K7N5M4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;0.1 M Tris, 12% PEG6000, 0.2 M magnesium chloride Resolution 2.35 Å R-free 0.255

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

Melanoma antigen recognized by T-cells 1

OrganismNot specified

UniProt Q16655

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 27–35 Fragment:peptide (UNP residues 27-35) HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) DMF5 alpha chain,DMF5 alpha chain × 1 (K7N5M3) DMF5 beta chain,DMF5 beta chain × 1 (K7N5M4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;0.1 M Tris, 12% PEG6000, 0.2 M magnesium chloride Resolution 2.35 Å R-free 0.255

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.

15 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MAR1_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 27–35

DMF5 alpha chain,DMF5 alpha chain

Homo sapiens

UniProt K7N5M3

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 118–206 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Melanoma antigen recognized by T-cells 1 × 1 (Q16655) DMF5 beta chain,DMF5 beta chain × 1 (K7N5M4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;0.1 M Tris, 12% PEG6000, 0.2 M magnesium chloride Resolution 2.35 Å R-free 0.255

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.

19 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name K7N5M3_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 112–200; UniProt 118–206

DMF5 beta chain,DMF5 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 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain E; UniProt 125–249 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Melanoma antigen recognized by T-cells 1 × 1 (Q16655) DMF5 alpha chain,DMF5 alpha chain × 1 (K7N5M3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;0.1 M Tris, 12% PEG6000, 0.2 M magnesium chloride Resolution 2.35 Å R-free 0.255

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 119–243; UniProt 125–249

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 6d78

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6d78
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6d78
Deposition date deposition_date2018-04-24
Structure title titleThe complex between high-affinity TCR DMF5(alpha-D26Y,beta-L98W) and human Class I MHC HLA-A2 with the bound MART-1(27-35)peptide
Keywords keywordsAlpha-beta T-cell receptor bound to class I MHC (HLA-A2) in complex with the Mart-1 peptide, 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_guinier36.75
Radius of gyration Rg (electron density) rg_electron36.90
Forward intensity I(0) i0138521000.00
Molecular weight molecular_weight91783.0 kDa
Excluded volume excluded_volume113410 ų
Envelope volume envelope_volume151370 ų
Hydration-shell volume shell_volume37299 ų
Envelope diameter envelope_diameter140.1
Shell Rg shell_rg38.90
Envelope Rg envelope_rg37.65
Shape Rg shape_rg36.88
Total Rg total_rg37.08
Total atoms total_atoms6475
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 dmax132.0
Rg (real space) rg_real37.33
Rg uncertainty (real space) rg_real_error1.46
I(0) (real space) i0_real1.3850e+08
I(0) uncertainty (real space) i0_real_error2.3310e+06
Rg (reciprocal space) rg_reciprocal36.97
I(0) (reciprocal space) i0_reciprocal138500000.0000
Solution quality estimate total_estimate0.7650
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.8
Skewness Skewness skewness0.681
Kurtosis Kurtosis kurtosis-0.092
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17710000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.592; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.460; Smooth: 0.705

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id6d78A01
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_id6d78A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6d78B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6d78D01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6d78E01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6d78E02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)