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- PDB-8dgm: 14-3-3 epsilon bound to phosphorylated PEAK1 (pT1165) peptide -

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Basic information

Entry
Database: PDB / ID: 8dgm
Title14-3-3 epsilon bound to phosphorylated PEAK1 (pT1165) peptide
Components
  • 14-3-3 protein epsilon
  • Inactive tyrosine-protein kinase PEAK1
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


negative regulation of peptidyl-serine dephosphorylation / regulation of heart rate by hormone / regulation of potassium ion transmembrane transporter activity / negative regulation of calcium ion transmembrane transporter activity / membrane repolarization during cardiac muscle cell action potential / regulation of membrane repolarization / NADE modulates death signalling / RAB GEFs exchange GTP for GDP on RABs / focal adhesion assembly / Signaling by Hippo ...negative regulation of peptidyl-serine dephosphorylation / regulation of heart rate by hormone / regulation of potassium ion transmembrane transporter activity / negative regulation of calcium ion transmembrane transporter activity / membrane repolarization during cardiac muscle cell action potential / regulation of membrane repolarization / NADE modulates death signalling / RAB GEFs exchange GTP for GDP on RABs / focal adhesion assembly / Signaling by Hippo / regulation of focal adhesion assembly / negative regulation of calcium ion export across plasma membrane / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / cytoplasmic pattern recognition receptor signaling pathway / regulation of heart rate by cardiac conduction / calcium channel regulator activity / protein localization to nucleus / phosphoserine residue binding / HSF1 activation / protein targeting / Regulation of HSF1-mediated heat shock response / Activation of BAD and translocation to mitochondria / potassium channel regulator activity / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / signaling adaptor activity / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / regulation of mitotic cell cycle / regulation of cytosolic calcium ion concentration / Anchoring of the basal body to the plasma membrane / substantia nigra development / substrate adhesion-dependent cell spreading / AURKA Activation by TPX2 / protein sequestering activity / positive regulation of protein export from nucleus / Translocation of SLC2A4 (GLUT4) to the plasma membrane / mitochondrial membrane / hippocampus development / TP53 Regulates Metabolic Genes / phosphoprotein binding / neuron migration / non-membrane spanning protein tyrosine kinase activity / cerebral cortex development / histone deacetylase binding / Regulation of PLK1 Activity at G2/M Transition / MAPK cascade / cell migration / melanosome / actin cytoskeleton / MHC class II protein complex binding / cellular response to heat / scaffold protein binding / protein phosphatase binding / transmembrane transporter binding / protein autophosphorylation / protein kinase activity / intracellular signal transduction / cadherin binding / protein heterodimerization activity / protein domain specific binding / protein phosphorylation / focal adhesion / ubiquitin protein ligase binding / enzyme binding / signal transduction / RNA binding / extracellular exosome / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site ...14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
14-3-3 protein epsilon / Inactive tyrosine-protein kinase PEAK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsRoy, M.J. / Hardy, J.M. / Lucet, I.S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1144149 Australia
CitationJournal: Nat Commun / Year: 2023
Title: Structural mapping of PEAK pseudokinase interactions identifies 14-3-3 as a molecular switch for PEAK3 signaling.
Authors: Roy, M.J. / Surudoi, M.G. / Kropp, A. / Hou, J. / Dai, W. / Hardy, J.M. / Liang, L.Y. / Cotton, T.R. / Lechtenberg, B.C. / Dite, T.A. / Ma, X. / Daly, R.J. / Patel, O. / Lucet, I.S.
History
DepositionJun 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_validate_planes
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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_validate_planes.type
Revision 1.2Aug 16, 2023Group: Data collection
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_validate_planes
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_validate_planes.type
Revision 1.3Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein epsilon
B: Inactive tyrosine-protein kinase PEAK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9084
Polymers31,7842
Non-polymers1242
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, Binding of phosphorylated PEAK1 (pT1165) peptide to 14-3-3 confirmed by SPR, fitting 1:1 stoichiometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-6 kcal/mol
Surface area10460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.423, 91.423, 139.872
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)

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Components

#1: Protein 14-3-3 protein epsilon / 14-3-3E


Mass: 29454.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAE / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P62258
#2: Protein/peptide Inactive tyrosine-protein kinase PEAK1 / Pseudopodium-enriched atypical kinase 1 / Sugen kinase 269 / Tyrosine-protein kinase SgK269


Mass: 2329.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H792
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
Has ligand of interestY

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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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.8 M ammonium sulfate, 0.1 M HEPES pH 7.5, 5% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.2→45.71 Å / Num. obs: 6156 / % possible obs: 99.8 % / Redundancy: 18.8 % / CC1/2: 1 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.106 / Net I/σ(I): 20.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.2-3.3919.41.4572.139480.7441.49599.2
3.39-3.6219.60.7684.34177430.9090.789100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.2 Å45.71 Å
Translation3.2 Å45.71 Å

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDS20161205data reduction
Aimless0.5.21data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
Coot0.9.8.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BR9

