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- PDB-8tv2: Structure of apo FabS1C_L1 -

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Basic information

Entry
Database: PDB / ID: 8tv2
TitleStructure of apo FabS1C_L1
Components
  • S1C variant of Fab_L1 heavy chain
  • S1C variant of Fab_L1 light chain
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / Cell signalling / antibody / agonist / high affinity / clustering / activation / SIGNALING PROTEIN-IMMUNE SYSTEM complex / IMMUNE SYSTEM
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSinger, A.U. / Bruce, H.A. / Blazer, L. / Adams, J.J. / Sicheri, F. / Sidhu, S.S.
Funding support United States, 2items
OrganizationGrant numberCountry
Celgene CorporationOperating Contract United States
Bristol-Myers Squibb (BMS) ResearchCollaboration and Option Agreement United States
CitationJournal: Protein Sci. / Year: 2025
Title: Synthetic antibodies targeting EphA2 induce diverse signaling-competent clusters with differential activation.
Authors: Adams, J.J. / Bruce, H.A. / Subramania, S. / Ploder, L. / Garcia, J. / Pot, I. / Blazer, L.L. / Singer, A.U. / Sidhu, S.S.
History
DepositionAug 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 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
Revision 1.2May 7, 2025Group: 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.title / _citation.year
Revision 1.3Jun 18, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: S1C variant of Fab_L1 heavy chain
E: S1C variant of Fab_L1 light chain
A: S1C variant of Fab_L1 heavy chain
B: S1C variant of Fab_L1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,56014
Polymers96,2314
Non-polymers33010
Water55831
1
D: S1C variant of Fab_L1 heavy chain
E: S1C variant of Fab_L1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3168
Polymers48,1152
Non-polymers2006
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-83 kcal/mol
Surface area19280 Å2
MethodPISA
2
A: S1C variant of Fab_L1 heavy chain
B: S1C variant of Fab_L1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2456
Polymers48,1152
Non-polymers1294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-64 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.259, 74.259, 370.837
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Antibody S1C variant of Fab_L1 heavy chain


Mass: 25257.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fab produced by randomization of CDR regions and selected by phage display. Fabs utilize IMGT (LeClerc et al., Dev Comp Immunol. 2003 Jan;27(1):55-77) numbering.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pSCSTa / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody S1C variant of Fab_L1 light chain


