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- PDB-8eq8: The crystal structure of 14-3-3 Beta containing 3-nitrotyrosine a... -

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Basic information

Entry
Database: PDB / ID: 8eq8
TitleThe crystal structure of 14-3-3 Beta containing 3-nitrotyrosine at position Y130
Components14-3-3 protein beta/alpha
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / MTOR signalling / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / Signaling by Hippo / vacuolar membrane / negative regulation of G protein-coupled receptor signaling pathway ...Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / MTOR signalling / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / Signaling by Hippo / vacuolar membrane / negative regulation of G protein-coupled receptor signaling pathway / negative regulation of protein import into nucleus / protein phosphatase inhibitor activity / Frs2-mediated activation / protein kinase inhibitor activity / mTORC1-mediated signalling / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / Transcriptional and post-translational regulation of MITF-M expression and activity / protein sequestering activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / phosphoprotein binding / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / histone deacetylase binding / Signaling by RAF1 mutants / Negative regulation of MAPK pathway / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / intracellular protein localization / melanosome / cadherin binding / protein domain specific binding / focal adhesion / perinuclear region of cytoplasm / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / nucleus / membrane / 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
Similarity search - Domain/homology
14-3-3 protein beta/alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsZhu, P. / Cooley, R.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RM1GM144227 United States
CitationJournal: Protein Sci. / Year: 2023
Title: Genetic encoding of 3-nitro-tyrosine reveals the impacts of 14-3-3 nitration on client binding and dephosphorylation.
Authors: Zhu, P. / Nguyen, K.T. / Estelle, A.B. / Sluchanko, N.N. / Mehl, R.A. / Cooley, R.B.
History
DepositionOct 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 25, 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

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Assembly

Deposited unit
B: 14-3-3 protein beta/alpha
A: 14-3-3 protein beta/alpha


Theoretical massNumber of molelcules
Total (without water)56,5632
Polymers56,5632
Non-polymers00
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-14 kcal/mol
Surface area22880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.400, 124.510, 55.230
Angle α, β, γ (deg.)90.000, 114.498, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein 14-3-3 protein beta/alpha / Protein 1054 / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 28281.623 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAB / Production host: Escherichia coli (E. coli) / References: UniProt: P31946
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O
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: 2.9 Å3/Da / Density % sol: 57.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20%-30% PEG 550 MME, 50 mM MgCl2, 100 mM HEPES pH 7-8.3

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Data collection

DiffractionMean temperature: 96 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.5→29.09 Å / Num. obs: 102662 / % possible obs: 99.8 % / Redundancy: 38.2 % / Biso Wilson estimate: 29.22 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.78
Reflection shellResolution: 1.5→1.55 Å / Num. unique obs: 9538 / CC1/2: 0.179 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BQ0

2bq0


Resolution: 1.5→29.09 Å / SU ML: 0.3066 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.224
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2049 5132 5 %
Rwork0.1785 97466 -
obs0.1799 102598 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.64 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3630 0 0 399 4029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01073731
X-RAY DIFFRACTIONf_angle_d0.99985049
X-RAY DIFFRACTIONf_chiral_restr0.0511567
X-RAY DIFFRACTIONf_plane_restr0.0063658
X-RAY DIFFRACTIONf_dihedral_angle_d14.06911411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.55551560.49613178X-RAY DIFFRACTION99.94
1.52-1.530.47181640.47223326X-RAY DIFFRACTION100
1.53-1.550.43551840.43713180X-RAY DIFFRACTION100
1.55-1.570.42061690.4043271X-RAY DIFFRACTION100
1.57-1.590.36031850.37063211X-RAY DIFFRACTION100
1.59-1.620.40161730.34613248X-RAY DIFFRACTION100
1.62-1.640.37931580.31513253X-RAY DIFFRACTION100
1.64-1.660.3081680.28913234X-RAY DIFFRACTION100
1.66-1.690.30791810.27123258X-RAY DIFFRACTION100
1.69-1.720.28811590.24823228X-RAY DIFFRACTION100
1.72-1.750.27781730.23033266X-RAY DIFFRACTION100
1.75-1.780.26671790.20773221X-RAY DIFFRACTION100
1.78-1.810.24351530.20323263X-RAY DIFFRACTION100
1.81-1.850.23661860.19173223X-RAY DIFFRACTION100
1.85-1.890.2531610.20293259X-RAY DIFFRACTION99.88
1.89-1.930.30831730.24783269X-RAY DIFFRACTION99.97
1.93-1.980.23361760.19753206X-RAY DIFFRACTION100
1.98-2.040.24341610.17163247X-RAY DIFFRACTION100
2.04-2.10.20611700.16513280X-RAY DIFFRACTION100
2.1-2.160.19111830.1563215X-RAY DIFFRACTION100
2.16-2.240.2051580.15773260X-RAY DIFFRACTION100
2.24-2.330.19981750.15233266X-RAY DIFFRACTION100
2.33-2.440.20721710.1563235X-RAY DIFFRACTION100
2.44-2.560.19971740.16273241X-RAY DIFFRACTION100
2.56-2.730.20141730.17133265X-RAY DIFFRACTION100
2.73-2.940.18571770.1723259X-RAY DIFFRACTION100
2.94-3.230.21411710.18853271X-RAY DIFFRACTION100
3.23-3.70.20241740.17013264X-RAY DIFFRACTION100
3.7-4.650.15591680.14243262X-RAY DIFFRACTION100
4.65-29.090.17021790.16253307X-RAY DIFFRACTION99.86

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