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- PDB-7kja: Crystal structure of the EphA2 intracellular KD-SAM domains -

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Basic information

Entry
Database: PDB / ID: 7kja
TitleCrystal structure of the EphA2 intracellular KD-SAM domains
ComponentsEphrin type-A receptor 2
KeywordsTRANSFERASE / Eph receptor / kinase / SAM / allostery
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) / 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 / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLechtenberg, B.C. / Pasquale, E.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131374 United States
CitationJournal: Nat Commun / Year: 2021
Title: Regulation of the EphA2 receptor intracellular region by phosphomimetic negative charges in the kinase-SAM linker.
Authors: Lechtenberg, B.C. / Gehring, M.P. / Light, T.P. / Horne, C.R. / Matsumoto, M.W. / Hristova, K. / Pasquale, E.B.
History
DepositionOct 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 12, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,41210
Polymers87,9172
Non-polymers1,4958
Water11,079615
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A: Ephrin type-A receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6725
Polymers43,9591
Non-polymers7144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ephrin type-A receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7405
Polymers43,9591
Non-polymers7814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.060, 55.030, 135.644
Angle α, β, γ (deg.)90.000, 94.858, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
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
d_1ens_1(chain "A" and (resid 590 through 635 or resid 638...
d_2ens_1(chain "B" and (resid 590 through 666 or resid 668...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPSERA4 - 49
d_12ens_1LYSILEA52 - 80
d_13ens_1GLYILEA84 - 91
d_14ens_1ARGVALA95 - 173
d_15ens_1ASPILEA175 - 187
d_16ens_1TYRGLUA189 - 213
d_17ens_1PROMETA216 - 226
d_18ens_1ALAPROA230 - 244
d_19ens_1ALATYRA248 - 250
d_110ens_1LEUVALA254 - 273
d_111ens_1ILEALAA277 - 292
d_112ens_1PHELEUA296 - 368
d_113ens_1GOLGOLC
d_21ens_1ASPILEB1 - 75
d_22ens_1GLYILEB79 - 86
d_23ens_1ARGVALB90 - 168
d_24ens_1ASPILEB172 - 184
d_25ens_1TYRTYRB187
d_26ens_1ARGGLUB190 - 213
d_27ens_1PROMETB215 - 225
d_28ens_1ALAPROB227 - 241
d_29ens_1ALAALAB244
d_210ens_1ILETYRB247 - 248
d_211ens_1LEUVALB250 - 269
d_212ens_1ILEALAB273 - 288
d_213ens_1PHETHRB290 - 301
d_214ens_1PROLEUB303 - 363
d_215ens_1GOLGOLH

NCS oper: (Code: givenMatrix: (-0.127501821399, 0.117185575186, 0.984891276491), (-0.534376339614, -0.844666124712, 0.0313219639441), (0.835574780137, -0.522308987796, 0.170317668099)Vector: 64. ...NCS oper: (Code: given
Matrix: (-0.127501821399, 0.117185575186, 0.984891276491), (-0.534376339614, -0.844666124712, 0.0313219639441), (0.835574780137, -0.522308987796, 0.170317668099)
Vector: 64.1760832642, 26.5227442022, 9.94284615523)

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Components

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


Mass: 43958.621 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)
References: UniProt: P29317, receptor protein-tyrosine kinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 615 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.2 M MgCl2, 0.1 M Bis-Tris pH5.5, 25% PEG 3350

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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: Nov 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→20.49 Å / Num. obs: 91439 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 23.19 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.056 / Rrim(I) all: 0.081 / Net I/σ(I): 13.4
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4522 / CC1/2: 0.599 / Rpim(I) all: 0.654 / Rrim(I) all: 0.953 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
MOSFLMversion 7.1.0data reduction
Aimlessversion 0.3.11data scaling
PHASER2.5.6phasing
Cootversion 0.9model building
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PDO, 3KKA

