4qok

Structural basis for ineffective T-cell responses to MHC anchor residue improved heteroclitic peptides

Method: X-RAY DIFFRACTION Dmax: 129.6 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 25–300 Not recorded Beta-2-microglobulin × 1 (P61769) Melanoma antigen recognized by T-cells 1 marker peptide × 1 (Q16655) Mel5 TCR chain alpha × 1 Mel5 TCR chain beta × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;291 K;0.1 M Sodium Cacodylate, pH 6.5, 15% PEG 4000, 15% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 291K Resolution 3.00 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.

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 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 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Melanoma antigen recognized by T-cells 1 marker peptide × 1 (Q16655) Mel5 TCR chain alpha × 1 Mel5 TCR chain beta × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;291 K;0.1 M Sodium Cacodylate, pH 6.5, 15% PEG 4000, 15% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 291K Resolution 3.00 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

Melanoma antigen recognized by T-cells 1 marker peptide

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 26–35 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Mel5 TCR chain alpha × 1 Mel5 TCR chain beta × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;291 K;0.1 M Sodium Cacodylate, pH 6.5, 15% PEG 4000, 15% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 291K Resolution 3.00 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.

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 1–10; UniProt 26–35

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 4qok

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4qok
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4qok
Deposition date deposition_date2014-06-20
Structure title titleStructural basis for ineffective T-cell responses to MHC anchor residue improved heteroclitic peptides
Keywords keywordsImmunoglobulin, HLA, TCR, Melanoma, 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_guinier37.12
Radius of gyration Rg (electron density) rg_electron37.24
Forward intensity I(0) i0143633000.00
Molecular weight molecular_weight93495.0 kDa
Excluded volume excluded_volume115580 ų
Envelope volume envelope_volume157790 ų
Hydration-shell volume shell_volume38352 ų
Envelope diameter envelope_diameter138.7
Shell Rg shell_rg39.21
Envelope Rg envelope_rg37.95
Shape Rg shape_rg37.23
Total Rg total_rg37.43
Total atoms total_atoms6596
Residues n_residues824
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 dmax129.6
Rg (real space) rg_real37.70
Rg uncertainty (real space) rg_real_error1.28
I(0) (real space) i0_real1.4360e+08
I(0) uncertainty (real space) i0_real_error2.4650e+06
Rg (reciprocal space) rg_reciprocal37.34
I(0) (reciprocal space) i0_reciprocal143600000.0000
Solution quality estimate total_estimate0.7716
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.2
Skewness Skewness skewness0.673
Kurtosis Kurtosis kurtosis-0.111
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19930000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.643; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.542; Smooth: 0.556

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id4qokA01
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_id4qokA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4qokB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4qokD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4qokD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4qokE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4qokE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)