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- PDB-7kjb: Crystal structure of the EphA2 S897E/S901E mutant intracellular K... -

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Basic information

Entry
Database: PDB / ID: 7kjb
TitleCrystal structure of the EphA2 S897E/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
: / Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1762
Polymers44,0431
Non-polymers1331
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.456, 94.456, 99.646
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
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

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


Mass: 44042.691 Da / Num. of mol.: 1 / Mutation: S897E, 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-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cs
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.91 Å3/Da / Density % sol: 57.78 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 4.5% Tacsimate, 0.09 M HEPES pH 7.0, 9% PEG-MME 5K, 0.1 M CsCl

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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: Apr 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→29.53 Å / Num. obs: 13051 / % possible obs: 99.9 % / Redundancy: 10.9 % / Biso Wilson estimate: 50.49 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.285 / Rpim(I) all: 0.13 / Rrim(I) all: 0.313 / Net I/σ(I): 10.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 11 % / Rmerge(I) obs: 1.956 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1871 / CC1/2: 0.554 / Rpim(I) all: 0.895 / Rrim(I) all: 2.153 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
XDSVERSION Oct 15, 2015data reduction
Aimlessversion 0.5.23data scaling
PHASER2.6.1phasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PDO, 3KKA

4pdo

3kka


Resolution: 2.8→29.53 Å / SU ML: 0.3866 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7528
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.246 665 5.11 %
Rwork0.1976 12360 -
obs0.2 13025 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.16 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2882 0 1 30 2913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00272944
X-RAY DIFFRACTIONf_angle_d0.49933973
X-RAY DIFFRACTIONf_chiral_restr0.0407436
X-RAY DIFFRACTIONf_plane_restr0.0027504
X-RAY DIFFRACTIONf_dihedral_angle_d14.73671111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.020.30241440.27732405X-RAY DIFFRACTION99.96
3.02-3.320.33791390.2372424X-RAY DIFFRACTION100
3.32-3.80.23571180.20282482X-RAY DIFFRACTION100
3.8-4.780.2231060.16312490X-RAY DIFFRACTION99.96
4.78-29.530.21631580.1852559X-RAY DIFFRACTION99.96
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)
10.5113254070620.51247984698-0.269615357681.86823476661-0.6725941757932.140737168960.04492373577770.26189415451-0.569288246728-0.214965746931-0.0726285880929-0.6416916761750.1069372736690.196200554139-6.72401896379E-50.451602272097-0.0838651373822-0.02392225767340.449361876289-0.02484662004010.783426671655108.8567841271.88026383310.636028189027
21.664421660461.79857176854-1.014112603763.76759476183-0.4947639288520.7730997914870.1070309346490.0427255628841-0.2661076562610.114979677613-0.0778737163597-0.4687758958890.0160262265760.1146307953798.78791052337E-50.478995303494-0.0407820472312-0.05709614953260.388330029024-0.0232514339070.432595220151101.85030912465.89471045515.15771379595
33.60831002180.8616754829561.539457153972.631508431020.1868480409843.408709653940.09013124236080.2834237319130.1375396109550.155153191448-0.05240123595110.219062197698-0.215836842189-0.2227738551710.003894706257940.422475422823-0.01300450434640.06170114998470.330901049069-0.01397171423150.32731906834583.544944022962.11284812244.84136725139
43.445265642292.22230088504-0.3419613250671.37244683598-0.300800989920.02442640188930.111545670872-0.61845706190.6340160434630.159407941247-0.05301804623260.488119046251-0.110549696523-0.0404228585978-0.05984762510010.71664847833-0.0281247275749-0.01602120173730.5050291447690.03506387713360.59863737282453.309323941551.335939305422.2168205616
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 591 through 640 )591 - 6401 - 45
22chain 'A' and (resid 641 through 732 )641 - 73246 - 137
33chain 'A' and (resid 733 through 863 )733 - 863138 - 268
44chain 'A' and (resid 864 through 965 )864 - 965269 - 361

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