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- PDB-7kql: Anti-Tim3 antibody Fab complex -

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Basic information

Entry
Database: PDB / ID: 7kql
TitleAnti-Tim3 antibody Fab complex
Components
  • Hepatitis A virus cellular receptor 2
  • Tim3.18 Fab heavy chain
  • Tim3.18 Fab light chain
KeywordsIMMUNE SYSTEM / Tim3 HAVCR2 Fab antibody
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 / positive regulation of macrophage activation / macrophage activation involved in immune response / anchoring junction / negative regulation of interleukin-2 production / negative regulation of NF-kappaB transcription factor activity / positive regulation of interleukin-4 production / negative regulation of interleukin-6 production / negative regulation of type II interferon production / immunological synapse / negative regulation of tumor necrosis factor production / maternal process involved in female pregnancy / positive regulation of chemokine production / negative regulation of T cell proliferation / positive 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 / negative regulation of gene expression / innate immune response / 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 / Immunoglobulins ...: / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Hepatitis A virus cellular receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsDeng, X.A. / West, S.M. / Strop, P.
CitationJournal: J.Clin.Invest. / Year: 2022
Title: Tim-3 mediates T cell trogocytosis to limit antitumor immunity.
Authors: Pagliano, O. / Morrison, R.M. / Chauvin, J.M. / Banerjee, H. / Davar, D. / Ding, Q. / Tanegashima, T. / Gao, W. / Chakka, S.R. / DeBlasio, R. / Lowin, A. / Kara, K. / Ka, M. / Zidi, B. / ...Authors: Pagliano, O. / Morrison, R.M. / Chauvin, J.M. / Banerjee, H. / Davar, D. / Ding, Q. / Tanegashima, T. / Gao, W. / Chakka, S.R. / DeBlasio, R. / Lowin, A. / Kara, K. / Ka, M. / Zidi, B. / Amin, R. / Raphael, I. / Zhang, S. / Watkins, S.C. / Sander, C. / Kirkwood, J.M. / Bosenberg, M. / Anderson, A.C. / Kuchroo, V.K. / Kane, L.P. / Korman, A.J. / Rajpal, A. / West, S.M. / Han, M. / Bee, C. / Deng, X. / Schebye, X.M. / Strop, P. / Zarour, H.M.
History
DepositionNov 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 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
H: Tim3.18 Fab heavy chain
L: Tim3.18 Fab light chain
T: Hepatitis A virus cellular receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2377
Polymers62,8683
Non-polymers3684
Water11,602644
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-38 kcal/mol
Surface area24290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.105, 63.856, 66.407
Angle α, β, γ (deg.)90.000, 94.254, 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

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Components

#1: Antibody Tim3.18 Fab heavy chain


Mass: 24986.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Tim3.18 Fab light chain


Mass: 23415.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Hepatitis A virus cellular receptor 2 / HAVcr-2 / T-cell immunoglobulin and mucin domain-containing protein 3 / TIMD-3 / T-cell ...HAVcr-2 / T-cell immunoglobulin and mucin domain-containing protein 3 / TIMD-3 / T-cell immunoglobulin mucin receptor 3 / TIM-3 / T-cell membrane protein 3


Mass: 14465.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HAVCR2, TIM3, TIMD3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8TDQ0
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / 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: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Crystals of Tim3.18 hTim3 IgV were grown in hanging drops at 22C containing 1 uL protein and 1 uL well solution consisting of optimized conditions of 0.1M MES pH 7.0 and 14.6-15.4% PEG 3350, ...Details: Crystals of Tim3.18 hTim3 IgV were grown in hanging drops at 22C containing 1 uL protein and 1 uL well solution consisting of optimized conditions of 0.1M MES pH 7.0 and 14.6-15.4% PEG 3350, Single crystals were harvested with glycerol as the cryoprotectant, and flash frozen in liquid nitrogen.

