6wzy

Structure of DbNA(10) peptides bound to H-2Db MHC-I

Method: X-RAY DIFFRACTION Dmax: 78.4 Å Quality: EXCELLENT

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

H-2 class I histocompatibility antigen, D-B alpha chain

Mus musculus

UniProt P01899

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 25–302 Not recorded Beta-2-microglobulin × 1 (P61769) Epitope from Neuraminidase Protein (NA-181-190) × 1 (P03468) EDO 1,2-ETHANEDIOL × 2 PEG DI(HYDROXYETHYL)ETHER × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.7;298 K;0.1M sodium citrate pH 5.7, 0.2M LiSO4 and 24-28% (w/v) PEG3350 Resolution 1.50 Å R-free 0.204

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.

93 other PDB entries and 202 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HA11_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–279; UniProt 25–302

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 Not recorded H-2 class I histocompatibility antigen, D-B alpha chain × 1 (P01899) Epitope from Neuraminidase Protein (NA-181-190) × 1 (P03468) EDO 1,2-ETHANEDIOL × 2 PEG DI(HYDROXYETHYL)ETHER × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.7;298 K;0.1M sodium citrate pH 5.7, 0.2M LiSO4 and 24-28% (w/v) PEG3350 Resolution 1.50 Å R-free 0.204

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 1–99; UniProt 21–119

Epitope from Neuraminidase Protein (NA-181-190)

OrganismNot specified

UniProt P03468

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 181–190 Fragment:Residues 181-190 H-2 class I histocompatibility antigen, D-B alpha chain × 1 (P01899) Beta-2-microglobulin × 1 (P61769) EDO 1,2-ETHANEDIOL × 2 PEG DI(HYDROXYETHYL)ETHER × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.7;298 K;0.1M sodium citrate pH 5.7, 0.2M LiSO4 and 24-28% (w/v) PEG3350 Resolution 1.50 Å R-free 0.204

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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NRAM_I34A1
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–10; UniProt 181–190

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 6wzy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6wzy
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id6wzy
Deposition date deposition_date2020-05-14
Structure title titleStructure of DbNA(10) peptides bound to H-2Db MHC-I
Keywords keywordsmouse, MHC, Class I MHC, histocompatibility, 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_guinier24.29
Radius of gyration Rg (electron density) rg_electron23.37
Forward intensity I(0) i035721200.00
Molecular weight molecular_weight44941.0 kDa
Excluded volume excluded_volume55652 ų
Envelope volume envelope_volume68860 ų
Hydration-shell volume shell_volume24707 ų
Envelope diameter envelope_diameter79.5
Shell Rg shell_rg30.14
Envelope Rg envelope_rg23.46
Shape Rg shape_rg23.34
Total Rg total_rg24.24
Total atoms total_atoms3172
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 dmax78.4
Rg (real space) rg_real24.22
Rg uncertainty (real space) rg_real_error0.44
I(0) (real space) i0_real3.5720e+07
I(0) uncertainty (real space) i0_real_error4.9610e+05
Rg (reciprocal space) rg_reciprocal24.24
I(0) (reciprocal space) i0_reciprocal35720000.0000
Solution quality estimate total_estimate0.9037
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.6
Skewness Skewness skewness0.245
Kurtosis Kurtosis kurtosis-0.498
Angular range angular_range— – 0.3250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9070000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.997

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)