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- PDB-8szy: Crystal Structure of Heterotrimeric Anti-TIGIT Fabs in complex wi... -

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Basic information

Entry
Database: PDB / ID: 8szy
TitleCrystal Structure of Heterotrimeric Anti-TIGIT Fabs in complex with human TIGIT
Components
  • BMS-986207 Fab Heavy Chain
  • BMS-986207 light chain
  • CHA.9.543 Fab heavy chain
  • CHA.9.543 light chain
  • T-cell immunoreceptor with Ig and ITIM domains
KeywordsIMMUNE SYSTEM / PROTEIN BINDING / Antibody / TIGIT / PVR-Family
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: 2.31 Å
AuthorsDiong, S.J. / Lee, P.S.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Mabs / Year: 2023
Title: Biophysical characterization of PVR family interactions and therapeutic antibody recognition to TIGIT.
Authors: Diong, S.J. / Jashnani, A. / Drake, A.W. / Bee, C. / Findeisen, F. / Dollinger, G. / Wang, F. / Rajpal, A. / Strop, P. / Lee, P.S.
History
DepositionMay 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHA.9.543 Fab heavy chain
B: CHA.9.543 light chain
H: BMS-986207 Fab Heavy Chain
L: BMS-986207 light chain
T: T-cell immunoreceptor with Ig and ITIM domains
C: CHA.9.543 Fab heavy chain
D: CHA.9.543 light chain
I: BMS-986207 Fab Heavy Chain
M: BMS-986207 light chain
U: T-cell immunoreceptor with Ig and ITIM domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,15812
Polymers220,71510
Non-polymers4422
Water2,018112
1
A: CHA.9.543 Fab heavy chain
B: CHA.9.543 light chain
H: BMS-986207 Fab Heavy Chain
L: BMS-986207 light chain
T: T-cell immunoreceptor with Ig and ITIM domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5796
Polymers110,3585
Non-polymers2211
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: CHA.9.543 Fab heavy chain
D: CHA.9.543 light chain
I: BMS-986207 Fab Heavy Chain
M: BMS-986207 light chain
U: T-cell immunoreceptor with Ig and ITIM domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5796
Polymers110,3585
Non-polymers2211
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.850, 216.910, 109.450
Angle α, β, γ (deg.)90.000, 95.970, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Antibody , 4 types, 8 molecules ACBDHILM

#1: Antibody CHA.9.543 Fab heavy chain


Mass: 24309.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody CHA.9.543 light chain


Mass: 24072.754 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 BMS-986207 Fab Heavy Chain


Mass: 25870.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#4: Antibody BMS-986207 light chain


Mass: 23621.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars / Non-polymers , 3 types, 116 molecules TU

#5: 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: 12483.785 Da / Num. of mol.: 2 / Mutation: C69S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIGIT, VSIG9, VSTM3 / Production host: Homo sapiens (human) / References: UniProt: Q495A1
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium phosphate monobasic monohydrate, 20% w/v Polyethylene glycol 1,000

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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: Feb 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.306→108.856 Å / Num. obs: 65410 / % possible obs: 70.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 35.04 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.091 / Rrim(I) all: 0.168 / Net I/σ(I): 7.5
Reflection shellResolution: 2.306→2.479 Å / Rmerge(I) obs: 0.694 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3271 / CC1/2: 0.6 / Rpim(I) all: 0.491 / Rrim(I) all: 0.854

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
STARANISOdata scaling
XSCALEdata scaling
Cootmodel building
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→45.6 Å / SU ML: 0.3176 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.0909
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2686 3191 4.88 %
Rwork0.227 62187 -
obs0.229 65378 70.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.66 Å2
Refinement stepCycle: LAST / Resolution: 2.31→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14751 0 28 112 14891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004915147
X-RAY DIFFRACTIONf_angle_d0.881320659
X-RAY DIFFRACTIONf_chiral_restr0.10082346
X-RAY DIFFRACTIONf_plane_restr0.01442630
X-RAY DIFFRACTIONf_dihedral_angle_d16.09055351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.340.2633280.2909383X-RAY DIFFRACTION10.26
2.34-2.380.3883290.315517X-RAY DIFFRACTION13.5
2.38-2.420.3163330.3151662X-RAY DIFFRACTION17.12
2.42-2.460.3477480.3283976X-RAY DIFFRACTION25.64
2.46-2.50.3817790.32031285X-RAY DIFFRACTION33.93
2.5-2.550.3274760.31931692X-RAY DIFFRACTION43.01
2.55-2.60.34241090.32411913X-RAY DIFFRACTION50.94
2.6-2.660.39291190.31982184X-RAY DIFFRACTION56.92
2.66-2.720.35371490.31942493X-RAY DIFFRACTION64.96
2.72-2.790.32681370.31752812X-RAY DIFFRACTION73.52
2.79-2.860.33111560.30413021X-RAY DIFFRACTION77.45
2.86-2.950.32611830.30043369X-RAY DIFFRACTION89.43
2.95-3.040.3151840.29713801X-RAY DIFFRACTION97.24
3.04-3.150.34121860.29453804X-RAY DIFFRACTION99.58
3.15-3.280.31552050.28613893X-RAY DIFFRACTION99.56
3.28-3.430.32441850.25233772X-RAY DIFFRACTION99.12
3.43-3.610.2811790.22853814X-RAY DIFFRACTION98.69
3.61-3.830.28311520.21422940X-RAY DIFFRACTION75.58
3.83-4.130.24552020.19033740X-RAY DIFFRACTION97.6
4.13-4.550.2021870.15493750X-RAY DIFFRACTION96.8
4.55-5.20.18761710.14913766X-RAY DIFFRACTION97.09
5.2-6.550.21942060.17583809X-RAY DIFFRACTION98.36
6.55-45.60.19941880.19043791X-RAY DIFFRACTION97.31
Refinement TLS params.Method: refined / Origin x: 11.5172330803 Å / Origin y: 39.7083482266 Å / Origin z: -26.4063142197 Å
111213212223313233
T0.0377147752385 Å20.0123720508454 Å2-0.00777820795839 Å2-0.121751130453 Å2-0.00976466635721 Å2--0.11618036816 Å2
L-0.00406046283219 °2-0.0269015134386 °2-0.0411445605458 °2-0.150143361703 °20.158191688689 °2--0.279974593236 °2
S-0.01028216234 Å °-0.00124123420841 Å °0.00464861116361 Å °-0.00142670602003 Å °0.0268035693408 Å °0.0156291612282 Å °-0.00563681411091 Å °-0.00966878573869 Å °-0.0157897420394 Å °
Refinement TLS groupSelection details: all

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