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- PDB-7kjc: Crystal structure of the EphA2 S901E mutant intracellular KD-SAM ... -

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Basic information

Entry
Database: PDB / ID: 7kjc
TitleCrystal structure of the EphA2 S901E mutant 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 / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
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: 2.3 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)89,4049
Polymers88,0012
Non-polymers1,4037
Water6,179343
1
A: Ephrin type-A receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7145
Polymers44,0011
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)44,6904
Polymers44,0011
Non-polymers6893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.639, 54.587, 135.538
Angle α, β, γ (deg.)90.000, 95.223, 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 587 through 608 or resid 610...
d_2ens_1(chain "B" and (resid 587 through 608 or resid 610...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYILEA1 - 22
d_12ens_1PROTHRA24 - 48
d_13ens_1LYSILEA50 - 77
d_14ens_1GLYASNA81 - 157
d_15ens_1LEUVALA161 - 170
d_16ens_1ASPGLYA172 - 174
d_17ens_1PROILEA190 - 199
d_18ens_1TYRLEUA201 - 259
d_19ens_1METMETA262
d_110ens_1GLNLEUA265 - 372
d_111ens_1GOLGOLF
d_21ens_1GLYILEB1 - 22
d_22ens_1PROTHRB26 - 50
d_23ens_1LYSILEB52 - 79
d_24ens_1GLYASNB83 - 159
d_25ens_1LEUVALB163 - 172
d_26ens_1ASPILEB176 - 188
d_27ens_1TYRLEUB192 - 250
d_28ens_1METMETB253
d_29ens_1GLNLEUB256 - 363
d_210ens_1GOLGOLJ

NCS oper: (Code: givenMatrix: (-0.136612496901, 0.126746094463, 0.982482800475), (-0.527598930366, -0.848724970349, 0.0361288441977), (0.8384368756, -0.513421223018, 0.182817541249)Vector: 63. ...NCS oper: (Code: given
Matrix: (-0.136612496901, 0.126746094463, 0.982482800475), (-0.527598930366, -0.848724970349, 0.0361288441977), (0.8384368756, -0.513421223018, 0.182817541249)
Vector: 63.5112026331, 27.0786350015, 10.102050003)

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Components

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


Mass: 44000.656 Da / Num. of mol.: 2 / Mutation: S901E
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-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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.55 Å3/Da / Density % sol: 51.69 %
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: 287 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: Dec 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→29.25 Å / Num. obs: 39708 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 31.98 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.086 / Rrim(I) all: 0.125 / Net I/σ(I): 12
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3887 / CC1/2: 0.643 / Rpim(I) all: 0.621 / Rrim(I) all: 0.905

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Processing

Software
NameVersionClassification
CrystalCleardata collection
XDSVERSION January 10, 2014data reduction
Aimlessversion 0.5.32data scaling
PHASER2.5.6phasing
Coot0.9model building
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PDO, 3KKA

4pdo

3kka


Resolution: 2.3→29.25 Å / SU ML: 0.2703 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.9104
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2257 2026 5.1 %
Rwork0.1884 37677 -
obs0.1903 39703 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.08 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5798 0 87 343 6228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00236070
X-RAY DIFFRACTIONf_angle_d0.51998211
X-RAY DIFFRACTIONf_chiral_restr0.0417896
X-RAY DIFFRACTIONf_plane_restr0.00311029
X-RAY DIFFRACTIONf_dihedral_angle_d14.18742317
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 8.6362275569 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.35481360.26812672X-RAY DIFFRACTION99.79
2.36-2.420.27771200.25042672X-RAY DIFFRACTION99.64
2.42-2.490.27751600.23822670X-RAY DIFFRACTION99.79
2.49-2.570.30071280.22572663X-RAY DIFFRACTION99.89
2.57-2.660.26761360.21752701X-RAY DIFFRACTION99.75
2.66-2.770.2761520.21672669X-RAY DIFFRACTION99.93
2.77-2.90.2591560.21382657X-RAY DIFFRACTION99.86
2.9-3.050.25761340.20962688X-RAY DIFFRACTION99.68
3.05-3.240.23471500.1942673X-RAY DIFFRACTION99.86
3.24-3.490.22871550.17062687X-RAY DIFFRACTION99.93
3.49-3.840.20821500.17152680X-RAY DIFFRACTION99.89
3.84-4.40.17171280.15162725X-RAY DIFFRACTION99.93
4.4-5.530.16831710.15432715X-RAY DIFFRACTION99.9
5.53-29.250.21481500.18552805X-RAY DIFFRACTION99.83
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)
11.646440799110.441052264738-0.7242003649941.10971611938-0.06428542608651.827862960590.0858767606230.0672955386560.01578638657370.0750961555174-0.02505174494880.0557381616023-0.0581989157638-0.205144839870.0004728576048290.2431160396070.040512204758-0.00937530638250.2030439860010.008687650651380.239949869889-25.091513715220.1343952369-25.7040567676
22.1110570143-1.07620705321-0.3189827265581.659949283690.9370320551452.074384671220.0134753499682-0.189728891343-0.1533697147250.0710453192910.131692785197-0.159543554960.1001620700560.3640201003220.001256444945820.210540418002-0.00635990433758-0.01373844152480.307370499573-0.04110598214140.328517005579-2.6065243422617.1091122827-31.8278119924
31.0642041881-0.03233083342270.05270786244730.369442455230.002620196204910.380576500137-0.181083665996-0.007029915130570.4187550635360.1346376252370.05063550559790.0357066524167-0.499950146768-0.8432306271157.32037613107E-50.5966644138780.0869300137986-0.04197748457060.69066021233-0.08012420151910.5243169338715.582414973328.1762410996-11.9922561807
41.571280302750.3400782039250.360948960570.84038645601-0.5983265015791.07960001872-0.0330725954023-0.07591922704310.1385800066360.117349743494-0.0159788473937-0.168012256757-0.2261773447310.1415336638470.007847229635130.227551773927-0.016413705748-0.03392327706880.3343602426220.04102929558750.34195119133646.176815402228.4479075917-33.0429262056
50.8159143695080.0506180763013-0.2548261216790.642866230393-0.08053077156162.059861355860.0143250436311-0.06480272841770.006662327060.231321497537-0.052304057714-0.04622499011570.01953373001030.166439779171-7.60243661435E-50.288840200690.00372861698044-0.04189957480680.2138284532370.008207793567250.24866577098939.610897935516.4191503677-13.6667180289
60.661436877399-0.113603762399-0.2114835588030.4991628453970.020894621520.3026657938830.2696224925290.530524307671-0.0402537728788-1.29437726433-0.199270810267-0.122576819025-0.186477819749-0.1454418065260.001912499420730.8482029939060.04232579509220.03748833832190.545454079660.004605622882780.41572969147649.7938528582-11.46227837627.05331950601
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 752 )AA587 - 7521 - 167
22chain 'A' and (resid 753 through 896 )AA753 - 896168 - 309
33chain 'A' and (resid 897 through 976 )AA897 - 976310 - 383
44chain 'B' and (resid 587 through 653 )BB587 - 6531 - 66
55chain 'B' and (resid 654 through 896 )BB654 - 89667 - 300
66chain 'B' and (resid 897 through 965 )BB897 - 965301 - 363

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