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- PDB-2br9: 14-3-3 Protein Epsilon (Human) Complexed to Peptide -

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Basic information

Entry
Database: PDB / ID: 2br9
Title14-3-3 Protein Epsilon (Human) Complexed to Peptide
Components
  • 14-3-3 PROTEIN EPSILON
  • CONSENSUS PEPTIDE FOR 14-3-3 PROTEINS
KeywordsCELL REGULATOR PROTEIN / 14-3-3 / PHOSPHOSERINE / STRUCTURAL GENOMICS CONSORTIUM / SGC / YWHAE
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 / Signaling by Hippo / negative regulation of calcium ion export across plasma membrane ...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 / Signaling by Hippo / 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 / 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 / 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 / signal transduction / RNA binding / extracellular exosome / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
14-3-3 domain / Delta-Endotoxin; domain 1 / 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 ...14-3-3 domain / Delta-Endotoxin; domain 1 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein epsilon
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsYang, X. / Elkins, J.M. / Soundararajan, M. / Fedorov, O. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Doyle, D.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Structural Basis for Protein-Protein Interactions in the 14-3-3 Protein Family.
Authors: Yang, X. / Lee, W.H. / Sobott, F. / Papagrigoriou, E. / Robinson, C.V. / Grossmann, J.G. / Sundstrom, M. / Doyle, D.A. / Elkins, J.M.
History
DepositionMay 3, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 4, 2013Group: Derived calculations / Source and taxonomy
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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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
P: CONSENSUS PEPTIDE FOR 14-3-3 PROTEINS


Theoretical massNumber of molelcules
Total (without water)27,7442
Polymers27,7442
Non-polymers00
Water2,630146
1
A: 14-3-3 PROTEIN EPSILON
P: CONSENSUS PEPTIDE FOR 14-3-3 PROTEINS

A: 14-3-3 PROTEIN EPSILON
P: CONSENSUS PEPTIDE FOR 14-3-3 PROTEINS


Theoretical massNumber of molelcules
Total (without water)55,4894
Polymers55,4894
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3790 Å2
ΔGint-27.1 kcal/mol
Surface area22690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.011, 81.533, 80.966
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTHE PROTEIN EXISTS IN PHYSIOGICALLY STATE AS A DIMER, HOWEVER, SINCE IN THIS STRUCTURE THIS IS IN COMPLEX WITH A SHORT PEPTIDE (CHAIN P), THE OVERALL COMPLEX IS DESIGNATED AS A TETRAMER.

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Components

#1: Protein 14-3-3 PROTEIN EPSILON / 14-3-3E


Mass: 26791.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: THE MAMMALIAN GENE COLLECTION, I.M.A.G.E. CONSORTIUM CLONE ID 3139004
Plasmid: PLIC-SGC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62258
#2: Protein/peptide CONSENSUS PEPTIDE FOR 14-3-3 PROTEINS


Mass: 952.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PHOSPHOSERINE AT RESIDUE P 5 / Source: (synth.) HOMO SAPIENS (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE UNIPROT CROSS-REFERENCE GIVEN IN THE DBREF RECORDS BELOW CORRESPONDS TO GENBANK ENTRY BC000179. ...THE UNIPROT CROSS-REFERENCE GIVEN IN THE DBREF RECORDS BELOW CORRESPONDS TO GENBANK ENTRY BC000179.2 (HOMO SAPIENS TYROSINE 3-MONOOXYGENASE ACTIVATION PROTEIN EPSILON POLYPEPTIDE TRANSCRIPT VARIANT 2). THE FIRST RESIDUE IS A CLONING ARTEFACT.

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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: 2.4 Å3/Da / Density % sol: 48.5 %
Crystal growpH: 8
Details: 40% MPD, 5% PEG10000, 0.1M CACODYLATE PH6.5. PROTEIN IN 150MM NACL, 50MM TRIS PH8, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.968
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 23, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.75→36.42 Å / Num. obs: 138812 / % possible obs: 99.2 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.1
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.9 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O9D

1o9d


Resolution: 1.75→56.34 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.503 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 628 2.4 %RANDOM
Rwork0.188 ---
obs0.19 25529 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å20 Å20 Å2
2--0.59 Å20 Å2
3---1.19 Å2
Refinement stepCycle: LAST / Resolution: 1.75→56.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1857 0 0 146 2003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221896
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.982563
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9615234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50424.54588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02715.043348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2691513
X-RAY DIFFRACTIONr_chiral_restr0.1310.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021406
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.2925
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21359
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2134
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3931.51220
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81721890
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5023777
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2544.5673
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.313 40
Rwork0.238 1785
Refinement TLS params.Method: refined / Origin x: -18.8416 Å / Origin y: -5.327 Å / Origin z: 19.6695 Å
111213212223313233
T-0.1257 Å2-0.03 Å20.0037 Å2--0.1478 Å2-0.0058 Å2---0.1147 Å2
L1.3635 °2-0.483 °2-0.3692 °2-0.9972 °20.1461 °2--1.2913 °2
S-0.0528 Å °-0.0329 Å °-0.0713 Å °-0.004 Å °-0.0128 Å °0.0678 Å °-0.0069 Å °0.015 Å °0.0656 Å °

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