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

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Basic information

Entry
Database: PDB / ID: 8jel
TitleCrystal structure of TIGIT in complexed with Ociperlimab, crystal form I
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 / positive regulation of interleukin-10 production / 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: 2.45 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: antibody heavy chain
D: antibody light chain
J: T-cell immunoreceptor with Ig and ITIM domains
A: antibody heavy chain
B: antibody light chain
E: T-cell immunoreceptor with Ig and ITIM domains
F: antibody heavy chain
G: antibody light chain
H: T-cell immunoreceptor with Ig and ITIM domains
I: antibody heavy chain
K: antibody light chain
L: T-cell immunoreceptor with Ig and ITIM domains


Theoretical massNumber of molelcules
Total (without water)239,38712
Polymers239,38712
Non-polymers00
Water14,736818
1
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
2
A: antibody heavy chain
B: antibody light chain
E: 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
F: antibody heavy chain
G: antibody light chain
H: 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
I: antibody heavy chain
K: antibody light chain
L: 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
Unit cell
Length a, b, c (Å)135.530, 138.310, 196.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-378-

HOH

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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.: 818 / Source method: isolated from a natural source / Formula: H2O

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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: 3.85 Å3/Da / Density % sol: 68.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M citric acid pH 4.6, 1 M lithium chloride, 7% PEG6000

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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 PILATUS3 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: 2.45→135.53 Å / Num. obs: 136106 / % possible obs: 100 % / Redundancy: 10.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.208 / Rrim(I) all: 0.22 / Net I/σ(I): 5.23
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.45-2.62.824219930.5612.9791
2.6-2.781.447205000.8161.5291
2.78-30.826189070.9240.8721
3-3.290.417178380.9720.4391
3.29-3.680.243160120.9850.2571
3.68-4.240.181139370.9890.1911
4.24-5.20.147121450.9910.1551
5.2-7.350.12293930.9940.1281
7.35-100.0853810.9970.0851

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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: 2.45→48.4 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2492 6936 5.1 %
Rwork0.1917 --
obs0.1946 135976 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16276 0 0 818 17094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816655
X-RAY DIFFRACTIONf_angle_d1.06822678
X-RAY DIFFRACTIONf_dihedral_angle_d15.8132291
X-RAY DIFFRACTIONf_chiral_restr0.0552564
X-RAY DIFFRACTIONf_plane_restr0.0082896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.480.43482320.45734249X-RAY DIFFRACTION100
2.48-2.510.45562300.41894252X-RAY DIFFRACTION100
2.51-2.540.42732180.41824280X-RAY DIFFRACTION100
2.54-2.570.44252240.4014267X-RAY DIFFRACTION100
2.57-2.60.42552280.39164252X-RAY DIFFRACTION100
2.6-2.640.41612290.36044229X-RAY DIFFRACTION100
2.64-2.680.38482210.33064272X-RAY DIFFRACTION100
2.68-2.720.31042450.29344268X-RAY DIFFRACTION100
2.72-2.760.33562520.27154219X-RAY DIFFRACTION100
2.76-2.80.35322180.2724276X-RAY DIFFRACTION100
2.8-2.850.31232360.2554280X-RAY DIFFRACTION100
2.85-2.90.28622360.24614257X-RAY DIFFRACTION100
2.9-2.960.31042020.24924293X-RAY DIFFRACTION100
2.96-3.020.30992300.24334287X-RAY DIFFRACTION100
3.02-3.090.3112040.23264279X-RAY DIFFRACTION100
3.09-3.160.2692060.21514315X-RAY DIFFRACTION100
3.16-3.240.29682540.20854264X-RAY DIFFRACTION100
3.24-3.320.28742160.20224302X-RAY DIFFRACTION100
3.32-3.420.24732300.19274280X-RAY DIFFRACTION100
3.42-3.530.26342430.19384288X-RAY DIFFRACTION100
3.53-3.660.25412630.19174281X-RAY DIFFRACTION100
3.66-3.810.25092430.17574288X-RAY DIFFRACTION100
3.81-3.980.23832120.1674322X-RAY DIFFRACTION100
3.98-4.190.22062320.1554319X-RAY DIFFRACTION100
4.19-4.450.20222620.13664293X-RAY DIFFRACTION100
4.45-4.790.18892320.12674347X-RAY DIFFRACTION100
4.79-5.280.18032230.13614357X-RAY DIFFRACTION100
5.28-6.040.20442280.15344412X-RAY DIFFRACTION100
6.04-7.60.24922330.17454424X-RAY DIFFRACTION100
7.61-48.40.192540.16794588X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -34.2117 Å / Origin y: 14.6387 Å / Origin z: 42.5714 Å
111213212223313233
T0.4855 Å20.0064 Å2-0.0232 Å2-0.5833 Å20.0147 Å2--0.4949 Å2
L-0.0416 °20.0113 °2-0.0661 °2-0.0609 °2-0.0281 °2--0.0582 °2
S-0.0265 Å °0.0319 Å °-0.0054 Å °0.0024 Å °0.0362 Å °0.0149 Å °0.0118 Å °0.0087 Å °-0.009 Å °
Refinement TLS groupSelection details: all

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