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- PDB-8tv5: Structure of the EphA2 LBDCRD bound to FabS1CE_L1 in a 2:1 (EphA2... -

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Basic information

Entry
Database: PDB / ID: 8tv5
TitleStructure of the EphA2 LBDCRD bound to FabS1CE_L1 in a 2:1 (EphA2 to Fab) ratio
Components
  • Ephrin type-A receptor 2
  • S1CE variant of Fab_L1 heavy chain
  • S1CE variant of Fab_L1 light chain
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 / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / ephrin receptor activity / pericyte cell differentiation / cAMP metabolic process / positive regulation of bicellular tight junction assembly ...notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / ephrin receptor activity / pericyte cell differentiation / cAMP metabolic process / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration / leading edge membrane / negative regulation of chemokine production / bone remodeling / post-anal tail morphogenesis / response to growth factor / activation of GTPase activity / tight junction / regulation of lamellipodium assembly / EPH-Ephrin signaling / branching involved in mammary gland duct morphogenesis / neural tube development / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / mammary gland epithelial cell proliferation / RHOV GTPase cycle / EPHA-mediated growth cone collapse / growth factor binding / regulation of cell adhesion mediated by integrin / lamellipodium membrane / RHOU GTPase cycle / ephrin receptor signaling pathway / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RAC2 GTPase cycle / RAC3 GTPase cycle / vasculogenesis / regulation of angiogenesis / keratinocyte differentiation / transmembrane receptor protein tyrosine kinase activity / RAC1 GTPase cycle / regulation of ERK1 and ERK2 cascade / negative regulation of angiogenesis / osteoclast differentiation / cell chemotaxis / skeletal system development / molecular function activator activity / protein localization to plasma membrane / cell motility / positive regulation of protein localization to plasma membrane / receptor protein-tyrosine kinase / neuron differentiation / ruffle membrane / osteoblast differentiation / intrinsic apoptotic signaling pathway in response to DNA damage / cell migration / lamellipodium / virus receptor activity / receptor complex / cell adhesion / defense response to Gram-positive bacterium / positive regulation of cell migration / inflammatory response / cadherin binding / 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 / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type III domain / 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: 4.6 Å
AuthorsSinger, A.U. / Bruce, H.A. / Blazer, L. / Adams, J.J. / Sicheri, F. / Sidhu, S.S.
Funding support2items
OrganizationGrant numberCountry
Other privateOperating Contract
Other privateCollaboration and Option Agreement
CitationJournal: To be published
Title: Synthetic Antibodies targeting EPHA2 Induce Diverse Signaling-Competent Clusters with Differential Activation
Authors: Adams, J.J. / Bruce, H.A. / Ploder, L. / Garcia, J. / Khutoreskaya, G. / Jarvik, N. / Costa, L.E. / Gorelik, M. / Pot, I. / Sicheri, F. / Blazer, L.L. / Singer, A.U. / Sidhu, S.S.
History
DepositionAug 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S1CE variant of Fab_L1 heavy chain
B: S1CE variant of Fab_L1 light chain
F: Ephrin type-A receptor 2
C: Ephrin type-A receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,1386
Polymers116,0894
Non-polymers492
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-70 kcal/mol
Surface area46310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.879, 72.888, 241.962
Angle α, β, γ (deg.)90.000, 89.040, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "C" and (resid 27 through 47 or (resid 48...
d_2ens_1(chain "F" and (resid 27 through 61 or (resid 62...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LYSLYSPROPROCD27 - 2385 - 216
d_12GLUGLULEULEUCD241 - 327219 - 305
d_21LYSLYSARGARGFC27 - 3155 - 293
d_22METMETLEULEUFC323 - 327301 - 305

NCS oper: (Code: givenMatrix: (-0.69289488864, 0.374683381214, -0.616043048121), (0.394187019528, -0.518561210881, -0.7587561296), (-0.603749341144, -0.768574416964, 0.211613087159)Vector: 139. ...NCS oper: (Code: given
Matrix: (-0.69289488864, 0.374683381214, -0.616043048121), (0.394187019528, -0.518561210881, -0.7587561296), (-0.603749341144, -0.768574416964, 0.211613087159)
Vector: 139.442780131, -3.492576941, 67.7195814914)

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Components

#1: Antibody S1CE variant of Fab_L1 heavy chain


Mass: 25326.221 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. Residues SSASTK replaced by FNQIK.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pSCSTa / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody S1CE variant of Fab_L1 light chain


Mass: 22858.264 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. Residues SPHAGLSSP replaced ...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. Residues SPHAGLSSP replaced by QGTTS; Q165S, K167Y.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pSCSTa / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Protein Ephrin type-A receptor 2 / Epithelial cell kinase / Tyrosine-protein kinase receptor ECK


