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- PDB-8tbb: F9S, novel TIM-3 targeting antibody, bound to IgV domain of TIM-3 -

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Basic information

Entry
Database: PDB / ID: 8tbb
TitleF9S, novel TIM-3 targeting antibody, bound to IgV domain of TIM-3
Components
  • F9S Fab heavy chain
  • F9S Fab light chain
  • T-cell immunoglobulin mucin receptor 3
KeywordsIMMUNE SYSTEM / Fab / IgV domain of TIM-3 / complex
Function / homology
Function and homology information


regulation of tolerance induction dependent upon immune response / negative regulation of interleukin-3 production / negative regulation of granulocyte colony-stimulating factor production / negative regulation of myeloid dendritic cell activation / Interleukin-2 family signaling / negative regulation of interferon-alpha production / negative regulation of T-helper 1 type immune response / negative regulation of defense response to bacterium / toll-like receptor 7 signaling pathway / natural killer cell tolerance induction ...regulation of tolerance induction dependent upon immune response / negative regulation of interleukin-3 production / negative regulation of granulocyte colony-stimulating factor production / negative regulation of myeloid dendritic cell activation / Interleukin-2 family signaling / negative regulation of interferon-alpha production / negative regulation of T-helper 1 type immune response / negative regulation of defense response to bacterium / toll-like receptor 7 signaling pathway / natural killer cell tolerance induction / negative regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / positive regulation of defense response to bacterium / negative regulation of immunological synapse formation / toll-like receptor 3 signaling pathway / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / positive regulation of interleukin-1 production / toll-like receptor 9 signaling pathway / mediator complex / macrophage activation involved in immune response / positive regulation of macrophage activation / anchoring junction / negative regulation of interleukin-2 production / positive regulation of interleukin-4 production / negative regulation of NF-kappaB transcription factor activity / negative regulation of interleukin-6 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / immunological synapse / maternal process involved in female pregnancy / positive regulation of T cell proliferation / positive regulation of chemokine production / negative regulation of T cell proliferation / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / cellular response to lipopolysaccharide / adaptive immune response / early endosome / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / inflammatory response / innate immune response / negative regulation of gene expression / regulation of transcription by RNA polymerase II / cell surface / metal ion binding / plasma membrane
Similarity search - Function
: / 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
Hepatitis A virus cellular receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOganesyan, V. / van Dyk, N. / Mazor, Y. / Yang, C.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To be published
Title: Generation of AZD7789, a novel PD-1 and TIM-3 targeting bispecific antibody, which binds to a differentiated epitope of TIM-3
Authors: Clancy-Thompson, E. / Perry, T. / Pryts, S. / Jaiswal, A. / Oganesyan, V. / van Dyk, N. / Yang, C. / Garcia, A. / Yu, W. / Moynihan, J. / Miller, C. / Mulgrew, K. / Cobbold, M. / Mazor, Y. / ...Authors: Clancy-Thompson, E. / Perry, T. / Pryts, S. / Jaiswal, A. / Oganesyan, V. / van Dyk, N. / Yang, C. / Garcia, A. / Yu, W. / Moynihan, J. / Miller, C. / Mulgrew, K. / Cobbold, M. / Mazor, Y. / Hammond, S. / Pollizzi, K.
History
DepositionJun 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: T-cell immunoglobulin mucin receptor 3
H: F9S Fab heavy chain
L: F9S Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0554
Polymers59,8343
Non-polymers2211
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-36 kcal/mol
Surface area23490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.805, 57.005, 80.453
Angle α, β, γ (deg.)90.000, 106.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein T-cell immunoglobulin mucin receptor 3 / TIM-3 / Hepatitis A virus cellular receptor 2 / HAVcr-2 / T-cell immunoglobulin and mucin domain- ...TIM-3 / Hepatitis A virus cellular receptor 2 / HAVcr-2 / T-cell immunoglobulin and mucin domain-containing protein 3 / TIMD-3 / T-cell membrane protein 3


Mass: 12395.116 Da / Num. of mol.: 1 / Fragment: IgV domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HAVCR2, TIM3, TIMD3 / Production host: Homo sapiens (human) / References: UniProt: Q8TDQ0
#2: Antibody F9S Fab heavy chain


