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- PDB-8trs: Structure of the EphA2 CRD bound to FabS1CE_C1, trigonal form -

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Basic information

Entry
Database: PDB / ID: 8trs
TitleStructure of the EphA2 CRD bound to FabS1CE_C1, trigonal form
Components
  • (S1CE variant of Fab C1 ...) x 2
  • Ephrin type-A receptor 2
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / Cell signalling / antibody / agonist / high affinity / clustering / activation / SIGNALING PROTEIN-IMMUNE SYSTEM complex
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 / tight junction / RND3 GTPase cycle / 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
DI(HYDROXYETHYL)ETHER / Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
CitationJournal: Protein Sci. / Year: 2024
Title: Engineered antigen-binding fragments for enhanced crystallization of antibody:antigen complexes.
Authors: Bruce, H.A. / Singer, A.U. / Filippova, E.V. / Blazer, L.L. / Adams, J.J. / Enderle, L. / Ben-David, M. / Radley, E.H. / Mao, D.Y.L. / Pau, V. / Orlicky, S. / Sicheri, F. / Kurinov, I. / ...Authors: Bruce, H.A. / Singer, A.U. / Filippova, E.V. / Blazer, L.L. / Adams, J.J. / Enderle, L. / Ben-David, M. / Radley, E.H. / Mao, D.Y.L. / Pau, V. / Orlicky, S. / Sicheri, F. / Kurinov, I. / Atwell, S. / Kossiakoff, A.A. / Sidhu, S.S.
History
DepositionAug 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 13, 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
A: S1CE variant of Fab C1 heavy chain
G: S1CE variant of Fab C1 light chain
D: Ephrin type-A receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,82647
Polymers61,2783
Non-polymers2,54844
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13440 Å2
ΔGint-117 kcal/mol
Surface area24390 Å2
Unit cell
Length a, b, c (Å)71.376, 71.376, 235.014
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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Protein , 1 types, 1 molecules D

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


Mass: 13961.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: residues 203-330 / 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 AG

#1: Antibody S1CE variant of Fab C1 heavy chain


Mass: 23883.762 Da / Num. of mol.: 1 / Mutation: SSASTK replaced by FNQIK
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 S1CE variant of Fab C1 light chain


Mass: 23432.895 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 , 5 types, 281 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.82 Å3/Da / Density % sol: 56.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 200 mM ammonium chloride, 30% PEG600 (GRAS1 condition A8)
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: Apr 5, 2022 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.85→117.51 Å / Num. obs: 60648 / % possible obs: 100 % / Redundancy: 11.5 % / Biso Wilson estimate: 41.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.015 / Rrim(I) all: 0.052 / Net I/σ(I): 28.7
Reflection shellResolution: 1.85→1.89 Å / Rmerge(I) obs: 1.516 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3633 / CC1/2: 0.692 / Rpim(I) all: 0.458 / Rrim(I) all: 1.585 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FL7

