[English] 日本語
Yorodumi
- PDB-6fnb: Mono- and bivalent 14-3-3 inhibitors for characterizing supramole... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fnb
TitleMono- and bivalent 14-3-3 inhibitors for characterizing supramolecular lysine-PEG interactions in proteins
Components14-3-3 protein zeta/delta
KeywordsPROTEIN BINDING / Inhibition / Mono- and bivalent 14-3-3 inhibitors / Supramolecular lysine-PEG
Function / homology
Function and homology information


Golgi reassembly / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling ...Golgi reassembly / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / 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 / negative regulation of TORC1 signaling / negative regulation of innate immune response / protein sequestering activity / regulation of ERK1 and ERK2 cascade / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / melanosome / DNA-binding transcription factor binding / vesicle / transmembrane transporter binding / blood microparticle / cadherin binding / protein phosphorylation / focal adhesion / glutamatergic synapse / ubiquitin protein ligase binding / 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 / cytosol / cytoplasm
Similarity search - Function
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 ...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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BENZOIC ACID / Chem-DWQ / 14-3-3 protein zeta/delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsBier, D. / Ottmann, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationCRC1093 Germany
CitationJournal: Chemistry / Year: 2018
Title: Mono- and Bivalent 14-3-3 Inhibitors for Characterizing Supramolecular "Lysine Wrapping" of Oligoethylene Glycol (OEG) Moieties in Proteins.
Authors: Yilmaz, E. / Bier, D. / Guillory, X. / Briels, J. / Ruiz-Blanco, Y.B. / Sanchez-Garcia, E. / Ottmann, C. / Kaiser, M.
History
DepositionFeb 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 19, 2018Group: Data collection / Derived calculations / Category: struct_conn
Revision 1.3Jan 17, 2024Group: 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 zeta/delta
B: 14-3-3 protein zeta/delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,95915
Polymers52,6342
Non-polymers3,32513
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-82 kcal/mol
Surface area22290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.800, 103.310, 113.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#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

-
Non-polymers , 6 types, 191 molecules

#2: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-DWQ / [2-[2-oxidanylidene-2-[[3-[2-[5-[3-oxidanylidene-3-[3-[2-[2-[3-[3-[2-[2-[2-[[3-[2-(2-phosphonophenoxy)ethanoylamino]phenyl]carbonylamino]ethoxy]ethoxy]ethoxy]propanoylamino]propoxy]ethoxy]ethoxy]propylamino]propoxy]pentoxy]ethylcarbamoyl]phenyl]amino]ethoxy]phenyl]phosphonic acid


Mass: 1291.273 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H84N6O22P2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 3.98 Å3/Da / Density % sol: 69.12 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.09 M HEPES sodium salt pH 7.5 1.26 M tri-Sodium citrate 10 %(v/v) Glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→46.98 Å / Num. obs: 38130 / % possible obs: 100 % / Redundancy: 13.252 % / Biso Wilson estimate: 60.572 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.128 / Rrim(I) all: 0.134 / Χ2: 0.95 / Net I/σ(I): 12.09 / Num. measured all: 505296 / Scaling rejects: 27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.413.041.1062.4258603449744940.8581.15199.9
2.4-2.513.950.8413.2753037380238020.9260.872100
2.5-313.360.3546.7216546912385123850.9830.368100
3-413.3280.12617.45132023990699060.9940.131100
4-612.9630.09723.8467747522652260.9960.101100
6-812.9310.10224.716836130313020.9960.10699.9
8-1011.6670.09724.7855074724720.9940.101100
10-1210.7910.09523.8723742212200.9940.10199.5
12-1412.0350.09325.3513841151150.9950.098100
14-2011.880.08925.2715801331330.9980.092100
20-409.8170.09321.9569771710.9970.098100
40-46.989.750.08224391440.9960.08628.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.98 Å
Translation2.5 Å46.98 Å

-
Processing

Software
NameVersionClassificationNB
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASER2.3.0phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NKX

3nkx


Resolution: 2.3→46.98 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.254 / SU ML: 0.163 / SU R Cruickshank DPI: 0.2152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.215 / ESU R Free: 0.189
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2484 1904 5 %RANDOM
Rwork0.2143 ---
obs0.216 36165 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 137.39 Å2 / Biso mean: 60.153 Å2 / Biso min: 36.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.91 Å2-0 Å20 Å2
2--5.66 Å20 Å2
3----3.76 Å2
Refinement stepCycle: final / Resolution: 2.3→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3532 0 122 179 3833
Biso mean--60.76 63.97 -
Num. residues----457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.023698
X-RAY DIFFRACTIONr_bond_other_d0.0020.023361
X-RAY DIFFRACTIONr_angle_refined_deg1.0721.9964981
X-RAY DIFFRACTIONr_angle_other_deg0.8793.0077769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9455453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.6225.03165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10815632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3521521
X-RAY DIFFRACTIONr_chiral_restr0.0550.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024096
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02737
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 139 -
Rwork0.321 2630 -
all-2769 -
obs--99.93 %

+
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