Mass: 33952.336 Da / Num. of mol.: 2 / Fragment: residues 27-330
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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.53 Å3/Da / Density % sol: 65.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 16% PEG8000, 100 mM CHES 9.0, 200 mM Magnesium Sulfate
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: Sep 26, 2022 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 4.5→120.96 Å / Num. obs: 9743 / % possible obs: 99 % / Redundancy: 3.5 % / Biso Wilson estimate: 160 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.089 / Rrim(I) all: 0.168 / Net I/σ(I): 9.4
Reflection shellResolution: 4.5→4.58 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.164 / Mean I/σ(I) obs: 1 / Num. unique obs: 487 / CC1/2: 0.495 / Rpim(I) all: 0.754 / Rrim(I) all: 1.393 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.6→120.96 Å / SU ML: 0.83 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 38.32
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2982 911 10 %
Rwork0.2651 8195 -
obs0.2683 9106 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 267.41 Å2
Refinement stepCycle: LAST / Resolution: 4.6→120.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7734 0 2 0 7736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00347935
X-RAY DIFFRACTIONf_angle_d0.899110836
X-RAY DIFFRACTIONf_chiral_restr0.05021204
X-RAY DIFFRACTIONf_plane_restr0.00661413
X-RAY DIFFRACTIONf_dihedral_angle_d16.87882728
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.41219742177 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.6-4.840.3681220.3251121X-RAY DIFFRACTION97.11
4.84-5.150.37291280.31361158X-RAY DIFFRACTION98.85
5.15-5.540.37531280.28891178X-RAY DIFFRACTION99.54
5.54-6.10.34371300.32261167X-RAY DIFFRACTION99.46
6.1-6.980.38151310.30541172X-RAY DIFFRACTION99.39
6.99-8.80.27351300.29031178X-RAY DIFFRACTION98.87
8.8-120.960.23541420.20391221X-RAY DIFFRACTION98.34
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)
11.75755666466-0.83115190510.2096335103027.58822217667-3.581225950923.531400855160.910576070084-0.0245214959836-0.4268553663550.4466662725540.6682829390952.65186893826-1.99630872241-0.0853236336594-1.211673897362.477362258470.1827636236040.3655470553991.76952633060.09434685804792.1589557755242.8329911056-6.866247918587.6788883392
23.60367261021-0.669580499869-3.131455131043.578070814663.553806996625.17969431297-0.6294712542310.719138075203-3.79216954479-0.531493250778-0.379627423575-0.4647924741773.05062708716-0.4225381146210.6960505646992.98178282102-0.482700912941-1.054565381332.523418667490.9891496938312.9120686904932.2731501075-4.04570447837118.593619439
33.95641962991.236951444952.750361564823.75229720881-2.269769625867.083743246860.0293363649637-1.03174166620.197636863154-0.922918058596-0.6993679059371.008549656030.3963486611530.03656027387240.5426625801882.85613255495-0.08565296786620.02151549671791.8917944373-0.1995048306622.1354054665923.02016926375.61107320515116.568479351
47.00189770699-3.54896606442-1.790163250286.486624070157.620241037436.555990145571.66620838019-0.6468816547851.175537609951.403617157830.3112808306430.88954738468-3.972911285580.789350065713-1.284774789373.57586543347-0.3779502768711.135822975292.051764492540.1602534685242.7313142359743.515285439615.159813830787.0091219374
56.64293846321-3.47157418984-2.34414592331.300587988393.967287434412.304806927291.95209804129-1.62658388361-3.331950460991.72765563544-1.70356743504-1.19817053588-1.626156648250.764026000088-0.1169830401784.944952669380.01487447178350.3428451077711.856856498840.3437204300721.7359725282142.432734348914.490325092494.4354029238
66.75970203045-3.51945636803-0.9682312340674.150257232294.461141311748.590928138080.661057840250.6550098684360.103121567972-1.62554542257-0.258501645238-0.962674966449-0.980958233594-0.219989949441-0.3162865429332.16902943121-0.078161819408-0.05123741176091.40477510080.02294184882441.4461204663131.844889022916.5261863468123.300894426
70.3504446150161.261830517070.1306034699182.17719460515-4.066434742297.42743804163-0.6118369933550.241843975171-0.896360347020.241430470412-0.203731866971-1.165257800990.648114967210.5982717305640.6325029389861.531395899420.602164780361-0.1803772758282.15932132967-0.1952195955252.3470509644169.7065842133-23.433063192449.7539704814
80.8936621233621.80879535514-3.42539516743-1.46160845563-1.555029647757.2715572899-0.9561602624310.02393256031170.482002036392-0.964271516467-0.552891289215-0.6929901406831.959076987161.307211213621.38386946782.62612743890.6665592160870.3950941337053.278902082320.1865892749693.4451676946679.6918765685-0.6207161738023.53800918629
92.77733691534-2.06042786139-1.800155323763.535027260782.252304529674.399908603220.106668818570.840137746293-0.299098866310.345896943496-0.0801008230870.68533565096-0.423185454091-0.4715902622750.2451430112721.44518059110.541860776397-0.3533849463112.119624795740.03953993169591.8439590220851.292666456-2.1205320638254.5650874288
103.84301325704-0.93982782506-0.1642206350145.43586043505-0.7443242356691.31797462065-0.1239035267561.667812955650.3321808155490.06600550594860.679123125602-0.809396860382-0.153225045960.216784554176-0.268996434922.674022146190.539083193118-0.2996652854673.046433549490.1899515012212.2716510166880.357033893325.001879298922.0080535848
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 135 )AA1 - 1351 - 127
22chain 'A' and (resid 136 through 148 )AA136 - 148128 - 139
33chain 'A' and (resid 149 through 240 )AA149 - 240140 - 231
44chain 'B' and (resid 2 through 106 )BB2 - 1061 - 89
55chain 'B' and (resid 107 through 129 )BB107 - 12990 - 109
66chain 'B' and (resid 130 through 232 )BB130 - 232110 - 210
77chain 'F' and (resid 27 through 199 )FC27 - 1991 - 173
88chain 'F' and (resid 200 through 327 )FC200 - 327174 - 299
99chain 'C' and (resid 27 through 199 )CD27 - 1991 - 173
1010chain 'C' and (resid 200 through 327 )CD200 - 327174 - 294

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