9qwj

Crystal structure of S2c TCR in complex with CD1c

Method: X-RAY DIFFRACTION Dmax: 184.7 Å Quality: GOOD

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

Beta-2-microglobulin,T-cell surface glycoprotein CD1c

Homo sapiens

UniProt P29017

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 Heteromer Protein × 3 其他Polymer 1 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 24–297 Not recorded TCR alpha × 1 TCR beta × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 BMA beta-D-mannopyranose × 1 D12 DODECANE × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.1 M Sodium cacodylate trihydrate pH 6.4, 0.2 M Calcium chloride dihydrate, 16 % (w/v) PEG 3350 and 3 % (w/v) 1,6-Hexanediol Resolution 2.04 Å R-free 0.235
2 Insufficient information Heteromer Protein × 3 其他Polymer 1 PDB declaration: trimeric(3) Consistent with protein copy count Chain N; UniProt 24–297 Not recorded TCR alpha × 1 TCR beta × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 BMA beta-D-mannopyranose × 1 CA CALCIUM ION × 2 D10 DECANE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.1 M Sodium cacodylate trihydrate pH 6.4, 0.2 M Calcium chloride dihydrate, 16 % (w/v) PEG 3350 and 3 % (w/v) 1,6-Hexanediol Resolution 2.04 Å R-free 0.235

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.

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

View Construct and Data Evidence
UniProt name CD1C_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain B; PDBConstruct 135–408; UniProt 24–297 Author chain N; PDBConstruct 135–408; UniProt 24–297

Beta-2-microglobulin,T-cell surface glycoprotein CD1c

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 Heteromer Protein × 3 其他Polymer 1 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 21–118 Not recorded TCR alpha × 1 TCR beta × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 BMA beta-D-mannopyranose × 1 D12 DODECANE × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.1 M Sodium cacodylate trihydrate pH 6.4, 0.2 M Calcium chloride dihydrate, 16 % (w/v) PEG 3350 and 3 % (w/v) 1,6-Hexanediol Resolution 2.04 Å R-free 0.235
2 Insufficient information Heteromer Protein × 3 其他Polymer 1 PDB declaration: trimeric(3) Consistent with protein copy count Chain N; UniProt 21–118 Not recorded TCR alpha × 1 TCR beta × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 BMA beta-D-mannopyranose × 1 CA CALCIUM ION × 2 D10 DECANE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.1 M Sodium cacodylate trihydrate pH 6.4, 0.2 M Calcium chloride dihydrate, 16 % (w/v) PEG 3350 and 3 % (w/v) 1,6-Hexanediol Resolution 2.04 Å R-free 0.235

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 1997 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 B; PDBConstruct 21–118; UniProt 21–118 Author chain N; PDBConstruct 21–118; UniProt 21–118

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 9qwj

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9qwj
Deposition date deposition_date2025-04-14
最后修订 last_revision2025-08-20
Structure title titleCrystal structure of S2c TCR in complex with CD1c
Keywords keywordsT cell receptor, TCR, CD1c, lipids, 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_guinier53.10
Radius of gyration Rg (electron density) rg_electron53.26
Forward intensity I(0) i0512206000.00
Molecular weight molecular_weight184960.0 kDa
Excluded volume excluded_volume230290 ų
Envelope volume envelope_volume341500 ų
Hydration-shell volume shell_volume59161 ų
Envelope diameter envelope_diameter195.0
Shell Rg shell_rg48.62
Envelope Rg envelope_rg52.84
Shape Rg shape_rg53.21
Total Rg total_rg53.24
Total atoms total_atoms13055
Residues n_residues1604
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 dmax184.7
Rg (real space) rg_real53.63
Rg uncertainty (real space) rg_real_error2.23
I(0) (real space) i0_real5.1220e+08
I(0) uncertainty (real space) i0_real_error1.1260e+07
Rg (reciprocal space) rg_reciprocal52.65
I(0) (reciprocal space) i0_reciprocal511500000.0000
Solution quality estimate total_estimate0.8075
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary55.4
Skewness Skewness skewness0.607
Kurtosis Kurtosis kurtosis-0.066
Angular range angular_range— – 0.1500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha25320000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.786; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.890; Smooth: 0.246

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (11)

8. Citations (1)

9. Files and Curves (10)