7vyt

Crystal structure of human TIGIT(23-129) in complex with the scFv fragment of anti-TIGIT antibody MG1131

Method: X-RAY DIFFRACTION Dmax: 93.8 Å Quality: GOOD

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

T-cell immunoreceptor with Ig and ITIM domains

Homo sapiens

UniProt Q495A1

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 23–129 Not recorded MG1131 heavy chain variable region × 1 MG1131 light chain variable region × 1 FLC CITRATE ANION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293.15 K;200mM ammonium citrate, 20% (v/v) polyethylene glycol 3350 Resolution 1.53 Å R-free 0.219
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain T; UniProt 23–129 Not recorded MG1131 heavy chain variable region × 1 MG1131 light chain variable region × 1 FLC CITRATE ANION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293.15 K;200mM ammonium citrate, 20% (v/v) polyethylene glycol 3350 Resolution 1.53 Å R-free 0.219

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.

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

View Construct and Data Evidence
UniProt name TIGIT_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–107; UniProt 23–129 Author chain T; PDBConstruct 1–107; UniProt 23–129

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 7vyt

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id7vyt
Deposition date deposition_date2021-11-15
Structure title titleCrystal structure of human TIGIT(23-129) in complex with the scFv fragment of anti-TIGIT antibody MG1131
Keywords keywordsAntibody, Immune Checkpoint, TIGIT, 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_guinier29.08
Radius of gyration Rg (electron density) rg_electron28.55
Forward intensity I(0) i089849800.00
Molecular weight molecular_weight73033.0 kDa
Excluded volume excluded_volume90539 ų
Envelope volume envelope_volume112250 ų
Hydration-shell volume shell_volume32975 ų
Envelope diameter envelope_diameter103.5
Shell Rg shell_rg35.37
Envelope Rg envelope_rg28.38
Shape Rg shape_rg28.50
Total Rg total_rg29.34
Total atoms total_atoms5140
Residues n_residues664
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 dmax93.8
Rg (real space) rg_real29.10
Rg uncertainty (real space) rg_real_error0.64
I(0) (real space) i0_real8.9850e+07
I(0) uncertainty (real space) i0_real_error1.3620e+06
Rg (reciprocal space) rg_reciprocal29.09
I(0) (reciprocal space) i0_reciprocal89850000.0000
Solution quality estimate total_estimate0.8750
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary92.1
Skewness Skewness skewness0.382
Kurtosis Kurtosis kurtosis-0.253
Angular range angular_range— – 0.2750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha22340000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.676

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id7vytB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7vytH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)