6c09

Ternary crystal structure of the 3C8 TCR-CD1c-monoacylglycerol complex

Method: X-RAY DIFFRACTION Dmax: 132.8 Å Quality: GOOD

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

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 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 19–297 Not recorded Beta-2-microglobulin × 1 (P61769) 3C8 T cell receptor alpha-chain × 1 3C8 T cell receptor beta-chain × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EKG (2R)-2,3-dihydroxypropyl hexadecanoate × 1 D10 DECANE × 2 K POTASSIUM ION × 3 EDO 1,2-ETHANEDIOL × 3 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;293 K;20% PEG 3350, 0.2M potassium thiocynate Resolution 2.95 Å R-free 0.208

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 13 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 A; PDBConstruct 4–282; UniProt 19–297

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 21–119 Not recorded T-cell surface glycoprotein CD1c × 1 (P29017) 3C8 T cell receptor alpha-chain × 1 3C8 T cell receptor beta-chain × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EKG (2R)-2,3-dihydroxypropyl hexadecanoate × 1 D10 DECANE × 2 K POTASSIUM ION × 3 EDO 1,2-ETHANEDIOL × 3 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;293 K;20% PEG 3350, 0.2M potassium thiocynate Resolution 2.95 Å R-free 0.208

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 4–102; UniProt 21–119

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 6c09

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6c09
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6c09
Deposition date deposition_date2017-12-28
Structure title titleTernary crystal structure of the 3C8 TCR-CD1c-monoacylglycerol complex
Keywords keywordsT cell Receptor, Antigen Presentation, 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_guinier37.77
Radius of gyration Rg (electron density) rg_electron38.12
Forward intensity I(0) i0117862000.00
Molecular weight molecular_weight87779.0 kDa
Excluded volume excluded_volume109760 ų
Envelope volume envelope_volume146950 ų
Hydration-shell volume shell_volume35760 ų
Envelope diameter envelope_diameter139.1
Shell Rg shell_rg38.84
Envelope Rg envelope_rg38.48
Shape Rg shape_rg38.12
Total Rg total_rg38.20
Total atoms total_atoms6204
Residues n_residues803
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 dmax132.8
Rg (real space) rg_real38.43
Rg uncertainty (real space) rg_real_error1.61
I(0) (real space) i0_real1.1790e+08
I(0) uncertainty (real space) i0_real_error2.0680e+06
Rg (reciprocal space) rg_reciprocal38.02
I(0) (reciprocal space) i0_reciprocal117800000.0000
Solution quality estimate total_estimate0.7717
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary31.6
Skewness Skewness skewness0.657
Kurtosis Kurtosis kurtosis-0.195
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14620000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.621; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.651; Smooth: 0.519

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (11)

7. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (7 domains)

Domain ID domain_idd6c09a1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.0 — automated matches
Domain ID domain_idd6c09a2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd6c09b_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd6c09c1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd6c09c2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd6c09d1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd6c09d2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id6c09A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id6c09A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6c09B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6c09C01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6c09D01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6c09D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (2)

9. Files and Curves (10)