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- PDB-6njz: EphA2 LBD in complex with YSA-GSGSK-bio peptide -

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Basic information

Entry
Database: PDB / ID: 6njz
TitleEphA2 LBD in complex with YSA-GSGSK-bio peptide
Components
  • Ephrin type-A receptor 2
  • YSA-GSGSK-bio peptide
KeywordsTRANSFERASE / protein-peptide interaction / kinase / ephrin / eph receptor / drug development / 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 / pericyte cell differentiation / cAMP metabolic process / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration ...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 / 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 / post-anal tail morphogenesis / bone remodeling / transmembrane-ephrin receptor activity / response to growth factor / tight junction / activation of GTPase activity / regulation of lamellipodium assembly / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / 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 / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / RAC2 GTPase cycle / RAC3 GTPase cycle / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / vasculogenesis / regulation of angiogenesis / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / negative regulation of angiogenesis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of ERK1 and ERK2 cascade / 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 / axon guidance / receptor protein-tyrosine kinase / 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 / cadherin binding / inflammatory response / phosphorylation / focal adhesion / dendrite / 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. / Eph receptor ligand-binding domain profile. ...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) / Galactose-binding domain-like / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Jelly Rolls / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
BIOTIN / Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLechtenberg, B.C. / Pasquale, E.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS087070 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA030199 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Engineering nanomolar peptide ligands that differentially modulate EphA2 receptor signaling.
Authors: Gomez-Soler, M. / Petersen Gehring, M. / Lechtenberg, B.C. / Zapata-Mercado, E. / Hristova, K. / Pasquale, E.B.
History
DepositionJan 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_site / struct_site_gen
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id / _struct_site_gen.symmetry
Revision 1.2Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ephrin type-A receptor 2
B: Ephrin type-A receptor 2
C: YSA-GSGSK-bio peptide
D: YSA-GSGSK-bio peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,00511
Polymers46,2084
Non-polymers7977
Water3,765209
1
A: Ephrin type-A receptor 2
C: YSA-GSGSK-bio peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6256
Polymers23,1042
Non-polymers5214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-14 kcal/mol
Surface area10320 Å2
MethodPISA
2
B: Ephrin type-A receptor 2
D: YSA-GSGSK-bio peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3805
Polymers23,1042
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-15 kcal/mol
Surface area10230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.775, 88.224, 153.414
Angle α, β, γ (deg.)90.000, 90.790, 90.000
Int Tables number5
Space group name H-MI121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 27 through 43 or resid 45...
21(chain B and (resid 27 through 43 or resid 45...
12(chain C and resid 1 through 10)
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYTRPTRP(chain A and (resid 27 through 43 or resid 45...AA27 - 437 - 23
121THRTHRTRPTRP(chain A and (resid 27 through 43 or resid 45...AA45 - 5225 - 32
131LEULEUASPASP(chain A and (resid 27 through 43 or resid 45...AA54 - 12734 - 107
141ASPASPCYSCYS(chain A and (resid 27 through 43 or resid 45...AA129 - 188109 - 168
151ALAALAHISHIS(chain A and (resid 27 through 43 or resid 45...AA190 - 205170 - 185
211GLYGLYTRPTRP(chain B and (resid 27 through 43 or resid 45...BB27 - 437 - 23
221THRTHRTRPTRP(chain B and (resid 27 through 43 or resid 45...BB45 - 5225 - 32
231LEULEUASPASP(chain B and (resid 27 through 43 or resid 45...BB54 - 12734 - 107
241ASPASPCYSCYS(chain B and (resid 27 through 43 or resid 45...BB129 - 188109 - 168
251ALAALAHISHIS(chain B and (resid 27 through 43 or resid 45...BB190 - 205170 - 185
112TYRTYRMETMET(chain C and resid 1 through 10)CC1 - 101 - 10
212TYRTYRMETMETchain DDD1 - 101 - 10

NCS ensembles :
ID
1
2

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Components

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


Mass: 21339.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA2, ECK / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2(DE3)
References: UniProt: P29317, receptor protein-tyrosine kinase
#2: Protein/peptide YSA-GSGSK-bio peptide


Mass: 1764.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: biotin linked to lysine 17 side-chain / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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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: 3.48 Å3/Da / Density % sol: 64.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.09M BIS-TRIS pH5.5, 22.5% w/v PEG 3,350, 3% w/v 6-aminohexanoic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Mar 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→29.98 Å / Num. obs: 44891 / % possible obs: 95.7 % / Redundancy: 2.8 % / Biso Wilson estimate: 34.85 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.9
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2943 / CC1/2: 0.672 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX1.14rc2_3191refinement
XDSJan 26, 2018data reduction
Aimless0.6.2data scaling
PHASER2.8.2phasing
Coot0.8.9.1model building
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HEI