Mass: 22858.264 Da / Num. of mol.: 2 / Mutation: SPHAGLSSP replaced by QGTTS; Q165S, K167Y
Source method: isolated from a genetically manipulated source
Details: Fab produced by randomization of CDR regions and selected by phage display. Fabs utilize IMGT (LeClerc et al., Dev Comp Immunol. 2003 Jan;27(1):55-77) numbering.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pSCSTa / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.07 Å3/Da / Density % sol: 59.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 18% PEG6000, 1M Lithium Chloride, 100 mM Sodium citrate 5.0
PH range: 5 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2022 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.65→92.71 Å / Num. obs: 33902 / % possible obs: 94.1 % / Redundancy: 8.9 % / Biso Wilson estimate: 67.19 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.045 / Rrim(I) all: 0.136 / Net I/σ(I): 9.3
Reflection shellResolution: 2.65→2.78 Å / Redundancy: 8.7 % / Rmerge(I) obs: 1.136 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3816 / CC1/2: 0.702 / Rpim(I) all: 0.405 / Rrim(I) all: 1.209 / % possible all: 82.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→64.31 Å / SU ML: 0.3998 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.8604
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2473 2002 5.94 %
Rwork0.2043 31713 -
obs0.207 33715 93.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.09 Å2
Refinement stepCycle: LAST / Resolution: 2.65→64.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6502 0 10 31 6543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00946672
X-RAY DIFFRACTIONf_angle_d1.19699117
X-RAY DIFFRACTIONf_chiral_restr0.06781041
X-RAY DIFFRACTIONf_plane_restr0.01061157
X-RAY DIFFRACTIONf_dihedral_angle_d17.46142269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.710.5847970.48781498X-RAY DIFFRACTION65.05
2.71-2.790.40591450.38572375X-RAY DIFFRACTION99.6
2.79-2.870.37661500.30012354X-RAY DIFFRACTION99.33
2.87-2.960.34121450.2712379X-RAY DIFFRACTION99.64
2.96-3.070.27421550.25272378X-RAY DIFFRACTION99.92
3.07-3.190.28951460.25922347X-RAY DIFFRACTION99.92
3.19-3.340.31221510.26282374X-RAY DIFFRACTION99.72
3.34-3.510.30881210.24871917X-RAY DIFFRACTION80.14
3.51-3.730.26491230.21452002X-RAY DIFFRACTION83.11
3.73-4.020.26991320.19342092X-RAY DIFFRACTION86.67
4.02-4.420.19881530.17082415X-RAY DIFFRACTION100
4.42-5.060.1681570.15032440X-RAY DIFFRACTION99.88
5.07-6.380.19471540.17742493X-RAY DIFFRACTION100
6.38-64.310.24071730.17322649X-RAY DIFFRACTION99.96
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)
17.38788876117-2.202197023680.1287710026183.045452294440.3576636437393.50400336406-0.379492497644-0.4199441522581.597040198250.6415425763560.553197369161-0.194988482787-0.699280122758-0.053050441745-0.1675999450860.7525797947370.03277018620580.2337341663540.458646920712-0.1124303892790.940658350139.238498443279.4634952544419.0707440268
25.63049124447-2.86244037063-2.142699111093.485152399550.9974732300443.17260063009-0.06205537551160.1334286709970.233753926140.02139488102080.135789680329-0.1699845350140.16173654704-0.0905977189539-0.07978871207050.366194362599-0.08918624171530.1239136071620.3026781886880.03398585761920.48777179772717.7490802892-10.05043767267.84478762338
36.86154755651.690310717172.849402965862.71099270759-0.2012852792263.837641139810.004180533069450.156978552989-0.0126781223709-0.2035109577580.212662249941-0.2072666178220.115651363225-0.0584921590708-0.2202174185880.31063546359-0.03003870311380.1476928087520.36286218816-0.06451497463030.56364210932520.9248213921-14.82177874790.314804091605
47.32904494734-0.5220426086741.102697693470.0729999661917-0.3487489113222.341786672760.3311170908140.984501187709-0.394559196317-0.252831945855-0.502691311364-0.1330500601280.5189544316850.2261952315360.110283082840.785926927687-0.1351328568680.2606468430350.610440322402-0.09587396499520.76526391261828.866692042-15.6106580683-6.79219253384
54.86667237344-0.3326691720051.179840667634.7630980435-0.4815919809172.43308449842-0.384580163642-0.484872444463-0.6831504035031.002237251220.1117488758970.9044740981770.194361588673-0.6567372930560.2734848247830.7551659412620.09419754233560.4568932547390.5259074949350.05533893036371.08352196122-5.50816109413-9.1041731222720.1366592359