4pdo

3kka


Resolution: 1.75→20.49 Å / SU ML: 0.1992 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.29
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2175 4492 4.94 %
Rwork0.1884 86375 -
obs0.1898 90867 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.04 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5692 0 93 615 6400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00385994
X-RAY DIFFRACTIONf_angle_d0.71458112
X-RAY DIFFRACTIONf_chiral_restr0.0454884
X-RAY DIFFRACTIONf_plane_restr0.00391017
X-RAY DIFFRACTIONf_dihedral_angle_d13.28292297
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 8.4733596137 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.30311370.2682918X-RAY DIFFRACTION99.84
1.77-1.790.30591400.2642863X-RAY DIFFRACTION99.8
1.79-1.810.2851550.25982840X-RAY DIFFRACTION99.97
1.81-1.840.28621670.2562939X-RAY DIFFRACTION99.97
1.84-1.860.27391670.24852812X-RAY DIFFRACTION99.93
1.86-1.890.26751390.25132881X-RAY DIFFRACTION99.9
1.89-1.910.45281730.39862728X-RAY DIFFRACTION94.74
1.91-1.940.48411360.44792781X-RAY DIFFRACTION96.33
1.94-1.970.28291650.22652852X-RAY DIFFRACTION99.9
1.97-20.26971750.19942838X-RAY DIFFRACTION99.9
2-2.040.23071360.19232971X-RAY DIFFRACTION99.94
2.04-2.070.18341510.18262819X-RAY DIFFRACTION99.97
2.07-2.110.17961460.18012926X-RAY DIFFRACTION99.87
2.11-2.160.20121580.16952835X-RAY DIFFRACTION99.9
2.16-2.20.22721540.17492917X-RAY DIFFRACTION99.87
2.2-2.260.39871490.37452663X-RAY DIFFRACTION93.92
2.26-2.310.30511380.26822758X-RAY DIFFRACTION95.89
2.31-2.370.19731610.17782902X-RAY DIFFRACTION99.97
2.37-2.440.17741480.16452887X-RAY DIFFRACTION100
2.44-2.520.20191540.16342896X-RAY DIFFRACTION99.97
2.52-2.610.17011610.15612931X-RAY DIFFRACTION99.97
2.61-2.720.20221350.162879X-RAY DIFFRACTION100
2.72-2.840.17671310.1632918X-RAY DIFFRACTION99.93
2.84-2.990.20371430.17182922X-RAY DIFFRACTION100
2.99-3.180.19711450.16432920X-RAY DIFFRACTION100
3.18-3.420.17411540.15852932X-RAY DIFFRACTION100
3.42-3.760.1881530.16652884X-RAY DIFFRACTION99.74
3.76-4.30.15661360.14542956X-RAY DIFFRACTION99.77
4.3-5.40.17691300.14082977X-RAY DIFFRACTION100
5.41-20.490.22931550.19093030X-RAY DIFFRACTION99.84
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)
10.4936390042120.0443781989409-0.5244233209391.0841215211-0.2653049211911.76990291880.0174361874045-0.217274643327-0.02199496909230.112095153339-0.02407970576350.05382749518170.0378176230318-0.263094440371-1.64205050004E-50.1978784676990.01487016170430.01035545542160.265316942763-0.01145277294930.227398655706-29.571069888119.0994563202-18.414142346
20.8345912155430.7743002486410.4097046727180.6280970042910.2532482546531.19914749389-0.101786601587-0.0662896325443-0.02085512508410.2251128842720.2301468913940.514305309413-0.07358524912-0.6428582385030.03123055742860.2668865493360.05078661030780.01236666071250.3327575162390.01411756065410.28354890308-36.818230276617.8149624855-26.7981408015
30.7741773337610.527117071378-0.006272473201670.3468372464860.3734436768370.9473674758650.0270779223921-0.148900445052-0.07853418488930.034970334603-0.0467099603501-0.007968167406110.111323093205-0.2527375990461.5326920664E-50.192132947339-0.001080773090150.01364280530670.2205017814680.004055678463640.199751255174-28.332216095818.1685618659-19.3767875763
41.10727385223-0.0628291096046-0.9316042779290.341747874868-0.1501901689780.6835909365060.08952785269430.1755204069770.0173219974214-0.0451671832067-0.0557426241833-0.0347150328009-0.119864725061-0.2565276857663.16656041266E-60.2062101654370.0301712685719-0.000803695384030.211632613312-0.01540526901860.215751823735-17.913338655123.2150006901-35.684151899
51.273666466470.0827543432967-0.4519469441510.9052322950160.6903175033271.183374618020.0192877432514-0.223161459316-0.1737717503540.1890394730710.0285414909142-0.02466866417270.1202565312550.1292511189130.0001918465279280.1603378143390.0105032707758-0.008198395154980.1626695744520.009217345463290.187933611512-12.040722617417.087498299-25.4290393313
