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- PDB-8jeo: Crystal structure of TIGIT in complexed with Tiragolumab -

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Basic information

Entry
Database: PDB / ID: 8jeo
TitleCrystal structure of TIGIT in complexed with Tiragolumab
Components
  • T-cell immunoreceptor with Ig and ITIM domains
  • antibody heavy chain
  • antibody light chain
KeywordsIMMUNE SYSTEM / immunotherapy / antibody / checkpoint inhibitor
Function / homology
Function and homology information


negative regulation of T cell activation / negative regulation of interleukin-12 production / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-10 production / signaling receptor activity / signaling receptor binding / cell surface / identical protein binding / plasma membrane
Similarity search - Function
T-cell immunoglobulin and ITIM domain receptor / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
T-cell immunoreceptor with Ig and ITIM domains
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsSun, J. / Zhang, X.X. / Song, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2024
Title: Structural insights into the unique pH-responsive characteristics of the anti-TIGIT therapeutic antibody Ociperlimab.
Authors: Sun, J. / Zhang, X. / Xue, L. / Cheng, L. / Zhang, J. / Chen, X. / Shen, Z. / Li, K. / Wang, L. / Huang, C. / Song, J.
History
DepositionMay 16, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 22, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T-cell immunoreceptor with Ig and ITIM domains
B: antibody heavy chain
C: antibody light chain
D: T-cell immunoreceptor with Ig and ITIM domains
E: antibody heavy chain
F: antibody light chain


Theoretical massNumber of molelcules
Total (without water)124,8336
Polymers124,8336
Non-polymers00
Water12,286682
1
A: T-cell immunoreceptor with Ig and ITIM domains
B: antibody heavy chain
C: antibody light chain


Theoretical massNumber of molelcules
Total (without water)62,4163
Polymers62,4163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: T-cell immunoreceptor with Ig and ITIM domains
E: antibody heavy chain
F: antibody light chain


Theoretical massNumber of molelcules
Total (without water)62,4163
Polymers62,4163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)214.161, 214.161, 66.885
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein T-cell immunoreceptor with Ig and ITIM domains / V-set and immunoglobulin domain-containing protein 9 / V-set and transmembrane domain-containing protein 3


Mass: 12759.214 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIGIT, VSIG9, VSTM3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q495A1
#2: Antibody antibody heavy chain


Mass: 25410.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody antibody light chain


Mass: 24246.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 682 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M ammonium citrate tribasic pH 7.4, 14% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→151.4 Å / Num. obs: 94450 / % possible obs: 99.5 % / Redundancy: 6.2 % / CC1/2: 0.991 / Rmerge(I) obs: 0.219 / Rrim(I) all: 0.239 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.06-2.181.633290630.4161.7911
2.18-2.331.19279740.6231.3051
2.33-2.520.865261240.8060.9441
2.52-2.760.579240230.9030.6331
2.76-3.080.371217170.9650.4031
3.08-3.560.239191530.9790.2611
3.56-4.350.171161930.9860.1861
4.35-6.130.133125680.9880.1461
6.13-100.08869780.9940.0961

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→48.81 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2055 4748 5.05 %
Rwork0.1722 --
obs0.174 94078 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8400 0 0 682 9082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078600
X-RAY DIFFRACTIONf_angle_d0.91211730
X-RAY DIFFRACTIONf_dihedral_angle_d13.5411166
X-RAY DIFFRACTIONf_chiral_restr0.0571337
X-RAY DIFFRACTIONf_plane_restr0.0071497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.080.33261340.30012635X-RAY DIFFRACTION88
2.08-2.10.37721330.27022982X-RAY DIFFRACTION100
2.1-2.130.27311690.24562950X-RAY DIFFRACTION100
2.13-2.160.22781670.22923014X-RAY DIFFRACTION100
2.16-2.190.27281560.21782913X-RAY DIFFRACTION100
2.19-2.220.24871430.21353023X-RAY DIFFRACTION100
2.22-2.250.24981660.21062926X-RAY DIFFRACTION100
2.25-2.280.24961400.20212984X-RAY DIFFRACTION100
2.28-2.320.22151550.19452988X-RAY DIFFRACTION100
2.32-2.350.24591750.19152936X-RAY DIFFRACTION100
2.35-2.390.23441370.19563014X-RAY DIFFRACTION100
2.39-2.440.24091570.19492966X-RAY DIFFRACTION100
2.44-2.490.25961720.19862998X-RAY DIFFRACTION100
2.49-2.540.23461350.19152953X-RAY DIFFRACTION100
2.54-2.590.23671640.18762983X-RAY DIFFRACTION100
2.59-2.650.23751780.18922956X-RAY DIFFRACTION100
2.65-2.720.24131460.18783036X-RAY DIFFRACTION100
2.72-2.790.22291570.17882954X-RAY DIFFRACTION100
2.79-2.870.24551300.18793019X-RAY DIFFRACTION100
2.87-2.970.26181410.19392986X-RAY DIFFRACTION100
2.97-3.070.22151630.1892986X-RAY DIFFRACTION100
3.07-3.190.24781320.1843023X-RAY DIFFRACTION100
3.19-3.340.22111750.18682992X-RAY DIFFRACTION100
3.34-3.520.20721790.17822973X-RAY DIFFRACTION100
3.52-3.740.20381930.16692964X-RAY DIFFRACTION100
3.74-4.020.18961460.1553018X-RAY DIFFRACTION100
4.03-4.430.15931610.13943040X-RAY DIFFRACTION100
4.43-5.070.15311760.12852976X-RAY DIFFRACTION100
5.07-6.380.19451880.14783022X-RAY DIFFRACTION100
6.39-48.810.16241800.16133120X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 82.4829 Å / Origin y: 47.3199 Å / Origin z: 35.3628 Å
111213212223313233
T0.263 Å20.0348 Å2-0.0398 Å2-0.2816 Å2-0.0135 Å2--0.2854 Å2
L0.2283 °2-0.0978 °20.0118 °2-0.3469 °20.0787 °2--0.3505 °2
S-0.0255 Å °-0.0172 Å °0.0462 Å °0.0202 Å °-0.0018 Å °-0.0164 Å °-0.0712 Å °-0.0151 Å °-0 Å °
Refinement TLS groupSelection details: all

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