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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: Mar 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→48.56 Å / Num. obs: 88986 / % possible obs: 98.74 % / Redundancy: 3.2 % / Biso Wilson estimate: 18.74 Å2 / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.05611 / Rpim(I) all: 0.03752 / Rrim(I) all: 0.06776 / Net I/σ(I): 13.01
Reflection shellResolution: 1.49→1.543 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.4747 / Mean I/σ(I) obs: 2.33 / Num. unique obs: 8955 / CC1/2: 0.884 / CC star: 0.969 / Rpim(I) all: 0.3076 / Rrim(I) all: 0.5676 / % possible all: 99.62

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F71, 4NZU

5f71

4nzu


Resolution: 1.49→48.56 Å / SU ML: 0.1607 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7946
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2002 4390 4.91 %
Rwork0.1766 85030 -
obs0.1778 88901 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.73 Å2
Refinement stepCycle: LAST / Resolution: 1.49→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4159 0 24 644 4827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00944357
X-RAY DIFFRACTIONf_angle_d1.33545948
X-RAY DIFFRACTIONf_chiral_restr0.1179662
X-RAY DIFFRACTIONf_plane_restr0.0094763
X-RAY DIFFRACTIONf_dihedral_angle_d16.276617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.50.32461590.27582848X-RAY DIFFRACTION99.73
1.5-1.520.28861650.26322784X-RAY DIFFRACTION99.63
1.52-1.540.2771380.2472861X-RAY DIFFRACTION99.57
1.54-1.560.28751390.24182892X-RAY DIFFRACTION99.67
1.56-1.580.24551390.23722860X-RAY DIFFRACTION99.63
1.58-1.60.2411390.22182803X-RAY DIFFRACTION99.36
1.6-1.620.25391300.21472849X-RAY DIFFRACTION99.6
1.62-1.650.24151500.21292881X-RAY DIFFRACTION99.74
1.65-1.670.26181300.20692897X-RAY DIFFRACTION99.54
1.67-1.70.24491810.19922798X-RAY DIFFRACTION99.33
1.7-1.730.2161560.19352826X-RAY DIFFRACTION99.37
1.73-1.760.20671240.1962834X-RAY DIFFRACTION99.16
1.76-1.80.23151630.18552836X-RAY DIFFRACTION99.24
1.8-1.830.20621630.18562810X-RAY DIFFRACTION99.53
1.83-1.870.21211540.1782852X-RAY DIFFRACTION99.37
1.87-1.920.17741500.17692829X-RAY DIFFRACTION99.04
1.92-1.970.2281420.18152821X-RAY DIFFRACTION98.37
1.97-2.020.20571550.17172791X-RAY DIFFRACTION98.89
2.02-2.080.21271480.18012861X-RAY DIFFRACTION98.98
2.08-2.140.21771540.18182829X-RAY DIFFRACTION98.68
2.14-2.220.20821440.17022791X-RAY DIFFRACTION98.23
2.22-2.310.17691360.17532847X-RAY DIFFRACTION98.29
2.31-2.420.2021450.17532812X-RAY DIFFRACTION97.98
2.42-2.540.19731460.17932835X-RAY DIFFRACTION98.06
2.54-2.70.22871590.18612760X-RAY DIFFRACTION97.2
2.7-2.910.22791510.1892832X-RAY DIFFRACTION98.16
2.91-3.20.211340.17442841X-RAY DIFFRACTION97.73
3.2-3.670.16671490.16142820X-RAY DIFFRACTION97.28
3.67-4.620.15771110.14272876X-RAY DIFFRACTION97.52
4.62-48.560.15841360.16462854X-RAY DIFFRACTION95.99
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)
11.212305315430.703642656595-1.008892779591.3438847916-0.05413948721914.05774589739-0.08320680317280.220444114026-0.141929704939-0.0297146041612-0.08129727270210.005415875415420.277970011794-0.3239896424020.1243441380180.156492015994-0.0116045789351-0.01133827713750.197361339104-0.03676649917840.178703199274-23.3369390291-18.1646888248-14.8898805082
22.46578577069-0.3888702507850.009165548367490.6361682739081.183921234212.51653759257-0.0460018941012-0.106276374055-0.1083728965050.04154688463090.0256451599780.09105699250230.150650212425-0.1326075740760.02881131933780.142417311599-0.01414871662740.004982255440620.118067071195-0.00540144806210.15665039239-26.2294482144-14.0794541404-2.56384882016
