[English] 日本語
Yorodumi
- PDB-8ah2: Crystal structure of human 14-3-3 zeta fused to the NPM1 peptide ... -

+
Open data


ID or keywords:

Loading...

-
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 eIF2 alpha phosphorylation by dsRNA / regulation of mRNA stability involved in cellular response to UV / regulation of endoribonuclease activity / negative regulation of centrosome duplication / regulation of endodeoxyribonuclease activity / positive regulation of cell cycle G2/M phase transition / regulation of centriole replication / granular component / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / negative regulation of protein kinase activity by regulation of protein phosphorylation ...regulation of eIF2 alpha phosphorylation by dsRNA / regulation of mRNA stability involved in cellular response to UV / regulation of endoribonuclease activity / negative regulation of centrosome duplication / regulation of endodeoxyribonuclease activity / positive regulation of cell cycle G2/M phase transition / regulation of centriole replication / granular component / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / negative regulation of protein kinase activity by regulation of protein phosphorylation / Golgi reassembly / synaptic target recognition / SARS-CoV-1-host interactions / Tat protein binding / respiratory system process / regulation of centrosome duplication / NOTCH4 Activation and Transmission of Signal to the Nucleus / regulation of synapse maturation / establishment of Golgi localization / tube formation / ALK mutants bind TKIs / spindle pole centrosome / Rap1 signalling / Nuclear import of Rev protein / negative regulation of protein localization to nucleus / centrosome cycle / nucleocytoplasmic transport / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / protein kinase inhibitor activity / ribosomal large subunit binding / Regulation of localization of FOXO transcription factors / ribosomal small subunit binding / NF-kappaB binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / ribosomal large subunit export from nucleus / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / protein targeting / ribosomal small subunit export from nucleus / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Nuclear events stimulated by ALK signaling in cancer / cellular response to glucose starvation / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / ribosomal subunit export from nucleus / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / core promoter sequence-specific DNA binding / Deposition of new CENPA-containing nucleosomes at the centromere / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / protein sequestering activity / ERK1 and ERK2 cascade / negative regulation of innate immune response / ribosome assembly / hippocampal mossy fiber to CA3 synapse / regulation of ERK1 and ERK2 cascade / SUMOylation of transcription cofactors / ribosomal large subunit biogenesis / positive regulation of translation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / protein-DNA complex / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / intracellular protein transport / lung development / regulation of protein stability / PKR-mediated signaling / protein localization / : / cellular response to UV / cellular senescence / Signaling by ALK fusions and activated point mutants / unfolded protein binding / nucleosome assembly / melanosome / ribosomal small subunit biogenesis / positive regulation of NF-kappaB transcription factor activity / histone binding / angiogenesis / DNA-binding transcription factor binding / vesicle / transmembrane transporter binding / transcription coactivator activity / blood microparticle / rRNA binding / chromatin remodeling / ribonucleoprotein complex / cadherin binding / negative regulation of cell population proliferation / protein domain specific binding / protein phosphorylation / DNA repair / focal adhesion / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / chromatin binding / positive regulation of cell population proliferation
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 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein ...Nucleophosmin, C-terminal / Nucleophosmin C-terminal domain / Nucleoplasmin core domain / Nucleoplasmin core domain superfamily / Nucleoplasmin/nucleophosmin domain / Nucleoplasmin family / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more