9c6x

Crystal Structure of a single chain trimer composed of HLA-B*39:01 Y84C variant, beta-2microglobulin, and NRVMLPKAA peptide from NLRP2

Method: X-RAY DIFFRACTION Dmax: 73.9 Å Quality: EXCELLENT

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

NACHT, LRR and PYD domains-containing protein 2,Beta-2-microglobulin,MHC class I antigen

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 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 21–119 Not recorded P4G 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;291 K;25% PEG 3350 and 0.1 M Tris Resolution 1.70 Å R-free 0.232

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 1
Chains and sequence ranges Author chain A; PDBConstruct 26–124; UniProt 21–119

NACHT, LRR and PYD domains-containing protein 2,Beta-2-microglobulin,MHC class I antigen

Homo sapiens

UniProt Q9NX02

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 323–331 Not recorded P4G 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;291 K;25% PEG 3350 and 0.1 M Tris Resolution 1.70 Å R-free 0.232

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.

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NALP2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–9; UniProt 323–331

NACHT, LRR and PYD domains-containing protein 2,Beta-2-microglobulin,MHC class I antigen

Homo sapiens

UniProt R5AK10

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 25–298 Not recorded P4G 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;291 K;25% PEG 3350 and 0.1 M Tris Resolution 1.70 Å R-free 0.232

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name R5AK10_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 145–418; UniProt 25–298

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 9c6x

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9c6x
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9c6x
Deposition date deposition_date2024-06-09
Structure title titleCrystal Structure of a single chain trimer composed of HLA-B*39:01 Y84C variant, beta-2microglobulin, and NRVMLPKAA peptide from NLRP2
Keywords keywordsHLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-39 ALPHA CHAIN, BETA-2-MICROGLOBULIN, NLRP2, 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_guinier24.07
Radius of gyration Rg (electron density) rg_electron22.93
Forward intensity I(0) i037596700.00
Molecular weight molecular_weight45100.0 kDa
Excluded volume excluded_volume55475 ų
Envelope volume envelope_volume67746 ų
Hydration-shell volume shell_volume24732 ų
Envelope diameter envelope_diameter77.5
Shell Rg shell_rg29.77
Envelope Rg envelope_rg23.03
Shape Rg shape_rg22.90
Total Rg total_rg23.81
Total atoms total_atoms3181
Residues n_residues390
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 dmax73.9
Rg (real space) rg_real23.99
Rg uncertainty (real space) rg_real_error0.48
I(0) (real space) i0_real3.7600e+07
I(0) uncertainty (real space) i0_real_error4.7260e+05
Rg (reciprocal space) rg_reciprocal24.01
I(0) (reciprocal space) i0_reciprocal37600000.0000
Solution quality estimate total_estimate0.9141
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.0
Skewness Skewness skewness0.221
Kurtosis Kurtosis kurtosis-0.491
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8436000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.994

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)