3hei


Resolution: 1.9→24.58 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2069 2320 5.17 %
Rwork0.1693 42564 -
obs0.1712 44884 95.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 265.03 Å2 / Biso mean: 57.3589 Å2 / Biso min: 23.62 Å2
Refinement stepCycle: final / Resolution: 1.9→24.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3047 0 114 209 3370
Biso mean--105.31 48.07 -
Num. residues----379
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1640X-RAY DIFFRACTION7.897TORSIONAL
12B1640X-RAY DIFFRACTION7.897TORSIONAL
21C90X-RAY DIFFRACTION7.897TORSIONAL
22D90X-RAY DIFFRACTION7.897TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.93880.36671350.27552446258193
1.9388-1.98090.30821340.25772418255294
1.9809-2.0270.2471290.23822462259194
2.027-2.07760.2291430.20482442258595
2.0776-2.13380.19931160.19772488260494
2.1338-2.19650.25731590.20152443260296
2.1965-2.26740.2221200.19532529264995
2.2674-2.34840.23261460.18612488263495
2.3484-2.44230.23531350.19382487262296
2.4423-2.55330.2281260.1922534266096
2.5533-2.68780.23761280.19012528265696
2.6878-2.8560.23051530.19232511266496
2.856-3.07610.22731410.18772520266197
3.0761-3.38490.20941440.16672544268897
3.3849-3.87310.18351340.14742525265996
3.8731-4.87350.15561330.12972597273097
4.8735-24.58170.19061440.15422602274697
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)
13.8950.7266-0.90961.97942.57084.4034-0.3217-0.04190.74470.15790.00750.1881-0.6347-1.00220.07030.39830.16640.05910.3884-0.03310.503717.9721.049938.0568
27.0947-0.4915-0.04333.89070.53130.91260.56270.38460.7416-0.3851-0.16640.2145-0.4072-0.6288-0.20210.36080.14540.0220.47470.12640.461511.5475-0.591625.6315
33.06140.21970.53412.4489-0.81092.92570.14630.3745-0.0706-0.10540.04220.01890.1443-0.3281-0.17330.21080.06020.02770.292-0.00690.339919.247-10.895327.9063
43.94391.54574.17693.56460.33045.1797-0.0830.2055-0.7421-0.38650.3249-0.1554-0.25120.353-0.29530.2920.01470.05840.34520.02170.545833.85770.95427.5626
56.0191-0.87211.4192.3978-0.3012.22370.10730.6491-0.3485-0.03190.15320.3440.1814-0.7853-0.160.224-0.0147-0.00670.48140.06240.361211.5101-13.895128.4251
62.08751.18492.50864.6143-0.86644.74030.4713-0.3135-0.31270.2974-0.3202-0.43130.1264-0.0433-0.14370.35530.0350.03370.2657-0.0210.349325.925-10.865639.567
72.4832-0.52311.08922.6576-0.42883.27970.0397-0.170.15940.28970.00610.026-0.0846-0.4257-0.07470.25930.02820.04410.2449-0.00330.367620.881-7.434236.9832
82.289-1.5681-1.00262.9098-1.1232.22350.38440.6937-0.5376-0.06120.0975-0.26471.18470.7872-0.34980.59040.2374-0.03180.45-0.07770.452242.66469.578128.6279
93.13250.2006-1.63394.7849-0.00222.185-0.11440.4697-0.3653-0.89990.2758-0.20591.19340.83240.28550.84030.27-0.05470.5633-0.14630.320838.224610.956114.2634
105.23921.4502-2.15694.4331-1.44621.5977-0.03921.38610.4288-0.67520.4450.67160.7073-0.6857-0.21780.49410.026-0.12040.54160.06460.453428.347921.499314.0089
114.1792.38070.28666.9625-0.93673.58080.3023-0.3365-0.00371.2258-0.41370.32510.4845-0.1072-0.17660.57020.05080.05840.25920.01910.34736.026613.024138.812
122.54970.51250.4453.4863-0.44862.7801-0.02780.50530.0297-0.11010.08230.3695-0.17030.1179-0.18710.30890.0718-0.00390.2807-0.00840.278233.093122.401122.9082
131.72670.0001-2.13071.13510.0932.6387-0.06961.0253-0.0196-0.65950.1988-0.2577-0.4051.4995-0.56170.57890.03630.05481.25890.01160.368148.762924.259.2244
142.66791.5523-0.24066.1123-1.75997.87970.4724-0.1969-0.01290.8083-0.27710.4115-0.67210.4426-0.15870.35390.08950.01110.2493-0.02340.265838.163521.606934.6853
152.48270.08341.73842.61850.22244.43670.15330.3732-0.1160.15380.0166-0.09550.27480.6194-0.24410.3490.09640.01640.2566-0.00940.329241.336317.942131.387
162.7755-0.632-0.54152.80490.11833.60740.27990.16910.3688-0.3611-0.06680.9645-0.4169-0.8748-0.19850.36730.2128-0.00680.67030.11710.56284.7275-3.37922.7324
174.93541.0893-0.42045.33011.21980.3745-0.11130.7811-0.9269-0.61740.4164-0.36790.56540.9262-0.24720.77670.234-0.00640.9454-0.18790.407541.096413.62967.7568
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 43 )A27 - 43
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 69 )A44 - 69
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 126 )A70 - 126
4X-RAY DIFFRACTION4chain 'A' and (resid 127 through 135 )A127 - 135
5X-RAY DIFFRACTION5chain 'A' and (resid 136 through 163 )A136 - 163
6X-RAY DIFFRACTION6chain 'A' and (resid 164 through 176 )A164 - 176
7X-RAY DIFFRACTION7chain 'A' and (resid 177 through 203 )A177 - 203
8X-RAY DIFFRACTION8chain 'B' and (resid 26 through 43 )B26 - 43
9X-RAY DIFFRACTION9chain 'B' and (resid 44 through 69 )B44 - 69
10X-RAY DIFFRACTION10chain 'B' and (resid 70 through 82 )B70 - 82
11X-RAY DIFFRACTION11chain 'B' and (resid 83 through 93 )B83 - 93
12X-RAY DIFFRACTION12chain 'B' and (resid 94 through 146 )B94 - 146
13X-RAY DIFFRACTION13chain 'B' and (resid 147 through 163 )B147 - 163
14X-RAY DIFFRACTION14chain 'B' and (resid 164 through 176 )B164 - 176
15X-RAY DIFFRACTION15chain 'B' and (resid 177 through 205 )B177 - 205
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 10 )C1 - 10
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 10 )D1 - 10

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