32.2011791956-0.00342459547685-0.622578934693.78267355974-0.7176865942082.43945713264-0.04591221682460.154294040873-0.3485502555020.07424226608390.0318013962420.3265554560940.07439430508-0.410979205640.0244708521350.143967451866-0.0172111809727-0.003380696671150.173064177656-0.01639092766340.190169763447-31.5390889984-15.5447703929-8.14228678698
41.99508318973-0.112413065366-1.318039566590.2769615350850.01357233824091.5135094238-0.0278619502537-0.0100266072436-0.0716266800858-0.0143252512952-0.0275423117420.02335439686740.0514565271735-0.04754242410850.04877365508190.136606274728-0.0132097769655-0.01704975115140.119366891819-0.01461006891660.160192105749-20.7074226326-13.1657563649-9.99544247963
51.978002774180.6327840408450.01432255928981.47238215270.7185575198272.07354707296-0.09267200028110.0190742525017-0.009672847302590.1757973646270.0115566911079-0.16839673710.2684581415890.05002992548150.07479629136250.1757233495280.0244839475436-0.0009166813741510.06930502009720.009332887874680.133449703148-0.859067763483-19.8703432053-24.4505041369
62.513337426970.4944999904831.050127021430.723931837143-0.1127316122411.488882486470.04472967099930.101225600048-0.3706969802330.3014399323790.0193641438241-0.3152690336190.6092608598740.4955441078050.008468720096720.3521998806870.196456962343-0.05332368319830.269713839357-0.005110680784470.2582834399798.07997846213-25.7471634641-22.8460223692
74.05084205477-0.678068086960.6533528070133.14171967082-0.1304848488021.533778204750.008779353165460.233137233201-0.3913556496260.187485293366-0.0238978457058-0.04580692947590.2929417787720.0140180482550.02716568480640.2255010971420.00671225471314-0.001602430647760.0831749214675-0.000626175064250.195869177719-2.14777174497-27.9346263278-27.7169146994
85.10328016025-0.1924677770140.510442882620.652085950985-0.3139870251971.41516386620.136970294162-0.3108383653970.7245050909970.08732677061910.0193069104297-0.106472592769-0.3097434820640.5292346256720.06794939047730.231632241446-0.09616478500890.01137602221130.333478931755-0.1186092508120.293216476611-5.160849826621.496631033091.76683144972
92.205548779210.469445639910.2218863336912.005717678-0.2865888995191.76925897210.0457844860684-0.6108599678020.1283160308670.2549579306980.121481049366-0.0500858739971-0.1098689709010.279136580011-0.1517351307160.159799138321-0.04360531001130.008004037535190.321183256008-0.07694374187440.157519587727-10.8878309955-6.072305776347.00904488138
101.309316657580.0806813173562-1.124542295590.260576414348-0.012699010551.359165761680.031682379248-0.3372555157490.09264071655230.04702152002550.0135075256462-0.0151440540050.02936616717080.303349318725-0.009347338593630.1423266291470.00629096571124-0.0269822312760.15887348485-0.01472252051950.150096170527-0.915102526899-9.32800086648-10.3297530455
111.592393546380.305271916428-0.02104801850240.8921653338990.3499318079753.0343015980.0454799803281-0.2784904450080.06431695401360.03342246663210.0351126901463-0.03613826517650.04132896366330.119795886473-0.0742863028830.1468912869630.0232615842818-0.0003899663844390.150617559116-0.01457983486070.1742167978858.02903072452-8.29174100748-22.5275502089
121.92983414530.368351767432-0.3451679798351.293331088030.4558747848024.35814670593-0.00826500361417-0.05275114135230.0303042805156-0.1307533543770.143925505828-0.141082652982-0.1316737296320.438196972373-0.1345112401530.166370397321-0.004226355574340.02280345101270.129740483628-0.01038909189320.17766631622213.1092268641-10.2274840143-33.0210188582
133.44285057506-1.19426602861.598084865529.08365413712-3.646860088936.549273316170.141853964571-1.074659293630.6986095921450.646101245753-0.3079453345530.11391182602-0.638783694015-0.4427832103950.1233046084540.31235182960.05209442831180.08422299204190.489780675668-0.1026195276940.357655910673-45.3010381858-4.6143520022528.8305380612
