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- PDB-8vtd: Co-structure of the Fab of the anti-TIGIT Vibostolimab antibody w... -

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Basic information

Entry
Database: PDB / ID: 8vtd
TitleCo-structure of the Fab of the anti-TIGIT Vibostolimab antibody with its antigen
Components
  • T-cell immunoreceptor with Ig and ITIM domains
  • Vibostolimab Fab Heavy chain
  • Vibostolimab Fab Light chain
KeywordsIMMUNE SYSTEM / antibody TIGIT immunotherapy
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 speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsFischmann, T.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Pharmacological and structural characterization of vibostolimab, a novel anti-human TIGIT blocking antibody for cancer immunotherapy
Authors: Fischmann, T.O. / Malashock, D. / Wang, H. / Grein, J. / Bahmanjah, S. / Ban, D. / Chien, E. / Hsieh, M. / Mayhood, T. / Yuan, J. / Beaumont, M. / Baker, J. / McCoy, M.A. / Wilson, D. / ...Authors: Fischmann, T.O. / Malashock, D. / Wang, H. / Grein, J. / Bahmanjah, S. / Ban, D. / Chien, E. / Hsieh, M. / Mayhood, T. / Yuan, J. / Beaumont, M. / Baker, J. / McCoy, M.A. / Wilson, D. / Williams, S.M.G. / Blumenschein, W. / Fayadat-Dilman, L. / Seghezzi, W. / Keenan, T. / Han, J.-H.
History
DepositionJan 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vibostolimab Fab Light chain
B: Vibostolimab Fab Heavy chain
C: T-cell immunoreceptor with Ig and ITIM domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6765
Polymers60,4913
Non-polymers1842
Water10,593588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-35 kcal/mol
Surface area23970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.775, 105.996, 71.758
Angle α, β, γ (deg.)90.00, 104.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Vibostolimab Fab Light chain


Mass: 23508.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody Vibostolimab Fab Heavy chain


Mass: 23569.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / 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: 13413.891 Da / Num. of mol.: 1
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 588 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / Details: 16% w/v PEG 20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.23→42.144 Å / Num. obs: 117862 / % possible obs: 67.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.029 / Rrim(I) all: 0.053 / Net I/σ(I): 12.3
Reflection shellResolution: 1.231→1.363 Å / % possible obs: 12.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.652 / Num. measured all: 20248 / Num. unique obs: 5892 / Rpim(I) all: 0.414 / Rrim(I) all: 0.775 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
Aimless0.7.2data scaling
XDS20180409data reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.23→42.14 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU R Cruickshank DPI: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.059 / SU Rfree Blow DPI: 0.059 / SU Rfree Cruickshank DPI: 0.057
RfactorNum. reflection% reflectionSelection details
Rfree0.204 5944 5.04 %RANDOM
Rwork0.185 ---
obs0.186 117862 67.8 %-
Displacement parametersBiso mean: 22.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.1065 Å20 Å2-0.2883 Å2
2--0.2759 Å20 Å2
3----0.3824 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: 1 / Resolution: 1.23→42.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4106 0 12 588 4706
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018298HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1114956HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1756SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1332HARMONIC5
X-RAY DIFFRACTIONt_it8298HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.82
X-RAY DIFFRACTIONt_other_torsion14.14
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion568SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9075SEMIHARMONIC4
LS refinement shellResolution: 1.23→1.32 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2186 132 5.6 %
Rwork0.2136 2226 -
all0.2139 2358 -
obs--6.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8418-0.19030.42590.92420.28081.15550.07140.0216-0.2186-0.0208-0.02220.05560.21730.015-0.0492-0.03150.0124-0.0062-0.05950.0101-0.01392.8897-26.9993-15.9196
20.7936-0.4275-0.21581.27460.20721.85210.08270.09480.0107-0.102-0.0413-0.20250.03150.2241-0.0414-0.05560.0166-0.003-0.051-0.002-0.04911.4994-33.9665-51.63
30.61040.06460.1790.7208-0.00050.954-0.0179-0.0096-0.0019-0.0876-0.00060.0661-0.04910.00080.0185-0.02760.006-0.0097-0.02870.006-0.0292-7.265-7.9974-21.6378
40.06950.0393-0.05062.97740.67710.56120.03190.0052-0.0506-0.0786-0.08910.1374-0.063-0.04850.0572-0.01380.0045-0.016-0.0311-0.006-0.0351-13.3062-28.0328-48.6985
50.6715-0.5489-0.52741.05750.46562.014-0.0458-0.13370.01940.15220.08490.0570.0080.0082-0.0391-0.04960.00390.0180.0070.014-0.07461.4446-7.08657.2254
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|106 }
2X-RAY DIFFRACTION2{ A|107 - A|214 }
3X-RAY DIFFRACTION3{ B|1 - B|116 }
4X-RAY DIFFRACTION4{ B|117 - B|217 }
5X-RAY DIFFRACTION5{ C|* }

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