8vz9

Crystal structure of mouse MAIT M2A TCR-MR1-5-OP-RU complex

Method: X-RAY DIFFRACTION Dmax: 129.3 Å Quality: GOOD

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

Major histocompatibility complex class I-related gene protein

Mus musculus

UniProt Q8HWB0

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 18–288 Not recorded Beta-2-microglobulin × 1 (P01887) Mouse MAIT TRAV1-TRAJ33 a-chain × 1 Mouse MAIT MBV13-2A b-chain × 1 GOL GLYCEROL × 2 2LJ 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;295 K;0.1M Bis-Tris Propane (pH 7.5 - 8.5), 16-22% PEG 3350 and 0.2M sodium acetate Resolution 3.40 Å R-free 0.263

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 HMR1_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–271; UniProt 18–288

Beta-2-microglobulin

Mus musculus

UniProt P01887

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 20–119 Not recorded Major histocompatibility complex class I-related gene protein × 1 (Q8HWB0) Mouse MAIT TRAV1-TRAJ33 a-chain × 1 Mouse MAIT MBV13-2A b-chain × 1 GOL GLYCEROL × 2 2LJ 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;295 K;0.1M Bis-Tris Propane (pH 7.5 - 8.5), 16-22% PEG 3350 and 0.2M sodium acetate Resolution 3.40 Å R-free 0.263

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.

290 other PDB entries and 483 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name B2MG_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–100; UniProt 20–119

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 8vz9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8vz9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8vz9
Deposition date deposition_date2024-02-11
Structure title titleCrystal structure of mouse MAIT M2A TCR-MR1-5-OP-RU complex
Keywords keywordsMouse MAIT TCR recognition of MR1, 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_guinier36.38
Radius of gyration Rg (electron density) rg_electron36.75
Forward intensity I(0) i0111631000.00
Molecular weight molecular_weight83695.0 kDa
Excluded volume excluded_volume103980 ų
Envelope volume envelope_volume141360 ų
Hydration-shell volume shell_volume35429 ų
Envelope diameter envelope_diameter136.6
Shell Rg shell_rg38.25
Envelope Rg envelope_rg37.43
Shape Rg shape_rg36.73
Total Rg total_rg36.90
Total atoms total_atoms5921
Residues n_residues787
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 dmax129.3
Rg (real space) rg_real36.97
Rg uncertainty (real space) rg_real_error1.47
I(0) (real space) i0_real1.1160e+08
I(0) uncertainty (real space) i0_real_error1.9380e+06
Rg (reciprocal space) rg_reciprocal36.60
I(0) (reciprocal space) i0_reciprocal111600000.0000
Solution quality estimate total_estimate0.7572
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.1
Skewness Skewness skewness0.693
Kurtosis Kurtosis kurtosis-0.076
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12970000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.607; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.464; Smooth: 0.555

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)