63.26237149387-3.08986503201-1.63822402358.24943000683.830821141283.28073721542-0.517842839939-0.295370863909-0.7948173256361.26246995218-0.02157797545011.157378777830.462037901276-0.3803360832260.531183543490.6655864244270.1204989402140.3521143883420.5886506050730.05137927688410.8954482610281.91512900936-14.827256980518.7763897954
70.0486978190923-0.5095360297580.1569463612765.44000367315-1.470828698142.64976472257-0.3013615811860.36839284309-1.262034834-0.2660520693830.0411360986422-1.162108285770.3617729753960.6774644847680.1590199827840.4394826067820.004742575702750.2167234168040.473828587699-0.1517498649730.84782831430730.1301492013-25.68761524220.486735569573
86.859207854123.169964050431.484248338766.43188227395-1.193069106633.19543281895-0.1437026439220.243069997072-0.6490006723580.5160293465540.0574332604127-0.3854429680710.1593648957920.1387663728150.07721354399740.499528407552-0.02498443880690.153715951160.342179620331-0.1272431734130.63139615736422.1113889679-30.9376632567.66003988804
94.22072063782-1.166542154490.8241679281383.01680138313-0.3926852026291.51661379853-0.569150591954-0.609177576725-0.448753258150.5278041750190.591233058154-0.08480001497560.090529070659-0.059829526621-0.01767185603830.7198144243010.2198969454730.2695699839920.5763955153640.0005316458760740.711436975838-18.212578561411.547710718535.879155962
103.66635271596-1.38673083880.4910770654243.034850293361.825588256465.73578375515-0.139930243716-0.0697789322575-0.264593756993-0.1464769245890.548176463329-0.293925298289-0.6350072314480.0643621262445-0.4090263861780.8106408526630.1885310899420.2772406453710.4600698252930.01438560500140.712580944136-23.177864143416.932122351227.8300623583
111.57774889653-0.5622683569450.5165961668992.67094913476-0.6571040584341.14509132423-0.330020858612-0.41851539808-0.1389974681950.222008461-0.05969403730770.4560357297380.481848469875-0.08012293447920.1470221024061.586749988280.9695087450720.5576211507010.6905342596530.6513628217210.864130655612-43.791249748611.775820178957.1459674369
125.382475076331.50929226559-3.309034955832.250778464611.257574412395.6078366545-0.847084274108-0.6451990289940.5015435548680.5764822635871.06362703559-0.351761943036-0.2277778564230.536855171556-0.1831436991241.358895567940.349333574110.4377827065420.6360934995660.1392374660121.0368577991-32.078254712337.869104430234.6955469929
135.13153533195-1.602604339473.762633874535.31725605030.3830795435724.76312299849-0.1234724685360.3699453293180.1772395841870.04592200971230.370402148046-0.0415530651402-0.4942086259630.142358685882-0.2419103433390.887205090490.2429214526460.3539774251510.5330086724760.1137257223550.643092175672-30.625703975529.680832185628.9642223184
140.251921113729-0.3559760516880.01279659289892.279269761410.2541013988270.06094008403110.293283374206-0.247654825672-0.08561969537450.5298371554890.227067741938-0.150808416459-0.1847946497930.422783776494-0.2042434350831.591619399461.159658037880.6364554018380.7192151773420.4349671649850.847061142857-44.541629674924.631542435358.1908924188
151.122335466760.348337668594-0.01229531223360.614476294379-0.5792253720962.544353833130.104830193758-0.3051309923810.2387427246390.3895909172220.325486750645-0.2969336201270.1118563056260.505151161403-0.4040350012121.602243998950.678561068450.5144718504361.012400252280.2884996619840.815006334636-45.154294426828.336280524464.5280521072
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 1 through 117 )DA1 - 1171 - 109
22chain 'D' and (resid 118 through 169 )DA118 - 169110 - 161
33chain 'D' and (resid 170 through 227 )DA170 - 227162 - 219
44chain 'D' and (resid 228 through 240 )DA228 - 240220 - 232
55chain 'E' and (resid 2 through 106 )EB2 - 1061 - 89
66chain 'E' and (resid 107 through 131 )EB107 - 13190 - 111
77chain 'E' and (resid 132 through 146 )EB132 - 146112 - 126
88chain 'E' and (resid 147 through 232 )EB147 - 232127 - 210
99chain 'A' and (resid 1 through 99 )AC1 - 991 - 91
1010chain 'A' and (resid 100 through 135 )AC100 - 13592 - 127
1111chain 'A' and (resid 136 through 238 )AC136 - 238128 - 225
1212chain 'B' and (resid 2 through 25 )BD2 - 251 - 24
1313chain 'B' and (resid 26 through 116 )BD26 - 11625 - 96
1414chain 'B' and (resid 117 through 155 )BD117 - 15597 - 135
1515chain 'B' and (resid 156 through 231 )BD156 - 231136 - 209

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