[English] 日本語
Yorodumi
- PDB-6kzh: 14-3-3 protein in Complex with CIC S173 phosphorylated peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kzh
Title14-3-3 protein in Complex with CIC S173 phosphorylated peptide
Components
  • 14-3-3 protein theta
  • CIC pS173 peptide
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 / Activation of BAD and translocation to mitochondria / protein targeting / 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 / Activation of BAD and translocation to mitochondria / protein targeting / 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 / 14-3-3 protein binding / substantia nigra development / 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 / intracellular membrane-bounded organelle / focal adhesion / negative regulation of DNA-templated transcription / synapse / chromatin / regulation of transcription by RNA polymerase II / signal transduction / protein-containing complex / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol
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: 2.645 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 S173 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 protein theta
C: CIC pS173 peptide
B: 14-3-3 protein theta
Q: CIC pS173 peptide


Theoretical massNumber of molelcules
Total (without water)61,6274
Polymers61,6274
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-26 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.169, 80.810, 107.064
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
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(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27348
#2: Protein/peptide CIC pS173 peptide / 8-mer from Protein capicua homolog


Mass: 955.970 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(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96RK0
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium chloride, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350

-
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: 2.645→44.628 Å / Num. obs: 18361 / % possible obs: 99.75 % / Redundancy: 12.8 % / CC1/2: 1 / Rmerge(I) obs: 0.147 / Net I/σ(I): 11.1
Reflection shellResolution: 2.645→2.74 Å / Rmerge(I) obs: 1.27 / Num. unique obs: 1800 / CC1/2: 0.8

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KZG

5kzg
PDB Unreleased entry


Resolution: 2.645→44.628 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.45
RfactorNum. reflection% reflection
Rfree0.2736 1834 10 %
Rwork0.2154 --
obs0.2212 18344 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 194.1 Å2 / Biso mean: 81.0218 Å2 / Biso min: 41.9 Å2
Refinement stepCycle: final / Resolution: 2.645→44.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3723 0 0 0 3723
Num. residues----471
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6453-2.71680.40171390.3771125099
2.7168-2.79670.3521400.31841258100
2.7967-2.8870.40871380.30871238100
2.887-2.99020.38781390.30661253100
2.9902-3.10980.36471380.27631244100
3.1098-3.25130.31351380.2691242100
3.2513-3.42270.30551400.2431267100
3.4227-3.6370.31171410.231264100
3.637-3.91770.26321410.2021264100
3.9177-4.31170.28631420.1831283100
4.3117-4.93490.22361430.17571281100
4.9349-6.21480.25841450.22281309100
6.2148-44.6280.22291500.1782135799
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

+
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