7mj7

HLA-A*02:01 bound to Neuroblastoma Derived IGFBPL1 peptide

Method: X-RAY DIFFRACTION Dmax: 76.2 Å Quality: EXCELLENT

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

MHC class I antigen

Homo sapiens

UniProt Q861F7

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 1–276 Not recorded Beta-2-microglobulin × 1 (P61769) Insulin-like growth factor-binding protein-like 1 peptide × 1 (Q8WX77) GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;295 K;1M Sodium Citrate Dibasic, 0.1M Sodium Cacodylate pH 6.5 Resolution 1.60 Å R-free 0.192

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.

31 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q861F7_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–277; UniProt 1–276

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 21–119 Fragment:UNP residues 21-119 MHC class I antigen × 1 (Q861F7) Insulin-like growth factor-binding protein-like 1 peptide × 1 (Q8WX77) GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;295 K;1M Sodium Citrate Dibasic, 0.1M Sodium Cacodylate pH 6.5 Resolution 1.60 Å R-free 0.192

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

Insulin-like growth factor-binding protein-like 1 peptide

OrganismNot specified

UniProt Q8WX77

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 C; UniProt 14–24 Fragment:Residues 14-24 MHC class I antigen × 1 (Q861F7) Beta-2-microglobulin × 1 (P61769) GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;295 K;1M Sodium Citrate Dibasic, 0.1M Sodium Cacodylate pH 6.5 Resolution 1.60 Å R-free 0.192

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.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IBPL1_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–11; UniProt 14–24

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 7mj7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7mj7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7mj7
Deposition date deposition_date2021-04-19
Structure title titleHLA-A*02:01 bound to Neuroblastoma Derived IGFBPL1 peptide
Keywords keywordsNEUROBLASTOMA TUMOR ANTIGEN, IGFBPL1, HUMAN MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I, MHC-I, COMPLEX, 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_guinier24.20
Radius of gyration Rg (electron density) rg_electron23.02
Forward intensity I(0) i035715300.00
Molecular weight molecular_weight44648.0 kDa
Excluded volume excluded_volume55193 ų
Envelope volume envelope_volume67127 ų
Hydration-shell volume shell_volume24450 ų
Envelope diameter envelope_diameter79.4
Shell Rg shell_rg29.90
Envelope Rg envelope_rg23.17
Shape Rg shape_rg23.00
Total Rg total_rg23.89
Total atoms total_atoms6135
Residues n_residues384
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 dmax76.2
Rg (real space) rg_real24.15
Rg uncertainty (real space) rg_real_error0.45
I(0) (real space) i0_real3.5720e+07
I(0) uncertainty (real space) i0_real_error5.1360e+05
Rg (reciprocal space) rg_reciprocal24.16
I(0) (reciprocal space) i0_reciprocal35720000.0000
Solution quality estimate total_estimate0.9095
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.8
Skewness Skewness skewness0.257
Kurtosis Kurtosis kurtosis-0.453
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7791000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.997

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)