7rym

CD1a-endo-gdTCR complex

Method: X-RAY DIFFRACTION Dmax: 122.6 Å Quality: GOOD

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

T-cell surface glycoprotein CD1a

Homo sapiens

UniProt P06126

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 18–295 Not recorded Beta-2-microglobulin × 1 (P61769) T cell receptor gamma variable 4,T cell receptor beta constant 1 × 1 (A0A0C4DH28,P01850) T cell receptor delta variable 1,T cell receptor alpha chain constant × 1 (A0A1B0GX56,P01848) PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;20% PEG3350, 0.2M Ammonium Sulfate Resolution 3.20 Å R-free 0.286

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.

14 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CD1A_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–280; UniProt 18–295

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 Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 21–119 Not recorded T-cell surface glycoprotein CD1a × 1 (P06126) T cell receptor gamma variable 4,T cell receptor beta constant 1 × 1 (A0A0C4DH28,P01850) T cell receptor delta variable 1,T cell receptor alpha chain constant × 1 (A0A1B0GX56,P01848) PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;20% PEG3350, 0.2M Ammonium Sulfate Resolution 3.20 Å R-free 0.286

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

T cell receptor gamma variable 4,T cell receptor beta constant 1

Homo sapiens

UniProt A0A0C4DH28

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 19–118 Not recorded T-cell surface glycoprotein CD1a × 1 (P06126) Beta-2-microglobulin × 1 (P61769) T cell receptor delta variable 1,T cell receptor alpha chain constant × 1 (A0A1B0GX56,P01848) PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;20% PEG3350, 0.2M Ammonium Sulfate Resolution 3.20 Å R-free 0.286

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.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRGV4_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 3–102; UniProt 19–118

T cell receptor gamma variable 4,T cell receptor beta constant 1

Homo sapiens

UniProt P01850

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 1–129 Not recorded T-cell surface glycoprotein CD1a × 1 (P06126) Beta-2-microglobulin × 1 (P61769) T cell receptor delta variable 1,T cell receptor alpha chain constant × 1 (A0A1B0GX56,P01848) PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;20% PEG3350, 0.2M Ammonium Sulfate Resolution 3.20 Å R-free 0.286

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.

24 other PDB entries and 40 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRBC1_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 120–248; UniProt 1–129

T cell receptor delta variable 1,T cell receptor alpha chain constant

Homo sapiens

UniProt A0A1B0GX56

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain D; UniProt 21–115 Not recorded T-cell surface glycoprotein CD1a × 1 (P06126) Beta-2-microglobulin × 1 (P61769) T cell receptor gamma variable 4,T cell receptor beta constant 1 × 1 (A0A0C4DH28,P01850) PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;20% PEG3350, 0.2M Ammonium Sulfate Resolution 3.20 Å R-free 0.286

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.

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRDV1_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 2–96; UniProt 21–115

T cell receptor delta variable 1,T cell receptor alpha chain constant

Homo sapiens

UniProt P01848

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain D; UniProt 1–93 Not recorded T-cell surface glycoprotein CD1a × 1 (P06126) Beta-2-microglobulin × 1 (P61769) T cell receptor gamma variable 4,T cell receptor beta constant 1 × 1 (A0A0C4DH28,P01850) PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;20% PEG3350, 0.2M Ammonium Sulfate Resolution 3.20 Å R-free 0.286

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.

34 other PDB entries and 51 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRAC_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 117–209; UniProt 1–93

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 7rym

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id7rym
Deposition date deposition_date2021-08-25
Structure title titleCD1a-endo-gdTCR complex
Keywords keywordsCD1, TCR, lipid antigen, 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_guinier35.56
Radius of gyration Rg (electron density) rg_electron35.33
Forward intensity I(0) i097666900.00
Molecular weight molecular_weight78279.0 kDa
Excluded volume excluded_volume97488 ų
Envelope volume envelope_volume136810 ų
Hydration-shell volume shell_volume34788 ų
Envelope diameter envelope_diameter131.5
Shell Rg shell_rg38.37
Envelope Rg envelope_rg35.72
Shape Rg shape_rg35.31
Total Rg total_rg35.64
Total atoms total_atoms5542
Residues n_residues732
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 dmax122.6
Rg (real space) rg_real35.92
Rg uncertainty (real space) rg_real_error1.26
I(0) (real space) i0_real9.7670e+07
I(0) uncertainty (real space) i0_real_error1.8470e+06
Rg (reciprocal space) rg_reciprocal35.70
I(0) (reciprocal space) i0_reciprocal97650000.0000
Solution quality estimate total_estimate0.8268
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.2
Skewness Skewness skewness0.579
Kurtosis Kurtosis kurtosis-0.206
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11220000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.774; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.760; Smooth: 0.662

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id7rymD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)