Mass: 24094.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody F9S Fab light chain


Mass: 23344.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: 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.: 1
Source method: isolated from a genetically manipulated 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Crystals for the TIM-3-F9S Fab complex were obtained in a condition made up of a combination of 0.1M BICINE, pH 9.0 and 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2017 / Details: Si (111) double crystal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.4→35 Å / Num. obs: 23828 / % possible obs: 99.8 % / Redundancy: 3.9 % / CC1/2: 0.97 / Net I/σ(I): 11.2
Reflection shellResolution: 2.4→2.8 Å / Redundancy: 3.3 % / Num. unique obs: 1422 / CC1/2: 0.88 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→35 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.895 / SU B: 9.957 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.517 / ESU R Free: 0.278
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2412 1117 5.034 %
Rwork0.1909 21071 -
all0.194 --
obs-22188 99.905 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.428 Å2
Baniso -1Baniso -2Baniso -3
1-4.523 Å20 Å2-0.607 Å2
2---2.429 Å20 Å2
3----1.499 Å2
Refinement stepCycle: LAST / Resolution: 2.5→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4145 0 14 157 4316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0114256
X-RAY DIFFRACTIONr_bond_other_d00.0163907
X-RAY DIFFRACTIONr_angle_refined_deg0.3751.6555791
X-RAY DIFFRACTIONr_angle_other_deg0.1391.579026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.585537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.287522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.97210670
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.13810173
X-RAY DIFFRACTIONr_chiral_restr0.020.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.025018
X-RAY DIFFRACTIONr_gen_planes_other00.02982
X-RAY DIFFRACTIONr_nbd_refined0.2270.2842
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2430.23957
X-RAY DIFFRACTIONr_nbtor_refined0.1870.22007
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.22271
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2550.2243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0050.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1280.215
X-RAY DIFFRACTIONr_nbd_other0.2410.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1730.27
X-RAY DIFFRACTIONr_mcbond_it3.8013.0062160
X-RAY DIFFRACTIONr_mcbond_other3.7943.0072160
X-RAY DIFFRACTIONr_mcangle_it5.4955.3872693
X-RAY DIFFRACTIONr_mcangle_other5.4945.392694
X-RAY DIFFRACTIONr_scbond_it5.1243.4582096
X-RAY DIFFRACTIONr_scbond_other5.1233.462097
X-RAY DIFFRACTIONr_scangle_it7.3166.1123098
X-RAY DIFFRACTIONr_scangle_other7.3156.1133099
X-RAY DIFFRACTIONr_lrange_it9.23329.9394671
X-RAY DIFFRACTIONr_lrange_other9.24129.9154657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5650.288650.2861535X-RAY DIFFRACTION99.9375
2.565-2.6340.281720.2671487X-RAY DIFFRACTION100
2.634-2.710.302800.2461487X-RAY DIFFRACTION99.9362
2.71-2.7930.232770.2181413X-RAY DIFFRACTION100
2.793-2.8840.246690.2071398X-RAY DIFFRACTION100
2.884-2.9850.31650.2011327X-RAY DIFFRACTION99.9282
2.985-3.0970.327570.1861281X-RAY DIFFRACTION100
3.097-3.2220.203830.181230X-RAY DIFFRACTION99.9239
3.222-3.3640.296630.1871181X-RAY DIFFRACTION99.9197
3.364-3.5270.235560.1881144X-RAY DIFFRACTION100
3.527-3.7150.254690.191074X-RAY DIFFRACTION99.9126
3.715-3.9380.215610.1771020X-RAY DIFFRACTION100
3.938-4.2060.202520.164984X-RAY DIFFRACTION99.9036
4.206-4.5370.188520.147895X-RAY DIFFRACTION100
4.537-4.9620.223480.152824X-RAY DIFFRACTION100
4.962-5.5340.193450.163766X-RAY DIFFRACTION100
5.534-6.3640.224310.185682X-RAY DIFFRACTION99.581
6.364-7.730.272320.194587X-RAY DIFFRACTION100
7.73-100.204300.176453X-RAY DIFFRACTION100
8-100.417100.272293X-RAY DIFFRACTION100

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