7m72

MHC-like protein complex structure

Method: X-RAY DIFFRACTION Dmax: 138.4 Å Quality: REASONABLE

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

Antigen-presenting glycoprotein CD1d1

Mus musculus

UniProt P11609

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 4 其他Polymer 3 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 19–297 Not recorded Beta-2-microglobulin × 1 (P01887) NKT Valpha14 (Mouse)-2C12 TCR,Human T-cell receptor sp3.4 alpha chain × 1 (K7N5N2) NKT Vbeta8.2 (Mouse)-2C12 TCR,Human nkt tcr beta chain × 1 (K7N5M4) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 QOD (3R)-N-[(2S,3R)-1-(alpha-D-galactopyranosyloxy)-3-hydroxy-15-methylhexadecan-2-yl]-3-hydroxyheptadecanamide × 1 HP6 HEPTANE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5;277 K;18-20% PEG 3350, 8% Tacsimate pH 5.0 Resolution 2.40 Å R-free 0.227

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.

64 other PDB entries and 78 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CD1D1_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–279; UniProt 19–297

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 Other combination Heteromer Protein × 4 其他Polymer 3 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 21–119 Not recorded Antigen-presenting glycoprotein CD1d1 × 1 (P11609) NKT Valpha14 (Mouse)-2C12 TCR,Human T-cell receptor sp3.4 alpha chain × 1 (K7N5N2) NKT Vbeta8.2 (Mouse)-2C12 TCR,Human nkt tcr beta chain × 1 (K7N5M4) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 QOD (3R)-N-[(2S,3R)-1-(alpha-D-galactopyranosyloxy)-3-hydroxy-15-methylhexadecan-2-yl]-3-hydroxyheptadecanamide × 1 HP6 HEPTANE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5;277 K;18-20% PEG 3350, 8% Tacsimate pH 5.0 Resolution 2.40 Å R-free 0.227

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 1–99; UniProt 21–119

NKT Valpha14 (Mouse)-2C12 TCR,Human T-cell receptor sp3.4 alpha chain

Homo sapiens

UniProt K7N5N2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 4 其他Polymer 3 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 115–207 Fragment:murine variable domain,human constant domain Antigen-presenting glycoprotein CD1d1 × 1 (P11609) Beta-2-microglobulin × 1 (P01887) NKT Vbeta8.2 (Mouse)-2C12 TCR,Human nkt tcr beta chain × 1 (K7N5M4) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 QOD (3R)-N-[(2S,3R)-1-(alpha-D-galactopyranosyloxy)-3-hydroxy-15-methylhexadecan-2-yl]-3-hydroxyheptadecanamide × 1 HP6 HEPTANE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5;277 K;18-20% PEG 3350, 8% Tacsimate pH 5.0 Resolution 2.40 Å R-free 0.227

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 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name K7N5N2_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 115–207; UniProt 115–207

NKT Vbeta8.2 (Mouse)-2C12 TCR,Human nkt tcr beta chain

Homo sapiens

UniProt K7N5M4

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 4 其他Polymer 3 PDB declaration: tetrameric(4) Consistent with protein copy count Chain D; UniProt 120–249 Fragment:murine variable domain,human constant domain Antigen-presenting glycoprotein CD1d1 × 1 (P11609) Beta-2-microglobulin × 1 (P01887) NKT Valpha14 (Mouse)-2C12 TCR,Human T-cell receptor sp3.4 alpha chain × 1 (K7N5N2) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 QOD (3R)-N-[(2S,3R)-1-(alpha-D-galactopyranosyloxy)-3-hydroxy-15-methylhexadecan-2-yl]-3-hydroxyheptadecanamide × 1 HP6 HEPTANE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5;277 K;18-20% PEG 3350, 8% Tacsimate pH 5.0 Resolution 2.40 Å R-free 0.227

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.

23 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name K7N5M4_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 113–242; UniProt 120–249

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 7m72

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7m72
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7m72
Deposition date deposition_date2021-03-26
Structure title titleMHC-like protein complex structure
Keywords keywords;MHC-like protein, CD1d1 antigen presenting molecule, lipid binding protein complex, LIPID BINDING PROTEIN, LIPID BINDING PROTEIN-IMMUNE SYSTEM complex ;; LIPID BINDING PROTEIN/IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier40.73
Radius of gyration Rg (electron density) rg_electron41.03
Forward intensity I(0) i0143792000.00
Molecular weight molecular_weight95575.0 kDa
Excluded volume excluded_volume118770 ų
Envelope volume envelope_volume163510 ų
Hydration-shell volume shell_volume37105 ų
Envelope diameter envelope_diameter149.7
Shell Rg shell_rg40.59
Envelope Rg envelope_rg41.08
Shape Rg shape_rg41.06
Total Rg total_rg40.93
Total atoms total_atoms6736
Residues n_residues840
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 dmax138.4
Rg (real space) rg_real41.29
Rg uncertainty (real space) rg_real_error1.66
I(0) (real space) i0_real1.4380e+08
I(0) uncertainty (real space) i0_real_error2.6420e+06
Rg (reciprocal space) rg_reciprocal40.74
I(0) (reciprocal space) i0_reciprocal143700000.0000
Solution quality estimate total_estimate0.7213
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.9
Skewness Skewness skewness0.642
Kurtosis Kurtosis kurtosis-0.315
Angular range angular_range— – 0.1950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12730000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.615; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.407; Smooth: 0.123

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

8. Citations (1)

9. Files and Curves (10)