3fqn

Phosphorylation of self-peptides alters Human Leukocyte Antigen Class I-restricted antigen presentation and generates tumor specific epitopes

Method: X-RAY DIFFRACTION Dmax: 74.9 Å Quality: EXCELLENT

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 25–299 Fragment:EXTRACELLULAR DOMAINS ALPHA1, ALPHA2, ALPHA3, UNP residues 25-299 Beta-2-microglobulin × 1 (P61769) peptide 30-39 from beta-Catenin: YLDSGIHSGA × 1 CD CADMIUM ION × 6 MG MAGNESIUM ION × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;293 K;13% PEG3350, 5mM CdCl2, 5mM MgCl2, 0.1M NaCl, pH7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.65 Å R-free 0.197

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 1–275; 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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 22–119 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) peptide 30-39 from beta-Catenin: YLDSGIHSGA × 1 CD CADMIUM ION × 6 MG MAGNESIUM ION × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;293 K;13% PEG3350, 5mM CdCl2, 5mM MgCl2, 0.1M NaCl, pH7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.65 Å R-free 0.197

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 1–98; UniProt 22–119

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 3fqn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3fqn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3fqn
Deposition date deposition_date2009-01-07
Structure title titlePhosphorylation of self-peptides alters Human Leukocyte Antigen Class I-restricted antigen presentation and generates tumor specific epitopes
Keywords keywords;IMMUNE SYSTEM, PHOSPHORYLATION, Glycoprotein, Immune response, Membrane, MHC I, Phosphoprotein, Transmembrane, Disease mutation, Immunoglobulin domain, Pyrrolidone carboxylic acid, Secreted, cancer, TCR, self-epitope ;; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.16
Radius of gyration Rg (electron density) rg_electron22.96
Forward intensity I(0) i038213300.00
Molecular weight molecular_weight44943.0 kDa
Excluded volume excluded_volume54811 ų
Envelope volume envelope_volume66765 ų
Hydration-shell volume shell_volume24390 ų
Envelope diameter envelope_diameter79.6
Shell Rg shell_rg29.71
Envelope Rg envelope_rg23.03
Shape Rg shape_rg22.91
Total Rg total_rg23.86
Total atoms total_atoms3139
Residues n_residues381
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 dmax74.9
Rg (real space) rg_real24.10
Rg uncertainty (real space) rg_real_error0.45
I(0) (real space) i0_real3.8210e+07
I(0) uncertainty (real space) i0_real_error5.4580e+05
Rg (reciprocal space) rg_reciprocal24.12
I(0) (reciprocal space) i0_reciprocal38210000.0000
Solution quality estimate total_estimate0.9122
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.3
Skewness Skewness skewness0.259
Kurtosis Kurtosis kurtosis-0.476
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9631000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.996

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3fqnb_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (3 domains)

Domain ID domain_id3fqnA01
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_id3fqnA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3fqnB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)