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- PDB-8dgn: 14-3-3 epsilon bound to phosphorylated PEAK2 (pS826) peptide -

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Basic information

Entry
Database: PDB / ID: 8dgn
Title14-3-3 epsilon bound to phosphorylated PEAK2 (pS826) peptide
Components
  • 14-3-3 protein epsilon
  • Phosphorylated PEAK2 (pS826) peptide
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 / negative regulation of toll-like receptor signaling pathway / regulation of membrane repolarization / protein localization to endoplasmic reticulum / NADE modulates death signalling / RAB GEFs exchange GTP for GDP on RABs ...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 / negative regulation of toll-like receptor signaling pathway / regulation of membrane repolarization / protein localization to endoplasmic reticulum / NADE modulates death signalling / RAB GEFs exchange GTP for GDP on RABs / Signaling by Hippo / negative regulation of calcium ion export across plasma membrane / cytoplasmic pattern recognition receptor signaling pathway / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of heart rate by cardiac conduction / protein localization to nucleus / calcium channel regulator activity / phosphoserine residue binding / Regulation of HSF1-mediated heat shock response / HSF1 activation / Activation of BAD and translocation to mitochondria / potassium channel regulator activity / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / signaling adaptor activity / 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 / Anchoring of the basal body to the plasma membrane / protein sequestering activity / regulation of mitotic cell cycle / regulation of cytosolic calcium ion concentration / substantia nigra development / AURKA Activation by TPX2 / 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 / cerebral cortex development / histone deacetylase binding / Regulation of PLK1 Activity at G2/M Transition / MAPK cascade / melanosome / MHC class II protein complex binding / cellular response to heat / scaffold protein binding / protein phosphatase binding / transmembrane transporter binding / intracellular signal transduction / cadherin binding / protein heterodimerization activity / protein domain specific binding / focal adhesion / ubiquitin protein ligase binding / enzyme binding / endoplasmic reticulum / signal transduction / RNA binding / extracellular exosome / identical protein binding / membrane / nucleus / cytoplasm / cytosol
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
Similarity search - Domain/homology
14-3-3 protein epsilon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.16 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 / diffrn_source
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
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein epsilon
B: Phosphorylated PEAK2 (pS826) peptide


Theoretical massNumber of molelcules
Total (without water)31,6302
Polymers31,6302
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, Binding of phosphorylated PEAK2 (pS826) peptide to 14-3-3 confirmed by SPR, fitting 1:1 stoichiometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-8 kcal/mol
Surface area10530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.131, 92.131, 137.439
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 Phosphorylated PEAK2 (pS826) peptide


Mass: 2175.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
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: 2.69 Å3/Da / Density % sol: 54.3 %
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: 3.16→46.07 Å / Num. obs: 6353 / % possible obs: 99.6 % / Redundancy: 18.9 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.013 / Rrim(I) all: 0.013 / Net I/σ(I): 18.97
Reflection shellResolution: 3.16→3.35 Å / Redundancy: 20.5 % / Rmerge(I) obs: 1.518 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 975 / CC1/2: 0.819 / Rrim(I) all: 1.558 / % possible all: 98.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.01 Å46.07 Å
Translation5.01 Å46.07 Å

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
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: 3.16→46.07 Å / SU ML: 0.5016 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3523
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2949 636 10.02 %
Rwork0.2417 5714 -
obs0.2471 6350 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 106.78 Å2
Refinement stepCycle: LAST / Resolution: 3.16→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 0 0 1510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00251535
X-RAY DIFFRACTIONf_angle_d0.52842097
X-RAY DIFFRACTIONf_chiral_restr0.0328251
X-RAY DIFFRACTIONf_plane_restr0.0052269
X-RAY DIFFRACTIONf_dihedral_angle_d4.8838222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.16-3.40.37941220.34791096X-RAY DIFFRACTION98.54
3.4-3.750.31721220.24991102X-RAY DIFFRACTION99.92
3.75-4.290.28221250.25431127X-RAY DIFFRACTION100
4.29-5.40.29411290.23221150X-RAY DIFFRACTION100
5.4-46.070.2821380.22371239X-RAY DIFFRACTION99.85
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)
14.20456486409-0.0539425152922-1.523444215233.08193335097-0.3540898713762.82181363967-0.1911587373250.471114608001-0.6166946615440.02694009586060.184852568627-0.0002951903547880.2669577178960.3111109363480.06549912087770.822032733142-0.1101355609-0.01688692769381.03991824299-0.0815714824110.786535874952-19.902057050529.615671674311.067516526
22.37442984980.816066003168-2.069016446551.341087872191.12274443861.79595411955-0.2884440000041.451259870670.837976209757-1.029983171710.6530881567231.358402568920.186800726414-0.6565041474290.3246019114251.06961028256-0.09428394020620.05554046651031.36071228845-0.04035857220631.09882044309-23.633777492424.08050312562.36918860981
32.41088941496-0.558223457436-0.136811629082.07455335316-2.665782155433.49065951089-0.09148959785080.4700413844330.810744886485-0.272427837694-0.3173218862560.110589694413-0.3152976484440.3335454225490.3211075581690.63156311963-0.05065866260190.06686185935961.076603304140.1311503742861.07670843399-7.1204314138233.52134167095.45837243146
44.26097719707-0.940764869036-0.3659180542674.121936249790.6398151349713.135121133560.5460890976020.386916471827-0.361538030748-0.685568323802-0.92325515951-0.1031579199290.398595204367-0.4740654521360.3547754649780.865459683457-0.004935422705440.07985506859221.246491704130.1706954308311.0483189555-2.4009959912728.444868028314.193926911
53.65292376985-1.53118994061-0.3489712771141.82125237662-1.201268668973.23146066163-0.148690021858-0.6849061262570.366586788177-0.06706151259360.233768823164-0.04038605626450.2310925255851.48241636964-0.1615531115390.681638572642-0.08731071265260.08822985960751.4125088970.2013247463761.08337089180.29362325921928.611560040123.8100385315
66.430353212681.39941969530.9750353868290.700945918023-0.5690844299736.436566288180.3449998413991.11525957480.5922253916220.053255747793-1.68323498641-1.16751284727-2.44510937378-0.1958463795130.3958834336271.194169328250.131871681810.2134570592291.111524119240.3576766999681.09655119319-11.43816323826.733822017217.7681230234
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 71 )AA33 - 711 - 39
22chain 'A' and (resid 72 through 106 )AA72 - 10640 - 71
33chain 'A' and (resid 107 through 162 )AA107 - 16272 - 127
44chain 'A' and (resid 163 through 187 )AA163 - 187128 - 152
55chain 'A' and (resid 188 through 232 )AA188 - 232153 - 197
66chain 'B' and (resid 66 through 72 )BB66 - 721 - 7

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