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- PDB-8tv1: Structure of the EphA2 LBDCRD bound to FabS1C_L1 -

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Basic information

Entry
Database: PDB / ID: 8tv1
TitleStructure of the EphA2 LBDCRD bound to FabS1C_L1
Components
  • (S1C variant of Fab_L1 ...) x 2
  • Ephrin type-A receptor 2
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / Cell signalling / antibody / agonist / high affinity / clustering / activation / SIGNALING PROTEIN-IMMUNE SYSTEM complex / SIGNALING PROTEIN
Function / homology
Function and homology information


notochord cell development / notochord formation / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / lens fiber cell morphogenesis / axial mesoderm formation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / pericyte cell differentiation / ephrin receptor activity ...notochord cell development / notochord formation / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / lens fiber cell morphogenesis / axial mesoderm formation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / pericyte cell differentiation / ephrin receptor activity / leading edge membrane / negative regulation of chemokine production / response to growth factor / post-anal tail morphogenesis / activation of GTPase activity / bone remodeling / positive regulation of bicellular tight junction assembly / regulation of lamellipodium assembly / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / central nervous system neuron differentiation / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / tight junction / neural tube development / mammary gland epithelial cell proliferation / RHOV GTPase cycle / growth factor binding / EPHA-mediated growth cone collapse / regulation of cell adhesion mediated by integrin / RHOU GTPase cycle / lamellipodium membrane / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RAC2 GTPase cycle / RAC3 GTPase cycle / regulation of angiogenesis / ephrin receptor signaling pathway / regulation of ERK1 and ERK2 cascade / vasculogenesis / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / osteoclast differentiation / molecular function activator activity / negative regulation of angiogenesis / skeletal system development / protein localization to plasma membrane / cell chemotaxis / positive regulation of protein localization to plasma membrane / cell motility / receptor protein-tyrosine kinase / ruffle membrane / intrinsic apoptotic signaling pathway in response to DNA damage / osteoblast differentiation / cell migration / lamellipodium / virus receptor activity / angiogenesis / receptor complex / cell adhesion / defense response to Gram-positive bacterium / positive regulation of cell migration / cadherin binding / inflammatory response / focal adhesion / cell surface / ATP binding / plasma membrane
Similarity search - Function
Ephrin type-A receptor 2, ligand binding domain / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / : / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. ...Ephrin type-A receptor 2, ligand binding domain / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / : / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. / Eph receptor ligand-binding domain profile. / Ephrin receptor ligand binding domain / Putative ephrin-receptor like / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Fibronectin type III domain / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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

Downloads & links

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Assembly

Deposited unit
D: S1C variant of Fab_L1 heavy chain
E: S1C variant of Fab_L1 light chain
C: Ephrin type-A receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2016
Polymers82,0683
Non-polymers1333
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-62 kcal/mol
Surface area32840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.437, 73.249, 118.570
Angle α, β, γ (deg.)90.000, 107.430, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules C

#3: Protein Ephrin type-A receptor 2 / Epithelial cell kinase / Tyrosine-protein kinase receptor ECK


Mass: 33952.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: expressed with a C-terminal thrombin cleavage site and 6-his sequence. The residues LTPR at the C-terminus are derived from the thrombin cleavage site
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA2, ECK / Plasmid: pSCSTa
Details (production host): expressed with a C-terminal thrombin cleavage site and 6-his sequence. The residues LTPR at the C-terminus are derived from the thrombin cleavage site
Cell line (production host): Expi293 / Production host: Homo sapiens (human)
References: UniProt: P29317, receptor protein-tyrosine kinase

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Antibody , 2 types, 2 molecules DE

#1: Antibody S1C variant of Fab_L1 heavy chain


Mass: 25257.072 Da / Num. of mol.: 1
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.: 1 / 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)