142.3752390752-0.7124673763180.8610315297572.05261175569-1.377830632483.139533805070.1963797825670.174815324397-0.0790595177551-0.1649044693290.08736895026810.3277872500710.213652296213-0.494513126315-0.2289923361740.174892823287-0.0347132477019-0.0286581827150.43869658157-0.01490935825250.255219697743-48.0598545832-12.57439238913.5168203785
152.146027931932.040330514340.4549028258564.216201243653.914599304565.623904537260.0534254863371-0.78182691112-0.3053547810040.164276009557-0.152071050725-0.212046622024-0.03923724867630.130128529350.005092912928360.144204966808-0.03249173571210.001889959640450.367720034123-0.004188829478470.186049336854-38.5595650009-12.524675810913.1914953281
162.94022804810.563991248251-0.4262678800011.59014845001-0.581335408743.26677891197-0.0911106419209-0.432192420391-0.360378057315-0.06107910925880.01077157570160.1751195798930.569341366537-0.09663731093390.05019856058530.238795938895-0.02876709107710.02963564469010.3210666484850.01536270784240.252776133467-35.2800390035-16.441796635912.1136486228
172.0911582748-1.373947546150.3463132187444.60875021089-2.039359967262.57581874011-0.001994680044880.218234519979-0.50072761022-0.391254933519-0.05495217552540.4105980973431.10544981894-0.03395700006520.002891868568270.4041706531650.002848102187240.03393670186680.479280594022-0.04834028655130.284791874092-46.1967444764-20.081558958316.3757237759
180.504344572337-0.3757671333650.2155216141790.6235303009140.5366755507972.167466666280.0289361099793-0.4962074736280.1308136285460.1705299005810.006161256506610.04937595888940.079482261270.439330257788-0.0204226302490.165617567246-0.01149580641530.0009322350104310.495816619266-0.04018165378910.181547249908-39.5163913361-11.998207665521.5028165036
192.074790553842.342419031021.44412337573.519940499011.791198988981.03663410631-0.6284955034910.6296168286420.566343742078-1.567553906770.297623118840.262517497143-0.910448607965-0.04392172560150.2519274164470.5713171190560.0272756839874-0.02366062993670.3534763020230.02296895481880.298936727176-41.200199778-5.067136956910.0806093148496
200.648185217392-0.0850386314634-0.259454585553.05897199292-2.818468570932.827495493420.33379257313-0.4493674162750.1726146577710.4641791252180.242280772820.134512978152-0.782660016441-0.0962356716121-0.7745513702060.199172897272-0.0198183163460.02926748597580.464746937142-0.07757854927860.228545675327-41.2896064929-5.8444649432123.4907411182
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 17 )HE1 - 171 - 17
22chain 'H' and (resid 18 through 62 )HE18 - 6218 - 63
33chain 'H' and (resid 63 through 84 )HE63 - 8464 - 86
44chain 'H' and (resid 85 through 129 )HE85 - 12987 - 133
55chain 'H' and (resid 130 through 185 )HE130 - 185134 - 182
66chain 'H' and (resid 186 through 204 )HE186 - 204183 - 201
77chain 'H' and (resid 205 through 226 )HE205 - 226202 - 223
88chain 'L' and (resid 1 through 25 )LF1 - 251 - 25
99chain 'L' and (resid 26 through 76 )LF26 - 7626 - 77
1010chain 'L' and (resid 77 through 129 )LF77 - 12978 - 132
1111chain 'L' and (resid 130 through 175 )LF130 - 175133 - 179
1212chain 'L' and (resid 176 through 215 )LF176 - 215180 - 221
1313chain 'T' and (resid 2 through 8 )TG2 - 81 - 7
1414chain 'T' and (resid 9 through 28 )TG9 - 288 - 27
1515chain 'T' and (resid 29 through 34 )TG29 - 3428 - 33
1616chain 'T' and (resid 35 through 55 )TG35 - 5534 - 54
1717chain 'T' and (resid 56 through 73 )TG56 - 7355 - 72
1818chain 'T' and (resid 74 through 92 )TG74 - 9273 - 91
1919chain 'T' and (resid 93 through 99 )TG93 - 9992 - 98
2020chain 'T' and (resid 100 through 111 )TG100 - 11199 - 110

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