9fe1

Cryo-EM structure of the ternary DARPin NY_1/HLA-A0201/NY-ESO1 complex.

Method: ELECTRON MICROSCOPY Dmax: 95.2 Å Quality: GOOD

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

MHC class I antigen

Homo sapiens

UniProt Q8WLS4

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 25–300 Not recorded Beta-2-microglobulin × 1 (P61769) Cancer/testis antigen 1 × 1 (P78358) DARPin NY_1 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4;25 mM HEPES, 150 mM NaCl, pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.10 Å

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.

10 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q8WLS4_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–277; 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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 21–119 Fragment:UNP residues 21-119 MHC class I antigen × 1 (Q8WLS4) Cancer/testis antigen 1 × 1 (P78358) DARPin NY_1 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4;25 mM HEPES, 150 mM NaCl, pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.10 Å

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

Cancer/testis antigen 1

OrganismNot specified

UniProt P78358

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 157–165 Not recorded MHC class I antigen × 1 (Q8WLS4) Beta-2-microglobulin × 1 (P61769) DARPin NY_1 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4;25 mM HEPES, 150 mM NaCl, pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.10 Å

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.

12 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CTG1B_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 157–165

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 9fe1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9fe1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9fe1
Deposition date deposition_date2024-05-17
Structure title titleCryo-EM structure of the ternary DARPin NY_1/HLA-A0201/NY-ESO1 complex.
Keywords keywordsDARPin targeting MHC molecules in complex with tumor-associated peptide antigens, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier27.62
Radius of gyration Rg (electron density) rg_electron26.95
Forward intensity I(0) i062882300.00
Molecular weight molecular_weight60808.0 kDa
Excluded volume excluded_volume75578 ų
Envelope volume envelope_volume93327 ų
Hydration-shell volume shell_volume29914 ų
Envelope diameter envelope_diameter97.8
Shell Rg shell_rg33.36
Envelope Rg envelope_rg27.23
Shape Rg shape_rg26.92
Total Rg total_rg27.72
Total atoms total_atoms8458
Residues n_residues539
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 dmax95.2
Rg (real space) rg_real27.74
Rg uncertainty (real space) rg_real_error0.71
I(0) (real space) i0_real6.2880e+07
I(0) uncertainty (real space) i0_real_error9.5450e+05
Rg (reciprocal space) rg_reciprocal27.70
I(0) (reciprocal space) i0_reciprocal62880000.0000
Solution quality estimate total_estimate0.8581
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.7
Skewness Skewness skewness0.502
Kurtosis Kurtosis kurtosis-0.139
Angular range angular_range— – 0.2850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11200000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.763; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.921

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)