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- PDB-4qli: A novel phospho-switch in the linker region of the snail zinc fin... -

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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 SNAI1
KeywordsSIGNALING PROTEIN / 14-3-3 / adapter protein / protein-protein interaction
Function / homology
Function and homology information


Regulation of CDH11 gene transcription / negative regulation of vitamin D biosynthetic process / epithelial to mesenchymal transition involved in endocardial cushion formation / heterochromatin organization / Epithelial-Mesenchymal Transition (EMT) during gastrulation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / mesoderm formation / aortic valve morphogenesis / regulation of bicellular tight junction assembly / positive regulation of epidermal cell differentiation ...Regulation of CDH11 gene transcription / negative regulation of vitamin D biosynthetic process / epithelial to mesenchymal transition involved in endocardial cushion formation / heterochromatin organization / Epithelial-Mesenchymal Transition (EMT) during gastrulation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / mesoderm formation / aortic valve morphogenesis / regulation of bicellular tight junction assembly / positive regulation of epidermal cell differentiation / regulation of epidermal cell division / protein kinase C inhibitor activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / E-box binding / regulation of cell-cell adhesion / canonical Wnt signaling pathway / establishment of skin barrier / Notch signaling pathway / Regulation of localization of FOXO transcription factors / epithelial to mesenchymal transition / Regulation of GBP-mediated host defense / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of protein localization to plasma membrane / positive regulation of epithelial to mesenchymal transition / cAMP/PKA signal transduction / protein export from nucleus / pericentric heterochromatin / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / release of cytochrome c from mitochondria / RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / negative regulation of protein kinase activity / positive regulation of protein export from nucleus / positive regulation of protein localization / positive regulation of cell adhesion / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of innate immune response / Regulation of PTEN gene transcription / RNA polymerase II transcription regulatory region sequence-specific DNA binding / TP53 Regulates Metabolic Genes / intrinsic apoptotic signaling pathway in response to DNA damage / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein sequestering activity / Negative Regulation of CDH1 Gene Transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / intracellular protein localization / osteoblast differentiation / kinase binding / sequence-specific double-stranded DNA binding / regulation of protein localization / positive regulation of cell growth / positive regulation of cell migration / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cadherin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / : / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
C2H2-type zinc finger / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 protein sigma / 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 ...C2H2-type zinc finger / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 protein sigma / 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, C2H2 type / 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
Revision 1.1Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / 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


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


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

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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

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Phasing

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

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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 %

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