[English] 日本語
Yorodumi
- PDB-5ewz: Small-molecule stabilization of the 14-3-3/Gab2 PPI interface -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ewz
TitleSmall-molecule stabilization of the 14-3-3/Gab2 PPI interface
Components
  • (GRB2-associated-binding protein 2) x 2
  • 14-3-3 protein zeta/delta
KeywordsSIGNALING PROTEIN / 14-3-3 / GAB2 / Protein / Diphosphorylation
Function / homology
Function and homology information


Golgi reassembly / synaptic target recognition / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / respiratory system process / establishment of Golgi localization / positive regulation of mast cell degranulation / STAT5 Activation / tube formation / Rap1 signalling ...Golgi reassembly / synaptic target recognition / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / respiratory system process / establishment of Golgi localization / positive regulation of mast cell degranulation / STAT5 Activation / tube formation / Rap1 signalling / phosphatidylinositol-3,4-bisphosphate binding / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by cytosolic FGFR1 fusion mutants / Interleukin-15 signaling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / STAT5 activation downstream of FLT3 ITD mutants / phosphatidylinositol-3,4,5-trisphosphate binding / Regulation of localization of FOXO transcription factors / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / protein targeting / Role of LAT2/NTAL/LAB on calcium mobilization / Interleukin receptor SHC signaling / 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 / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / negative regulation of TORC1 signaling / ERK1 and ERK2 cascade / Signaling by FLT3 fusion proteins / FLT3 Signaling / negative regulation of innate immune response / protein sequestering activity / hippocampal mossy fiber to CA3 synapse / osteoclast differentiation / regulation of ERK1 and ERK2 cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / lung development / regulation of protein stability / Signaling by SCF-KIT / Constitutive Signaling by Aberrant PI3K in Cancer / Signaling by CSF1 (M-CSF) in myeloid cells / melanosome / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA-binding transcription factor binding / angiogenesis / vesicle / transmembrane transporter binding / blood microparticle / cadherin binding / membrane raft / protein domain specific binding / protein phosphorylation / focal adhesion / glutamatergic synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GRB2-associated-binding protein 1-4-like / 14-3-3 domain / Delta-Endotoxin; domain 1 / 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 ...GRB2-associated-binding protein 1-4-like / 14-3-3 domain / Delta-Endotoxin; domain 1 / 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 / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BENZOIC ACID / 14-3-3 protein zeta/delta / GRB2-associated-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.34 Å
AuthorsBier, D. / Ottmann, C.
CitationJournal: Chemmedchem / Year: 2016
Title: Small-Molecule Stabilization of the 14-3-3/Gab2 Protein-Protein Interaction (PPI) Interface.
Authors: Bier, D. / Bartel, M. / Sies, K. / Halbach, S. / Higuchi, Y. / Haranosono, Y. / Brummer, T. / Kato, N. / Ottmann, C.
History
DepositionNov 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_symm_contact / struct_conn

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 protein zeta/delta
B: 14-3-3 protein zeta/delta
C: GRB2-associated-binding protein 2
D: GRB2-associated-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7506
Polymers54,5054
Non-polymers2442
Water5,909328
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-17 kcal/mol
Surface area23720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.660, 104.920, 116.030
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 zeta/delta / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 26316.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Production host: Escherichia coli (E. coli) / References: UniProt: P63104
#2: Protein/peptide GRB2-associated-binding protein 2 / GRB2-associated binder 2 / Growth factor receptor bound protein 2-associated protein 2 / pp100


Mass: 1137.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UQC2
#3: Protein/peptide GRB2-associated-binding protein 2 / GRB2-associated binder 2 / Growth factor receptor bound protein 2-associated protein 2 / pp100


Mass: 734.673 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UQC2
#4: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 4.13 Å3/Da / Density % sol: 70.25 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 1.2 M sodium hydrogen phosphate, 0.8 M dipotassium hydrogen phosphate, 0.2 M lithium sulfate, 0.1 M CAPS
PH range: 10.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.34→45.57 Å / Num. obs: 38368 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 43.575 Å2 / Rmerge F obs: 0.108 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.097 / Χ2: 1.001 / Net I/σ(I): 13.93 / Num. measured all: 195814
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.34-2.350.5390.633.1725124764760.695100
2.35-2.360.5330.6373.0224974734700.70299.4
2.36-2.370.4930.5873.3726025004970.64899.4
2.37-30.260.2925.989529518614185190.32299.5
3-40.060.07818.615377110606105450.08699.4
4-60.0310.04827.2127389556154890.05498.7
6-80.0260.04228.496953139213590.04697.6
8-100.0210.03532.5221755084820.03994.9
10-120.0180.03136.4910742392220.03492.9
120.0160.03235.5215463543090.03587.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.58 Å
Translation2.5 Å45.58 Å

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.3.0phasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→45.57 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.2418 / WRfactor Rwork: 0.1898 / FOM work R set: 0.8469 / SU B: 5.3 / SU ML: 0.128 / SU R Cruickshank DPI: 0.2058 / SU Rfree: 0.1933 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 1919 5 %RANDOM
Rwork0.194 ---
obs0.1964 36449 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 88.57 Å2 / Biso mean: 35.813 Å2 / Biso min: 15.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--1.09 Å20 Å2
3----1.16 Å2
Refinement stepCycle: final / Resolution: 2.34→45.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3685 0 18 328 4031
Biso mean--23.64 44.25 -
Num. residues----471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0223755
X-RAY DIFFRACTIONr_angle_refined_deg1.9411.9785061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7875466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.08225176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.94515.022683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5061524
X-RAY DIFFRACTIONr_chiral_restr0.1370.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022797
X-RAY DIFFRACTIONr_mcbond_it1.1891.52353
X-RAY DIFFRACTIONr_mcangle_it2.32123739
X-RAY DIFFRACTIONr_scbond_it3.55331402
X-RAY DIFFRACTIONr_scangle_it5.844.51322
LS refinement shellResolution: 2.34→2.401 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 140 -
Rwork0.243 2665 -
all-2805 -
obs--100 %

+
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