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- PDB-8ah2: Crystal structure of human 14-3-3 zeta fused to the NPM1 peptide ... -

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Basic information

Entry
Database: PDB / ID: 8ah2
TitleCrystal structure of human 14-3-3 zeta fused to the NPM1 peptide including phosphoserine-48
Components14-3-3 protein zeta/delta,Nucleophosmin
KeywordsSIGNALING PROTEIN / 14-3-3 / Nucleophosmin 1 / NPM1 / B23 / numatrin / Ser48 / phosphoserine binder / phosphothreonine binder / pentamer / phosphorylation
Function / homology
Function and homology information


regulation of mRNA stability involved in cellular response to UV / regulation of eIF2 alpha phosphorylation by dsRNA / regulation of endoribonuclease activity / negative regulation of centrosome duplication / positive regulation of cell cycle G2/M phase transition / regulation of endodeoxyribonuclease activity / regulation of centriole replication / positive regulation of centrosome duplication / granular component / positive regulation of protein localization to nucleolus ...regulation of mRNA stability involved in cellular response to UV / regulation of eIF2 alpha phosphorylation by dsRNA / regulation of endoribonuclease activity / negative regulation of centrosome duplication / positive regulation of cell cycle G2/M phase transition / regulation of endodeoxyribonuclease activity / regulation of centriole replication / positive regulation of centrosome duplication / granular component / positive regulation of protein localization to nucleolus / negative regulation of protein kinase activity by regulation of protein phosphorylation / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / synaptic target recognition / Golgi reassembly / SARS-CoV-1-host interactions / NOTCH4 Activation and Transmission of Signal to the Nucleus / regulation of centrosome duplication / establishment of Golgi localization / Tat protein binding / respiratory system process / spindle pole centrosome / ALK mutants bind TKIs / tube formation / negative regulation of mRNA splicing, via spliceosome / regulation of synapse maturation / Rap1 signalling / Nuclear import of Rev protein / cell volume homeostasis / centrosome cycle / negative regulation of protein localization to nucleus / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / nucleocytoplasmic transport / regulation of DNA damage response, signal transduction by p53 class mediator / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / protein kinase inhibitor activity / ribosomal large subunit binding / macrophage differentiation / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / ribosomal small subunit binding / ribosomal large subunit export from nucleus / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / NF-kappaB binding / protein targeting / regulation of ERK1 and ERK2 cascade / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / core promoter sequence-specific DNA binding / cellular response to glucose starvation / Nuclear events stimulated by ALK signaling in cancer / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / ribosomal small subunit export from nucleus / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / positive regulation of protein ubiquitination / ERK1 and ERK2 cascade / Deposition of new CENPA-containing nucleosomes at the centromere / Transcriptional and post-translational regulation of MITF-M expression and activity / protein sequestering activity / SUMOylation of transcription cofactors / Deactivation of the beta-catenin transactivating complex / negative regulation of innate immune response / hippocampal mossy fiber to CA3 synapse / ribosome assembly / positive regulation of translation / ribosomal large subunit biogenesis / Negative regulation of NOTCH4 signaling / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / intracellular protein transport / regulation of cell growth / lung development / positive regulation of NF-kappaB transcription factor activity / protein-DNA complex / PKR-mediated signaling / regulation of protein stability / Signaling by ALK fusions and activated point mutants / protein import into nucleus / cellular response to UV / cellular senescence / unfolded protein binding / melanosome / intracellular protein localization / nucleosome assembly / large ribosomal subunit / ribosomal small subunit biogenesis / small ribosomal subunit / blood microparticle / vesicle / angiogenesis / protein phosphatase binding / histone binding / molecular adaptor activity / DNA-binding transcription factor binding / transmembrane transporter binding / transcription coactivator activity / protein stabilization / rRNA binding
Similarity search - Function
Nucleophosmin, C-terminal / Nucleophosmin C-terminal domain / Nucleoplasmin core domain / Nucleoplasmin core domain superfamily / Nucleoplasmin/nucleophosmin domain / Nucleoplasmin family / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site ...Nucleophosmin, C-terminal / Nucleophosmin C-terminal domain / Nucleoplasmin core domain / Nucleoplasmin core domain superfamily / Nucleoplasmin/nucleophosmin domain / Nucleoplasmin family / 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
Nucleophosmin / 14-3-3 protein zeta/delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsBoyko, K.M. / Kapitonova, A.A. / Tugaeva, K.V. / Varfolomeeva, L.A. / Sluchanko, N.N.
Funding support Russian Federation, 2items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation075-15-2021-1354 Russian Federation
Russian Science Foundation19-74-10031 Russian Federation
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Structural basis for the recognition by 14-3-3 proteins of a conditional binding site within the oligomerization domain of human nucleophosmin.
Authors: Kapitonova, A.A. / Tugaeva, K.V. / Varfolomeeva, L.A. / Boyko, K.M. / Cooley, R.B. / Sluchanko, N.N.
History
DepositionJul 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein zeta/delta,Nucleophosmin
C: 14-3-3 protein zeta/delta,Nucleophosmin


