[English] 日本語
Yorodumi
- PDB-6zfd: 14-3-3 zeta bound to the phosphorylated 18E6 C-terminus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zfd
Title14-3-3 zeta bound to the phosphorylated 18E6 C-terminus
Components14-3-3 protein zeta/delta,Protein E6
KeywordsPROTEIN BINDING / HPV / E6 oncoprotein / 14-3-3
Function / homology
Function and homology information


Golgi reassembly / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling ...Golgi reassembly / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cellular response to glucose starvation / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / negative regulation of innate immune response / regulation of ERK1 and ERK2 cascade / protein sequestering activity / PDZ domain binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / : / melanosome / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / blood microparticle / DNA-binding transcription factor binding / vesicle / host cell cytoplasm / transmembrane transporter binding / cadherin binding / protein phosphorylation / focal adhesion / negative regulation of DNA-templated transcription / DNA-templated transcription / glutamatergic synapse / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ubiquitin protein ligase binding / host cell nucleus / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / DNA binding / extracellular space / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
E6 early regulatory protein / E6 superfamily / Early Protein (E6) / 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
Protein E6 / 14-3-3 protein zeta/delta
Similarity search - Component
Biological speciesHomo sapiens (human)
Human papillomavirus type 18
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGogl, G. / Tugaeva, K.V. / Sluchanko, N.N. / Trave, G.
CitationJournal: Nat Commun / Year: 2021
Title: Hierarchized phosphotarget binding by the seven human 14-3-3 isoforms.
Authors: Gogl, G. / Tugaeva, K.V. / Eberling, P. / Kostmann, C. / Trave, G. / Sluchanko, N.N.
History
DepositionJun 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 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,Protein E6
B: 14-3-3 protein zeta/delta,Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1586
Polymers54,7902
Non-polymers3684
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-16 kcal/mol
Surface area25190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.350, 78.530, 90.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein 14-3-3 protein zeta/delta,Protein E6 / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 27394.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Human papillomavirus type 18
Gene: YWHAZ, E6 / Production host: Escherichia coli (E. coli) / References: UniProt: P63104, UniProt: P06463
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 19% PEG4000, 0.1M cacodylate, 20%glycerol as a cryoprotectant

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→45.2 Å / Num. obs: 41285 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 26.54 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.166 / Net I/σ(I): 13.19
Reflection shellResolution: 1.9→1.95 Å / Mean I/σ(I) obs: 1.39 / Num. unique obs: 2986 / CC1/2: 0.547 / Rrim(I) all: 2.05

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O02

2o02


Resolution: 1.9→45.14 Å / SU ML: 0.2048 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5858 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2071 2015 4.89 %
Rwork0.1764 39202 -
obs0.178 41217 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.39 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 0 24 410 4234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00654130
X-RAY DIFFRACTIONf_angle_d0.82575597
X-RAY DIFFRACTIONf_chiral_restr0.0489605
X-RAY DIFFRACTIONf_plane_restr0.0064750
X-RAY DIFFRACTIONf_dihedral_angle_d26.12251601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.30941460.3012744X-RAY DIFFRACTION99.9
1.95-20.27321140.25332790X-RAY DIFFRACTION99.97
2-2.060.28561550.23622757X-RAY DIFFRACTION99.93
2.06-2.130.24861550.20872733X-RAY DIFFRACTION99.93
2.13-2.20.25881410.19432767X-RAY DIFFRACTION99.93
2.2-2.290.241310.18662785X-RAY DIFFRACTION99.97
2.29-2.390.22441230.17342798X-RAY DIFFRACTION99.97
2.39-2.520.23861190.17322804X-RAY DIFFRACTION100
2.52-2.680.21271290.17192808X-RAY DIFFRACTION100
2.68-2.880.19861580.17672792X-RAY DIFFRACTION100
2.88-3.170.20511600.1772784X-RAY DIFFRACTION100
3.17-3.630.17791710.15622807X-RAY DIFFRACTION99.97
3.63-4.580.15221530.14532844X-RAY DIFFRACTION100
4.58-39.260.21351600.17152989X-RAY DIFFRACTION99.94

+
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://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