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Non-polymers , 3 types, 64 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.12 Å3/Da / Density % sol: 60.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 14% PEG 20K, 100 mm HEPES 7.0, 200 mM KSCN / 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: 2.6→62.2 Å / Num. obs: 28513 / % possible obs: 91.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 54.37 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.072 / Rrim(I) all: 0.149 / Net I/σ(I): 6.2
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.102 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3018 / CC1/2: 0.612 / Rpim(I) all: 0.619 / Rrim(I) all: 1.269 / % possible all: 79.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→62.2 Å / SU ML: 0.349 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0652
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2462 1992 6.99 %
Rwork0.2016 26508 -
obs0.2048 28500 91.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.12 Å2
Refinement stepCycle: LAST / Resolution: 2.6→62.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5542 0 6 61 5609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00795701
X-RAY DIFFRACTIONf_angle_d1.04057781
X-RAY DIFFRACTIONf_chiral_restr0.0557869
X-RAY DIFFRACTIONf_plane_restr0.00891005
X-RAY DIFFRACTIONf_dihedral_angle_d17.7931969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.36011620.32252015X-RAY DIFFRACTION97.67
2.67-2.740.3131980.28671392X-RAY DIFFRACTION67
2.74-2.820.32461400.27262001X-RAY DIFFRACTION96.35
2.82-2.910.35351460.27381872X-RAY DIFFRACTION91.56
2.91-3.010.3231480.27542026X-RAY DIFFRACTION97.8
3.01-3.130.31861540.27412045X-RAY DIFFRACTION98.17
3.13-3.280.29821450.24512021X-RAY DIFFRACTION98.1
3.28-3.440.32521400.23721897X-RAY DIFFRACTION97.14
3.47-3.660.28581340.22871727X-RAY DIFFRACTION98.1
3.7-3.950.25191140.20721507X-RAY DIFFRACTION83.26
3.95-4.340.22761490.16821903X-RAY DIFFRACTION91.57
4.34-4.970.17361520.1462040X-RAY DIFFRACTION98.52
4.97-6.260.21551560.16112068X-RAY DIFFRACTION98.06
6.26-62.20.1711540.16091994X-RAY DIFFRACTION92.47
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)
12.81650113918-1.190911009512.717805854241.36491644234-1.397696857174.64994454706-0.117196056953-0.1747875669570.1671081581910.03537752798920.2196131351360.158618908794-0.400697790323-0.566782622153-0.1065187853520.36967977620.002856473092150.07151257004920.347908018783-7.76080140278E-50.353705970118-12.80707538617.8943902824236.1420774115
29.562418209691.30844599517-2.757884147238.502710941965.063078593737.63457074857-1.02223517587-1.2225282941-0.8719699218361.453100363260.894175454131-1.046924787571.042814489881.395759091580.1596407617090.5815582490650.116584805925-0.004753191408770.4908766367550.1192624011950.47455650232315.9319191654-10.65486044755.5612642659
34.408274433541.747403126450.1669757836252.40531677048-0.9966355256063.89073984037-0.0619532980755-0.0462339443498-0.0812057602857-0.311111324698-0.121807180011-0.2800684800910.1111670855720.2891033163550.154324971670.4168803763030.001728293624010.01222261827990.231742687722-0.02449521312430.34418079183112.2469253667-3.2755157541150.3225155094
42.99276941087-1.364698494911.205578479077.7395383181-1.186349833415.062353168340.2140107879160.22936844998-0.807097033609-0.05514407624410.1532663948430.8730934240010.908148786788-0.612885893553-0.3564814185310.566669960317-0.161189445471-0.09223360460260.436730001722-0.02647039786840.482327899078-15.9070901915-12.786137218831.5917652294
53.66370878378-0.600600476532.025561623911.5618345353-1.779217673732.405929479210.2737949765640.00466468648886-0.412309810123-0.361017932529-0.08486305004720.1499943451860.45883317885-0.0320714736673-0.150193802810.4447191110830.01235555771080.03562553806410.2742325306510.008377174484350.3419423204747.39352449867-14.753903640754.531009568
64.353775725660.6141185246752.245900833657.481480834711.241274514396.93721223320.0112381243862-0.330879630852-0.2465322897410.164966618218-0.09192717820720.484084291396-0.00338250572049-0.1654194591610.04592308079350.3328028250750.002579389648620.07897819626970.2444343259660.02247832382840.3447140902926.75605142723-17.401792005761.0475710511
74.607979016611.016578967891.767478850234.335715471881.145436998245.84626850189-0.2681155452070.184056969717-0.005397506781480.2025779016580.2504054608620.0606741830669-0.0656456544646-0.7929688796060.02748317903780.426085696048-0.0716603157096-0.03204343408080.6808629294860.07940646293290.379629065671-31.03083390516.610777418644.40086846588
84.201072288022.2386504484.732087793931.113785835852.171962061153.54879503721-0.7664056262210.7261746081850.346564345576-0.5228487298190.5270322703660.226509148742-0.4674261234150.5882278893620.2174350629680.614981786989-0.3789100170710.03188370794141.28873595606-0.03759739204880.691839081275-68.8665112078-16.5379583524-19.5228689835
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 148 )DA1 - 1481 - 140
22chain 'D' and (resid 149 through 169 )DA149 - 169141 - 161
33chain 'D' and (resid 170 through 238 )DA170 - 238162 - 230
44chain 'E' and (resid 2 through 119 )EC2 - 1191 - 99
55chain 'E' and (resid 120 through 146 )EC120 - 146100 - 126
66chain 'E' and (resid 147 through 232 )EC147 - 232127 - 210
77chain 'C' and (resid 27 through 188 )CD27 - 1881 - 162
88chain 'C' and (resid 189 through 329 )CD189 - 329163 - 303

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