6cx9

Structure of alpha-GSA[16,6P] bound by CD1d and in complex with the Va14Vb8.2 TCR

Method: X-RAY DIFFRACTION Dmax: 136.7 Å Quality: REASONABLE

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

Antigen-presenting glycoprotein CD1d1

Mus musculus

UniProt A0A0R4J090

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 1 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 19–297 Not recorded Beta-2-microglobulin × 1 (P01887) Chimeric T cell antigen receptor alpha chain Va14,Va24,Ja18 × 1 Chimeric T cell antigen receptor beta chain Vb8.2, vb11 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NA SODIUM ION × 7 EM4 N-[(2S,3S,4R)-3,4-dihydroxy-8-oxo-8-[(6-phenylhexyl)amino]-1-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}octan-2-yl]hexacosanamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 4;295 K;12% PEG 3350, 0.1M sodium malonate pH 4.0 Resolution 2.36 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.

30 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A0R4J090_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 1 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 21–119 Not recorded Antigen-presenting glycoprotein CD1d1 × 1 (A0A0R4J090) Chimeric T cell antigen receptor alpha chain Va14,Va24,Ja18 × 1 Chimeric T cell antigen receptor beta chain Vb8.2, vb11 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NA SODIUM ION × 7 EM4 N-[(2S,3S,4R)-3,4-dihydroxy-8-oxo-8-[(6-phenylhexyl)amino]-1-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}octan-2-yl]hexacosanamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 4;295 K;12% PEG 3350, 0.1M sodium malonate pH 4.0 Resolution 2.36 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.

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

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 6cx9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6cx9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6cx9
Deposition date deposition_date2018-04-02
Structure title titleStructure of alpha-GSA[16,6P] bound by CD1d and in complex with the Va14Vb8.2 TCR
Keywords keywordsimmune system, antigen-presentation, TCR, MHC-fold; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier39.22
Radius of gyration Rg (electron density) rg_electron39.79
Forward intensity I(0) i0133402000.00
Molecular weight molecular_weight92226.0 kDa
Excluded volume excluded_volume114790 ų
Envelope volume envelope_volume156770 ų
Hydration-shell volume shell_volume36510 ų
Envelope diameter envelope_diameter145.0
Shell Rg shell_rg40.04
Envelope Rg envelope_rg40.00
Shape Rg shape_rg39.80
Total Rg total_rg39.76
Total atoms total_atoms6491
Residues n_residues804
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 dmax136.7
Rg (real space) rg_real40.02
Rg uncertainty (real space) rg_real_error1.42
I(0) (real space) i0_real1.3340e+08
I(0) uncertainty (real space) i0_real_error2.3350e+06
Rg (reciprocal space) rg_reciprocal39.53
I(0) (reciprocal space) i0_reciprocal133300000.0000
Solution quality estimate total_estimate0.7386
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary34.2
Skewness Skewness skewness0.655
Kurtosis Kurtosis kurtosis-0.259
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12150000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.599; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.488; Smooth: 0.312

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

7. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (7 domains)

Domain ID domain_idd6cx9a1
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_idd6cx9a2
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_idd6cx9b_
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_idd6cx9c1
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_idd6cx9c2
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_idd6cx9d1
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_idd6cx9d2
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_id6cx9A01
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_id6cx9A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6cx9B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6cx9C01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6cx9D01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6cx9D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)