60.850131277403-0.543419661884-0.9061919557120.8137261652270.1972047668541.230706352710.0140310780794-0.157093943621-0.00530903961312-0.02168536303660.0184465774759-0.1402834234480.01805268747560.2003239358350.002087562379360.1277457416870.00414357963549-0.004411601656140.209996470923-0.01937286445180.195933543812-0.91415049110415.9872074822-33.4406531005
70.8375047611850.5552092317110.04936700571490.310832170441-0.03123933537441.202767231930.147647895916-0.006939011799280.191788473066-0.132040910209-0.0247468004821-0.216632916075-0.2849298532710.21549959365-2.9773136159E-50.267577413215-0.008282997027060.04301163794790.201148774945-0.006122049135550.2756984303870.014620688842226.0609537095-39.7222976996
80.739698102947-0.7370620476140.8455747012931.25807523385-1.144572152661.73926413227-0.591148336032-0.39155384580.5575431378520.3627897258920.346646063224-0.00448282642474-0.775663101008-1.30980376840.05148214091710.5194299947490.129127612649-0.1375348553480.715577976048-0.1732670550810.61130506460512.819285343529.0950009026-10.1131180932
90.9820186540130.01184962201170.3544734602270.6854345573120.4224934900340.546101793614-0.08119391869670.05852604436820.627405182919-0.1148978196370.4652723867430.0312927369839-0.422389016649-0.8664259828010.006933195475620.399842400670.04119240862360.01875596630380.483797622508-0.03985486216080.42207622123321.735264419625.7187307741-16.5180025934
102.91491162584-0.139371933281.221811402660.83825316175-0.282630417731.625991724890.000279840991158-0.07955391492490.005120273973710.038715860896-0.0218325373747-0.0473020072321-0.05098311332450.01925032665362.37686434114E-50.206782784417-0.0006832154010380.008152003354290.1940555343130.02713386398230.24897826327846.016288451629.2793382849-33.3196716105
110.7846200854090.381734471447-0.2405710518490.86276178143-0.4208972681651.130174794920.00318109296197-0.02495735483410.10215567270.0557625662905-0.0399613733225-0.01709496500040.02281846810090.01791146329342.11863767158E-50.1517256724160.00799415132282-0.008443287415690.126041057743-0.007422412041460.17963406676442.211280820820.6351023749-24.3166400971
121.20910341687-0.105484897681-0.4109636367230.851429449920.3686610652752.193672221070.0110550667584-0.234878277186-0.02296370904820.13091740254-0.00210747503744-0.02235900174010.1362691601010.0878081999935-0.0006083883821310.231434145789-0.018979348124-0.01796403554320.1993162775730.01261073250830.17341734394638.01317997213.5238544886-5.60362627616
131.270883594540.1348825089030.02934612344740.0422774589655-0.04261575785840.02630341034390.2829827660610.8106079791350.450915793197-1.182550102210.0490655416241-0.255959616851-0.518668000541-0.2686592078720.1333148523590.7454877064590.09928197342380.07424241975740.5347874646330.08441055050420.30402567514852.2236732617-7.420848484285.21699442621
141.251287230940.387844286577-0.2524705564180.352168430138-0.3868864501370.638409950178-0.2978702341450.592825254-0.515970741975-0.459269651875-0.6349681745760.7660221946970.937839286316-1.06676658501-0.5054705203230.489446776595-0.02273845981170.005610859315410.520848096314-0.2281707053610.44179768789547.9984167366-17.33372080129.37400578599
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 587 through 625 )AA587 - 6251 - 39
22chain 'A' and (resid 626 through 653 )AA626 - 65340 - 67
33chain 'A' and (resid 654 through 688 )AA654 - 68868 - 106
44chain 'A' and (resid 689 through 732 )AA689 - 732107 - 150
55chain 'A' and (resid 733 through 795 )AA733 - 795151 - 193
66chain 'A' and (resid 796 through 863 )AA796 - 863194 - 268
77chain 'A' and (resid 864 through 896 )AA864 - 896269 - 305
88chain 'A' and (resid 897 through 951 )AA897 - 951306 - 354
99chain 'A' and (resid 952 through 976 )AA952 - 976355 - 379
1010chain 'B' and (resid 590 through 653 )BB590 - 6531 - 62
1111chain 'B' and (resid 654 through 752 )BB654 - 75263 - 165
1212chain 'B' and (resid 753 through 896 )BB753 - 896166 - 299
1313chain 'B' and (resid 897 through 938 )BB897 - 938300 - 336
1414chain 'B' and (resid 939 through 965 )BB939 - 965337 - 363

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