[English] 日本語
Yorodumi
- PDB-4qli: A novel phospho-switch in the linker region of the snail zinc fin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qli
TitleA novel phospho-switch in the linker region of the snail zinc finger protein which regulates 14-3-3 association, DNA binding and epithelial-mesenchymal differentiation
Components
  • 14-3-3 protein sigma
  • Zinc finger protein SNAI1SNAI1
KeywordsSIGNALING PROTEIN / 14-3-3 / adapter protein / protein-protein interaction
Function / homology
Function and homology information


negative regulation of cell differentiation involved in embryonic placenta development / cartilage morphogenesis / left/right pattern formation / negative regulation of vitamin D biosynthetic process / Regulation of CDH11 gene transcription / epithelial cell migration / epithelial to mesenchymal transition involved in endocardial cushion formation / trophoblast giant cell differentiation / heterochromatin organization / Epithelial-Mesenchymal Transition (EMT) during gastrulation ...negative regulation of cell differentiation involved in embryonic placenta development / cartilage morphogenesis / left/right pattern formation / negative regulation of vitamin D biosynthetic process / Regulation of CDH11 gene transcription / epithelial cell migration / epithelial to mesenchymal transition involved in endocardial cushion formation / trophoblast giant cell differentiation / heterochromatin organization / Epithelial-Mesenchymal Transition (EMT) during gastrulation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / aortic valve morphogenesis / regulation of bicellular tight junction assembly / hair follicle morphogenesis / regulation of epidermal cell division / roof of mouth development / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / E-box binding / negative regulation of DNA damage response, signal transduction by p53 class mediator / Regulation of localization of FOXO transcription factors / mesoderm formation / keratinocyte proliferation / phosphoserine residue binding / canonical Wnt signaling pathway / Activation of BAD and translocation to mitochondria / epithelial to mesenchymal transition / positive regulation of epithelial to mesenchymal transition / negative regulation of keratinocyte proliferation / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / pericentric heterochromatin / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / Notch signaling pathway / protein export from nucleus / negative regulation of innate immune response / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / Regulation of PTEN gene transcription / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / fibrillar center / osteoblast differentiation / kinase binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / intrinsic apoptotic signaling pathway in response to DNA damage / sequence-specific double-stranded DNA binding / positive regulation of cell growth / regulation of cell cycle / positive regulation of cell migration / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
C2H2-type zinc finger / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 protein sigma / Zinc finger, C2H2 type / 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 ...C2H2-type zinc finger / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 protein sigma / Zinc finger, C2H2 type / 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 / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Zinc finger protein SNAI1 / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsBier, D. / Ottmann, C.
CitationJournal: To be Published
Title: A novel phospho-switch in the linker region of the snail zinc finger protein which regulates 14-3-3 association, DNA binding and epithelial-mesenchymal differentiation
Authors: Liu, Y. / Prokop, J.W. / Peng, H. / Karar, J. / White, D. / Hou, Z. / Qin, Y.S. / Bier, D. / Ottmann, C. / Waxman, S. / Halazonetis, T.D. / Rauscher III, F.J.
History
DepositionJun 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 protein sigma
B: Zinc finger protein SNAI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4205
Polymers27,2802
Non-polymers1413
Water3,351186
1
A: 14-3-3 protein sigma
B: Zinc finger protein SNAI1
hetero molecules

A: 14-3-3 protein sigma
B: Zinc finger protein SNAI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,84110
Polymers54,5594
Non-polymers2816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4730 Å2
ΔGint-35 kcal/mol
Surface area23440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.300, 111.900, 62.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 26541.971 Da / Num. of mol.: 1 / Fragment: UNP residues 1-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HME1, NM_006142, SFN / Plasmid: pPROEX HTB / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P31947
#2: Protein/peptide Zinc finger protein SNAI1 / SNAI1 / Protein snail homolog 1 / Protein sna


Mass: 737.739 Da / Num. of mol.: 1 / Fragment: phosphopeptide (UNP residues 175-180) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O95863
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 0.2 M calcium chloride, 28% PEG400, 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 27, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→45.44 Å / Num. all: 51357 / Num. obs: 51053 / % possible obs: 99.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.651 Å2 / Rmerge(I) obs: 0.066 / Χ2: 0.944 / Net I/σ(I): 17.37
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.45-1.70.1948.621221771904098.8
1.7-1.90.09915.0660278893899.8
1.9-20.07818.5119937321699.5
2-30.0625.14910781382199.9
3-40.0630.3523372342299.9
4-60.05929.1210931179899.8
6-80.06130.853136462100
8-100.05830.96109416599.4
10-120.06429.8347275100
12-140.0729.225843100
14-200.06229.327246100
200.06425.321282787.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.44 Å
Translation2.5 Å45.44 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→45.44 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.2122 / WRfactor Rwork: 0.181 / FOM work R set: 0.8917 / SU B: 0.864 / SU ML: 0.035 / SU R Cruickshank DPI: 0.0593 / SU Rfree: 0.0642 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.203 2553 5 %RANDOM
Rwork0.1694 ---
obs0.1711 51037 99.42 %-
all-51053 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.31 Å2 / Biso mean: 18.723 Å2 / Biso min: 6.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å2-0 Å2
2---0.09 Å2-0 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.45→45.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1890 0 8 186 2084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0192079
X-RAY DIFFRACTIONr_bond_other_d0.0010.028
X-RAY DIFFRACTIONr_angle_refined_deg2.6691.9862831
X-RAY DIFFRACTIONr_angle_other_deg0.758316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5545283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50124.52695
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08915399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7781515
X-RAY DIFFRACTIONr_chiral_restr0.1860.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021566
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 177 -
Rwork0.184 3300 -
all-3477 -
obs--97.75 %

+
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