2br9


Resolution: 3.2→45.71 Å / SU ML: 0.4446 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.5633
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2663 615 10.01 %
Rwork0.2075 5528 -
obs0.2134 6143 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 102.97 Å2
Refinement stepCycle: LAST / Resolution: 3.2→45.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1491 0 8 0 1499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911523
X-RAY DIFFRACTIONf_angle_d1.16442080
X-RAY DIFFRACTIONf_chiral_restr0.0594253
X-RAY DIFFRACTIONf_plane_restr0.0173263
X-RAY DIFFRACTIONf_dihedral_angle_d12.4711228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.520.32261400.26351346X-RAY DIFFRACTION99.93
3.52-4.030.26551490.20521337X-RAY DIFFRACTION100
4.03-5.080.2521610.20311372X-RAY DIFFRACTION100
5.08-45.710.2651650.20121473X-RAY DIFFRACTION99.76
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)
14.57472137016-0.306206493463-1.490444664216.21856852725-0.1178281784884.66592154514-0.191321332976-0.6266848165120.0457143960359-0.5079395313270.284917874195-0.9405873377840.04077883299220.488583295679-0.05118197636690.661821927759-0.01434206653430.02363614765940.5115421106840.0287843356980.592032568861-34.4589879691-3.3366593211-11.6583363787
27.081871605991.90554702824-1.185257577053.950652557680.22656583601210.1757135252-1.028490640330.493779519002-1.36116844490.7678552409541.142201997750.6092149966140.5507117364560.811918731376-0.07643433061090.737568304267-0.06830749588590.05666771034930.664297645607-0.06118538289670.714935917005-31.601103853-9.69326096472-20.2664754151
36.25245779993.153247466234.193523986056.5594512364.405090500514.25721764927-0.2948726227210.1146983519540.405571870146-0.807448242084-1.499695033453.76977662965-2.61555194711-1.740913138081.016153653471.37852633372-0.0239366744432-0.1653578229341.140968820840.357834012030.968052469332-44.0815285915.326301933-18.5406741454
47.16464377576-8.0540755277-0.09883375591957.73322627811-0.1213231467453.86227985012-0.5718489088350.1517201074551.26457884909-0.01504139769940.411518303133-1.558097477820.845563595497-0.1414379511840.1901528163891.00614708597-0.1490906754780.1441022103440.5026991971820.06791957204051.12872764181-32.55395769226.8520168321-16.0730012895
53.845737203660.592108299261-2.593570413672.995136023340.4176909594538.138494334780.05792559503360.4803158103080.453033329137-0.375084063978-0.0050947357112-0.02604411445-0.5681159179580.1675657194850.1166206884351.09967319116-0.123485492649-0.0355685080540.7465974555140.09557620223240.797317230236-26.11976455712.1913665467-14.0094536444
65.57946377007-5.32035264196-4.586532050864.991348147514.4043411884.115676421651.421899453810.4420760524752.992840186620.898142310538-0.220536858849-2.27968340785-0.617934703649-0.147409255282-0.860653930461.37632075217-0.366721069558-0.08565480600691.108973623050.09814089707421.29635059362-21.047873577617.9142371818-2.7286074817
77.584167331013.34348570851.935683860578.35184868254-2.255841616231.84090319822-1.63675089979-1.009547538312.68250139849-0.5384685357791.87182359997-0.162843897952-0.9497080309462.004227333360.3139551218811.74563071021-0.138426029866-0.1970860202011.51765012684-0.04979170420641.20596896217-35.508651697617.5263309357.06302569268
87.0592253155-1.64827179391-3.462212637172.889167908190.8115636981186.10966945182-0.178605857226-0.438935296825-0.106788770272-0.5014660845980.0519208795018-0.6631928874-1.01609084710.8532513689940.100916982381.32446035846-0.114238400368-0.188070532750.7785103652890.2120824378441.10199953716-21.46401522738.814458396940.609498037303
90.111386027774-0.213682289742-0.4342621840950.3358253109650.8592600086593.70871536271.59401354028-2.370425875861.259792260120.946239315005-0.0631077985383.347633321831.05616734274-1.76498178171-0.9376617330931.0812802737-0.4469137031850.3852649386041.106079295170.08395458592261.59661442647-29.29400851313.00066410872-4.93661540412
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 33 through 72 )AA33 - 721 - 40
22chain 'A' and (resid 73 through 106 )AA73 - 10641 - 74
33chain 'A' and (resid 107 through 114 )AA107 - 11475 - 82
44chain 'A' and (resid 115 through 137 )AA115 - 13783 - 105
55chain 'A' and (resid 138 through 187 )AA138 - 187106 - 155
66chain 'A' and (resid 188 through 208 )AA188 - 208156 - 176
77chain 'A' and (resid 209 through 217 )AA209 - 217177 - 185
88chain 'A' and (resid 218 through 232 )AA218 - 232186 - 200
99chain 'B' and (resid 67 through 72 )BD67 - 721 - 6

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