3RQ3 | pdb_00003rq3

Structure of T-cell immunoreceptor with immunoglobulin and ITIM domains (TIGIT) in hexagonal crystal form

PDB DOI: https://doi.org/10.2210/pdb3RQ3/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-04-27 Released: 2011-06-01
Deposition Author(s): Ramagopal, U.A., Rubinstein, R., Guo, H., Samanta, D., Nathenson, S.G., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC), Atoms-to-Animals: The Immune Function Network (IFN)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.253 (Depositor), 0.246 (DCC)
R-Value Work:
0.206 (Depositor), 0.202 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3RQ3

This is version 1.3 of the entry. See complete history.

Literature

Structure of T-cell immunoreceptor with immunoglobulin and ITIM domains (TIGIT) in hexagonal crystal form

Ramagopal, U.A., Rubinstein, R., Guo, H., Samanta, D., Nathenson, S.G., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC), Atoms-to-Animals: The Immune Function Network (IFN)

To be published.

Macromolecule Content

Total Structure Weight: 25.21 kDa
Atom Count: 1,688
Modeled Residue Count: 214
Deposited Residue Count: 232
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell immunoreceptor with Ig and ITIM domains	A, B	116	Homo sapiens	Mutation(s): 0 Gene Names: TIGIT, VSIG9, VSTM3
UniProt & NIH Common Fund Data Resources
Find proteins for Q495A1 (Homo sapiens) Explore Q495A1 Go to UniProtKB: Q495A1
PHAROS: Q495A1 GTEx: ENSG00000181847
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q495A1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.253 (Depositor), 0.246 (DCC)
R-Value Work: 0.206 (Depositor), 0.202 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.614	α = 90
b = 118.614	β = 90
c = 98.197	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-06-01

Deposition Author(s):

Ramagopal, U.A.

Nathenson, S.G.

New York Structural Genomics Research Consortium (NYSGRC)

Atoms-to-Animals: The Immune Function Network (IFN)

Revision History (Full details and data files)

Version 1.0: 2011-06-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.