Theoretical massNumber of molelcules
Total (without water)55,2742
Polymers55,2742
Non-polymers00
Water25214
1
A: 14-3-3 protein zeta/delta,Nucleophosmin

A: 14-3-3 protein zeta/delta,Nucleophosmin


Theoretical massNumber of molelcules
Total (without water)55,2742
Polymers55,2742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_455-x-1,-y+1/2,z1
2
C: 14-3-3 protein zeta/delta,Nucleophosmin

C: 14-3-3 protein zeta/delta,Nucleophosmin


Theoretical massNumber of molelcules
Total (without water)55,2742
Polymers55,2742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545-x,-y-1/2,z1
Unit cell
Length a, b, c (Å)79.696, 110.207, 163.413
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-309-

HOH

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Components

#1: Protein 14-3-3 protein zeta/delta,Nucleophosmin / Protein kinase C inhibitor protein 1 / KCIP-1 / NPM / Nucleolar phosphoprotein B23 / Nucleolar ...Protein kinase C inhibitor protein 1 / KCIP-1 / NPM / Nucleolar phosphoprotein B23 / Nucleolar protein NO38 / Numatrin


Mass: 27637.055 Da / Num. of mol.: 2 / Mutation: S58A,E75A,K76A,K77A,K157A,K158A,E159A
Source method: isolated from a genetically manipulated source
Details: N-termianl residues - GPH are tag. C-terminal GGGG - linker, and C-terminal LRTV(SEP)LGAGAKD is NPM1 peptide,N-termianl residues - GPH are tag. C-terminal GGGG - linker, and C-terminal ...Details: N-termianl residues - GPH are tag. C-terminal GGGG - linker, and C-terminal LRTV(SEP)LGAGAKD is NPM1 peptide,N-termianl residues - GPH are tag. C-terminal GGGG - linker, and C-terminal LRTV(SEP)LGAGAKD is NPM1 peptide,N-termianl residues - GPH are tag. C-terminal GGGG - linker, and C-terminal LRTV(SEP)LGAGAKD is NPM1 peptide,N-termianl residues - GPH are tag. C-terminal GGGG - linker, and C-terminal LRTV(SEP)LGAGAKD is NPM1 peptide
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ, NPM1, NPM / Production host: Escherichia coli (E. coli) / References: UniProt: P63104, UniProt: P06748
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.25 Å3/Da / Density % sol: 62.1 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: 0.01 M CoCl2, 0.1 M MES, pH 6.5, 2.2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jun 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.9→21.91 Å / Num. obs: 16235 / % possible obs: 99.5 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.058 / Rrim(I) all: 0.168 / Net I/σ(I): 10.4 / Num. measured all: 131674 / Scaling rejects: 680
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.9-3.0891.6592335626020.8830.5841.7611100
8.7-21.914.90.02230126180.9990.0110.02540.492.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.7.8data scaling
MOLREPphasing
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FNC

6fnc


Resolution: 2.9→21.91 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.887 / SU B: 64.541 / SU ML: 0.478 / SU R Cruickshank DPI: 2.3403 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.34 / ESU R Free: 0.479 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3226 730 4.8 %RANDOM
Rwork0.2697 ---
obs0.2722 14615 93.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 180.69 Å2 / Biso mean: 75.162 Å2 / Biso min: 34.96 Å2
Baniso -1Baniso -2Baniso -3
1-10.7 Å20 Å2-0 Å2
2---6.05 Å20 Å2
3----4.65 Å2
Refinement stepCycle: final / Resolution: 2.9→21.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3533 0 0 14 3547
Biso mean---46.58 -
Num. residues----479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123580
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163167
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.6314853
X-RAY DIFFRACTIONr_angle_other_deg0.4731.5477310
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7985475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.1711022
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.66810546
X-RAY DIFFRACTIONr_chiral_restr0.060.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024203
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02705
LS refinement shellResolution: 2.9→2.974 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.455 57 -
Rwork0.455 1059 -
all-1116 -
obs--95.79 %
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)
12.95230.4061-1.22351.80270.01283.298-0.4852-0.59410.07130.21030.4037-0.1080.04540.31980.08150.22640.2854-0.09160.4189-0.03370.293-20.524624.154820.3821
21.5498-0.06930.01875.60870.76071.38680.10540.1533-0.016-0.2758-0.2015-0.4572-0.13150.20190.09610.28580.30090.03970.41450.13070.38373.2603-8.037619.1678
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 243
2X-RAY DIFFRACTION2C2 - 241

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