3fl7


Resolution: 1.9→61.81 Å / SU ML: 0.229 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.437
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.214 2734 4.89 %
Rwork0.18 --
obs0.182 55894 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.17 Å2
Refinement stepCycle: LAST / Resolution: 1.9→61.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4190 0 143 237 4570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074425
X-RAY DIFFRACTIONf_angle_d0.9595986
X-RAY DIFFRACTIONf_dihedral_angle_d16.2291561
X-RAY DIFFRACTIONf_chiral_restr0.064662
X-RAY DIFFRACTIONf_plane_restr0.007768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.3371030.27372691X-RAY DIFFRACTION100
1.93-1.970.34081320.24482583X-RAY DIFFRACTION100
1.97-2.010.26151180.22532614X-RAY DIFFRACTION100
2.01-2.050.25231360.21532599X-RAY DIFFRACTION100
2.05-2.090.25671210.20552654X-RAY DIFFRACTION100
2.09-2.140.22091570.19542585X-RAY DIFFRACTION100
2.14-2.190.20251470.20532615X-RAY DIFFRACTION100
2.19-2.250.25761580.20032620X-RAY DIFFRACTION100
2.25-2.320.25811440.21772609X-RAY DIFFRACTION100
2.32-2.390.24261430.20872626X-RAY DIFFRACTION100
2.39-2.480.27451370.21142632X-RAY DIFFRACTION100
2.48-2.580.23031350.20212651X-RAY DIFFRACTION100
2.58-2.70.2738960.20572676X-RAY DIFFRACTION100
2.7-2.840.23581400.19842655X-RAY DIFFRACTION100
2.84-3.020.24591270.2052664X-RAY DIFFRACTION100
3.02-3.250.21971490.18422693X-RAY DIFFRACTION100
3.25-3.580.20241570.17782658X-RAY DIFFRACTION100
3.58-4.090.1881580.16692669X-RAY DIFFRACTION100
4.09-5.160.17081280.142771X-RAY DIFFRACTION100
5.16-61.810.20851480.17392895X-RAY DIFFRACTION100
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)
13.31090.5832-0.42411.75270.45384.59640.221-0.2991-0.0520.073-0.1518-0.1388-0.17830.1534-0.0580.3087-0.04060.01890.28720.03080.320728.9983-18.01265.5263
21.1028-0.24190.15510.6028-1.63554.6766-0.0242-0.47290.5340.17250.04140.1161-0.55540.3529-0.02440.3914-0.1182-0.00530.6263-0.0050.466129.8033-20.438227.2275
34.29541.507-0.20435.2778-0.53232.6561-0.013-0.1020.01760.0692-0.0710.17810.06030.20230.07840.2002-0.0032-0.01370.43110.00230.282716.1523-34.08535.9103
46.7115.8872-4.58786.9228-4.22384.6640.6776-0.12630.49750.5165-0.38680.5511-0.5878-0.145-0.30550.32480.10030.02940.4006-0.01630.352.1341-17.77688.032
53.83582.0158-1.37374.6266-0.58563.47080.11520.10980.2496-0.3794-0.01370.3117-0.2792-0.3748-0.09950.27510.0598-0.0160.2929-0.01790.26117.2215-19.5116-0.3427
65.19224.1841-1.92946.7943-2.37583.18330.2524-0.13250.09850.055-0.3136-0.03-0.3344-0.09370.01870.28630.08420.01170.2797-0.00990.275410.3437-18.81023.6248
73.01892.2462-4.36063.2012-4.60267.4950.0191-0.0082-0.1579-0.06210.0321-0.14770.0532-0.5613-0.04910.322-0.060.00550.56220.03110.3889-2.5492-27.709619.857
88.84940.13427.32295.36131.04838.0116-0.1273-1.3485-0.19770.34110.1868-0.42160.3541-0.3209-0.05830.33360.04110.03570.6975-0.00120.320912.7833-29.099146.0956
92.22050.4113.81832.06431.97177.4204-0.1012-0.04580.2454-0.06540.0092-0.0441-0.3088-0.04430.10290.2401-0.0740.02730.54410.04290.39982.9351-23.623235.9105
104.1750.08942.03069.3136.18884.9609-0.2527-0.46110.3470.19940.0260.3562-0.3434-0.05840.44570.3004-0.0004-0.01960.50970.08240.46865.9502-16.694541.3304
116.32511.00164.41999.18473.26197.7321-0.34520.1941-0.8093-0.64890.3376-0.9450.18840.79170.07080.3504-0.09880.03730.568-0.01080.52913.1658-31.447923.0192
124.71775.02966.67078.3256.10869.5793-0.2824-0.10610.24760.54740.305-0.4176-0.50710.62820.05990.33930.0229-0.03680.598-0.07250.553311.92-20.504247.6623
135.68832.01354.68884.5611.87023.86490.2538-1.00820.16760.37760.0645-0.20730.0773-0.5292-0.4910.34160.00730.03880.88590.01810.3863-0.0944-24.612745.8478
143.0403-4.409-1.3187.98831.97236.2760.24950.231-0.2404-0.1718-0.77410.23620.1913-0.69380.51910.53850.0402-0.00040.7798-0.14820.622528.7508-42.1579-31.6659
159.0361-9.0568-7.51779.38598.2727.81960.25090.7738-0.3975-0.0604-0.4921-0.11210.0741-0.28110.32280.47860.0571-0.01660.5653-0.04220.454228.2407-32.3141-24.5653
164.61020.8258-0.79824.649-1.4224.27890.23050.32230.37060.07740.0345-0.052-0.7643-0.0486-0.25360.52490.07680.0570.35710.06050.297322.1905-9.441-15.755
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 130 )
2X-RAY DIFFRACTION2chain 'A' and (resid 131 through 143 )
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 239 )
4X-RAY DIFFRACTION4chain 'G' and (resid 1 through 18 )
5X-RAY DIFFRACTION5chain 'G' and (resid 19 through 91 )
6X-RAY DIFFRACTION6chain 'G' and (resid 92 through 119 )
7X-RAY DIFFRACTION7chain 'G' and (resid 120 through 131 )
8X-RAY DIFFRACTION8chain 'G' and (resid 132 through 146 )
9X-RAY DIFFRACTION9chain 'G' and (resid 147 through 168 )
10X-RAY DIFFRACTION10chain 'G' and (resid 169 through 181 )
11X-RAY DIFFRACTION11chain 'G' and (resid 182 through 192 )
12X-RAY DIFFRACTION12chain 'G' and (resid 193 through 206 )
13X-RAY DIFFRACTION13chain 'G' and (resid 207 through 232 )
14X-RAY DIFFRACTION14chain 'D' and (resid 199 through 237 )
15X-RAY DIFFRACTION15chain 'D' and (resid 238 through 285 )
16X-RAY DIFFRACTION16chain 'D' and (resid 286 through 329 )

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