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- PDB-6kzg: 14-3-3 protein in Complex with CIC S301 phosphorylated peptide -

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Basic information

Entry
Database: PDB / ID: 6kzg
Title14-3-3 protein in Complex with CIC S301 phosphorylated peptide
Components
  • 14-3-3 protein theta
  • ARG-SER-MET-SER-GLU-THR-GLY-THR
KeywordsSIGNALING PROTEIN / 14-3-3 protein / CIC / phosphorylation / transcriptional regulation
Function / homology
Function and homology information


negative regulation of monoatomic ion transmembrane transport / small GTPase-mediated signal transduction / social behavior / Regulation of localization of FOXO transcription factors / protein targeting / Activation of BAD and translocation to mitochondria / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / 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 monoatomic ion transmembrane transport / small GTPase-mediated signal transduction / social behavior / Regulation of localization of FOXO transcription factors / protein targeting / Activation of BAD and translocation to mitochondria / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / substantia nigra development / 14-3-3 protein binding / learning / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / RNA polymerase II transcription regulatory region sequence-specific DNA binding / brain development / memory / transmembrane transporter binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein domain specific binding / focal adhesion / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / synapse / chromatin / regulation of transcription by RNA polymerase II / signal transduction / protein-containing complex / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
14-3-3 theta / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / 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 theta / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / 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
14-3-3 protein theta / Protein capicua homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWen, Y. / Shao, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaNO.31870132 China
National Natural Science Foundation of ChinaNO.81741088 China
National Natural Science Foundation of ChinaNO.31500051 China
CitationJournal: To Be Published
Title: 14-3-3 protein in Complex with CIC S301 phosphorylated peptide
Authors: Wen, Y. / Shao, Y.
History
DepositionSep 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein theta
C: ARG-SER-MET-SER-GLU-THR-GLY-THR
B: 14-3-3 protein theta
Q: ARG-SER-MET-SER-GLU-THR-GLY-THR


Theoretical massNumber of molelcules
Total (without water)61,6134
Polymers61,6134
Non-polymers00
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-28 kcal/mol
Surface area22780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.657, 79.487, 106.261
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 14-3-3 protein theta / 14-3-3 protein T-cell / 14-3-3 protein tau / Protein HS1


Mass: 29857.580 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAQ / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P27348
#2: Protein/peptide ARG-SER-MET-SER-GLU-THR-GLY-THR / 8-mer from Protein capicua homolog


Mass: 948.913 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CIC, KIAA0306 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q96RK0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 8% v/v TacsimateTM pH 6.0, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→44.17 Å / Num. obs: 40758 / % possible obs: 99.81 % / Redundancy: 12.8 % / CC1/2: 1 / Rmerge(I) obs: 0.113 / Net I/σ(I): 16.9
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 3950 / CC1/2: 0.61

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Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IQP

5iqp


Resolution: 2→44.17 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2306 --
Rwork0.1909 --
obs-40758 99.81 %
Displacement parametersBiso max: 129.51 Å2 / Biso mean: 52.403 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 2→44.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3775 0 0 165 3940
Refinement TLS params.Method: refined / Origin x: -69.3197 Å / Origin y: -0.6816 Å / Origin z: -2.95 Å
111213212223313233
T0.5618 Å2-0.0057 Å2-0.0423 Å2-0.4552 Å20.0418 Å2--0.4638 Å2
L2.6067 °20.259 °2-0.8221 °2-0.2505 °20.1561 °2--0.9768 °2
S0.0339 Å °-0.0758 Å °-0.2259 Å °0.0341 Å °-0.0861 Å °-0.0334 Å °0.3006 Å °-0.036 Å °0.041 Å °
Refinement TLS groupSelection details: all

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