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- PDB-7vyt: Crystal structure of human TIGIT(23-129) in complex with the scFv... -

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Basic information

Entry
Database: PDB / ID: 7vyt
TitleCrystal structure of human TIGIT(23-129) in complex with the scFv fragment of anti-TIGIT antibody MG1131
Components
  • MG1131 heavy chain variable region
  • MG1131 light chain variable region
  • T-cell immunoreceptor with Ig and ITIM domains
KeywordsIMMUNE SYSTEM / Antibody / Immune Checkpoint / TIGIT
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
CITRATE ANION / T-cell immunoreceptor with Ig and ITIM domains
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsJeong, B.-S. / Nam, H. / Kim, M. / Oh, B.-H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other privateMOGAM institute and GC Pharma Korea, Republic Of
CitationJournal: Mabs / Year: 2022
Title: Structural and functional characterization of a monoclonal antibody blocking TIGIT.
Authors: Jeong, B.S. / Nam, H. / Lee, J. / Park, H.Y. / Cho, K.J. / Sheen, J.H. / Song, E. / Oh, M. / Lee, S. / Choi, H. / Yang, J.E. / Kim, M. / Oh, B.H.
History
DepositionNov 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: MG1131 heavy chain variable region
T: T-cell immunoreceptor with Ig and ITIM domains
L: MG1131 light chain variable region
H: MG1131 heavy chain variable region
C: MG1131 light chain variable region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3438
Polymers76,9656
Non-polymers3782
Water6,990388
1
A: T-cell immunoreceptor with Ig and ITIM domains
B: MG1131 heavy chain variable region
C: MG1131 light chain variable region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6724
Polymers38,4833
Non-polymers1891
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
T: T-cell immunoreceptor with Ig and ITIM domains
L: MG1131 light chain variable region
H: MG1131 heavy chain variable region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6724
Polymers38,4833
Non-polymers1891
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.670, 79.820, 77.970
Angle α, β, γ (deg.)90.000, 100.554, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 25 through 35 or resid 37...
d_2ens_1(chain "T" and (resid 25 through 35 or resid 37...
d_1ens_2(chain "H" and (resid 2 through 12 or resid 14...
d_2ens_2(chain "B" and (resid 2 through 12 or resid 14...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYALAA1 - 11
d_12ens_1LYSLEUA13 - 19
d_13ens_1CYSGLNA21 - 38
d_14ens_1LEUPHEA41 - 57
d_15ens_1ASPGLUA59 - 104
d_21ens_1GLYALAC1 - 11
d_22ens_1LYSLEUC13 - 19
d_23ens_1CYSGLNC21 - 38
d_24ens_1LEUPHEC41 - 57
d_25ens_1ASPGLUC59 - 104
d_11ens_2VALLYSG3 - 13
d_12ens_2PROGLYG15 - 43
d_13ens_2GLYLEUG45 - 87
d_14ens_2SERSERG89 - 121
d_21ens_2VALLYSB2 - 12
d_22ens_2PROGLYB14 - 42
d_23ens_2GLYLEUB44 - 86
d_24ens_2SERSERB88 - 120

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.0889832869727, -0.00770410505748, 0.996003323993), (-0.0176608851662, -0.99980067648, -0.00931130733973), (0.995876532395, -0.0184188510633, 0.0888294891961)-11.4347053778, 160.968170546, 12.4874891734
2given(-0.0657336045095, -0.0113429005643, 0.997772735569), (-0.0178203255276, -0.9997625699, -0.012539530499), (0.997678068936, -0.0186049034889, 0.0655158631927)-12.5064334578, 161.038078765, 13.319999235
3given(-0.146513933408, -0.0189031359242, 0.989027976737), (-0.0307336464689, -0.999247745926, -0.0236513262977), (0.988731060649, -0.0338616850311, 0.145822755408)-7.93451347419, 162.270455887, 10.4410263669

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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: 11643.942 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 MG1131 heavy chain variable region


Mass: 13277.817 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody MG1131 light chain variable region


Mass: 13560.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: (G4S)4 is a linker. / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.76 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 200mM ammonium citrate, 20% (v/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97957 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.53→29.33 Å / Num. obs: 126325 / % possible obs: 99.94 % / Redundancy: 7 % / Biso Wilson estimate: 21.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06538 / Rsym value: 0.07068 / Net I/σ(I): 16
Reflection shellResolution: 1.53→1.585 Å / Num. unique obs: 12553 / CC1/2: 0.703

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EHV, 3UCR

6ehv

3ucr


Resolution: 1.53→29.33 Å / SU ML: 0.1966 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.8121
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.219 6315 5 %
Rwork0.2012 119998 -
obs0.2021 126313 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.78 Å2
Refinement stepCycle: LAST / Resolution: 1.53→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5114 0 26 390 5530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01175252
X-RAY DIFFRACTIONf_angle_d1.19657132
X-RAY DIFFRACTIONf_chiral_restr0.093782
X-RAY DIFFRACTIONf_plane_restr0.0077916
X-RAY DIFFRACTIONf_dihedral_angle_d11.5814742
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONNCS constraints0.54177228003
ens_2d_2HX-RAY DIFFRACTIONNCS constraints0.463225853019
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.550.35572080.32923946X-RAY DIFFRACTION99.9
1.55-1.570.35492090.31353979X-RAY DIFFRACTION99.88
1.57-1.580.30842100.29493986X-RAY DIFFRACTION99.9
1.58-1.60.31762100.28133990X-RAY DIFFRACTION99.95
1.6-1.630.25652100.26723984X-RAY DIFFRACTION99.95
1.63-1.650.27572080.25493959X-RAY DIFFRACTION100
1.65-1.670.29132100.2654008X-RAY DIFFRACTION99.95
1.67-1.70.26612120.26314022X-RAY DIFFRACTION100
1.7-1.720.29772080.25163951X-RAY DIFFRACTION100
1.72-1.750.26942100.23463985X-RAY DIFFRACTION99.95
1.75-1.780.272080.21643975X-RAY DIFFRACTION99.9
1.78-1.810.24072100.21323994X-RAY DIFFRACTION100
1.81-1.850.21842110.21414004X-RAY DIFFRACTION99.86
1.85-1.890.22052100.21053989X-RAY DIFFRACTION99.9
1.89-1.930.22462100.21033998X-RAY DIFFRACTION99.95
1.93-1.970.23262090.20763952X-RAY DIFFRACTION99.93
1.97-2.020.22442100.20783992X-RAY DIFFRACTION100
2.02-2.080.24942110.20084007X-RAY DIFFRACTION99.95
2.08-2.140.22732110.21044012X-RAY DIFFRACTION100
2.14-2.210.20882110.19984021X-RAY DIFFRACTION100
2.21-2.290.22952110.20883999X-RAY DIFFRACTION100
2.29-2.380.21862100.20653986X-RAY DIFFRACTION99.95
2.38-2.480.23912120.21034028X-RAY DIFFRACTION100
2.48-2.620.25792090.21523973X-RAY DIFFRACTION99.98
2.62-2.780.21662140.20624060X-RAY DIFFRACTION100
2.78-2.990.24212090.2083975X-RAY DIFFRACTION100
2.99-3.290.19362120.20244033X-RAY DIFFRACTION99.98
3.29-3.770.19552120.18644030X-RAY DIFFRACTION99.81
3.77-4.750.14942130.15164049X-RAY DIFFRACTION100
4.75-29.330.21162170.17084111X-RAY DIFFRACTION99.84

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