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- PDB-8jen: Crystal structure of TIGIT in complexed with Ociperlimab, crystal... -

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Basic information

Entry
Database: PDB / ID: 8jen
TitleCrystal structure of TIGIT in complexed with Ociperlimab, crystal form II
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: 2.71 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 20, 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: antibody heavy chain
B: antibody light chain
C: antibody heavy chain
D: antibody light chain
E: antibody heavy chain
F: antibody light chain
I: T-cell immunoreceptor with Ig and ITIM domains
J: T-cell immunoreceptor with Ig and ITIM domains
M: T-cell immunoreceptor with Ig and ITIM domains
P: T-cell immunoreceptor with Ig and ITIM domains
G: antibody heavy chain
H: antibody light chain


Theoretical massNumber of molelcules
Total (without water)239,38712
Polymers239,38712
Non-polymers00
Water7,116395
1
A: antibody heavy chain
B: antibody light chain
I: T-cell immunoreceptor with Ig and ITIM domains


Theoretical massNumber of molelcules
Total (without water)59,8473
Polymers59,8473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: antibody heavy chain
D: antibody light chain
J: T-cell immunoreceptor with Ig and ITIM domains


Theoretical massNumber of molelcules
Total (without water)59,8473
Polymers59,8473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: antibody heavy chain
F: antibody light chain
M: T-cell immunoreceptor with Ig and ITIM domains


Theoretical massNumber of molelcules
Total (without water)59,8473
Polymers59,8473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
P: T-cell immunoreceptor with Ig and ITIM domains
G: antibody heavy chain
H: antibody light chain


Theoretical massNumber of molelcules
Total (without water)59,8473
Polymers59,8473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.320, 79.350, 173.690
Angle α, β, γ (deg.)90.00, 101.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
antibody heavy chain


Mass: 23784.613 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
antibody light chain


Mass: 23302.881 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: 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.: 4
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate tribasic dihydrate pH 5.2, 17% PEG 20000

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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 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.71→170.1 Å / Num. obs: 72920 / % possible obs: 99.8 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.171 / Rrim(I) all: 0.205 / Net I/σ(I): 6.37
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.71-2.871.094114350.5571.3151
2.87-3.070.707111590.7820.8421
3.07-3.320.402104580.9210.481
3.32-3.640.21295300.9710.2561
3.64-4.060.13983940.9880.1661
4.06-4.690.08976360.9950.1061
4.69-5.750.08164560.9950.0981
5.75-8.130.07650290.9960.091
8.13-100.04228230.9970.0511

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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: 2.71→49.12 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2893 3669 5.04 %
Rwork0.2178 --
obs0.2214 72727 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.71→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16341 0 0 395 16736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916721
X-RAY DIFFRACTIONf_angle_d1.09422764
X-RAY DIFFRACTIONf_dihedral_angle_d14.5052302
X-RAY DIFFRACTIONf_chiral_restr0.0562569
X-RAY DIFFRACTIONf_plane_restr0.0072910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.750.42381480.3532612X-RAY DIFFRACTION100
2.75-2.780.43941580.34152643X-RAY DIFFRACTION100
2.78-2.820.39421490.32082612X-RAY DIFFRACTION100
2.82-2.870.36461420.31812628X-RAY DIFFRACTION100
2.87-2.910.40041080.29762687X-RAY DIFFRACTION100
2.91-2.960.36351470.29142633X-RAY DIFFRACTION100
2.96-3.010.36311230.2822654X-RAY DIFFRACTION100
3.01-3.060.3881620.27472628X-RAY DIFFRACTION100
3.06-3.120.33091570.26892645X-RAY DIFFRACTION100
3.12-3.190.38971370.26432643X-RAY DIFFRACTION99
3.19-3.260.33031290.2582634X-RAY DIFFRACTION100
3.26-3.330.33441380.24122651X-RAY DIFFRACTION100
3.33-3.410.33961370.24122636X-RAY DIFFRACTION99
3.41-3.510.28661380.20922646X-RAY DIFFRACTION99
3.51-3.610.28551390.20472691X-RAY DIFFRACTION100
3.61-3.730.28871360.20842637X-RAY DIFFRACTION100
3.73-3.860.26671140.20252678X-RAY DIFFRACTION100
3.86-4.010.29151310.19932673X-RAY DIFFRACTION100
4.01-4.20.21311360.18672647X-RAY DIFFRACTION99
4.2-4.420.24691570.17432657X-RAY DIFFRACTION99
4.42-4.690.23621270.16472662X-RAY DIFFRACTION99
4.69-5.060.24561550.15662642X-RAY DIFFRACTION99
5.06-5.560.2071360.16872701X-RAY DIFFRACTION100
5.56-6.370.25431590.19072664X-RAY DIFFRACTION100
6.37-8.020.24991670.20912693X-RAY DIFFRACTION100
8.02-49.120.26471390.20782761X-RAY DIFFRACTION99

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