[English] 日本語
Yorodumi
- PDB-6yp2: 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yp2
Title14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-011
Components
  • 14-3-3 protein sigma
  • p65pS45
KeywordsPEPTIDE BINDING PROTEIN / covalent fragment / p65 / 1433
Function / homology
Function and homology information


acetaldehyde metabolic process / prolactin signaling pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / IkBA variant leads to EDA-ID / positive regulation of Schwann cell differentiation / cellular response to peptidoglycan / Regulated proteolysis of p75NTR / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 ...acetaldehyde metabolic process / prolactin signaling pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / IkBA variant leads to EDA-ID / positive regulation of Schwann cell differentiation / cellular response to peptidoglycan / Regulated proteolysis of p75NTR / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / CLEC7A/inflammasome pathway / SUMOylation of immune response proteins / negative regulation of protein sumoylation / nucleotide-binding oligomerization domain containing 2 signaling pathway / postsynapse to nucleus signaling pathway / defense response to tumor cell / Interleukin-1 processing / cellular response to interleukin-6 / actinin binding / NF-kappaB complex / negative regulation of non-canonical NF-kappaB signal transduction / cellular response to angiotensin / response to UV-B / interleukin-1-mediated signaling pathway / vascular endothelial growth factor signaling pathway / Regulation of NFE2L2 gene expression / positive regulation of leukocyte adhesion to vascular endothelial cell / positive regulation of miRNA metabolic process / toll-like receptor 4 signaling pathway / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / positive regulation of T cell receptor signaling pathway / response to cobalamin / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / phosphate ion binding / non-canonical NF-kappaB signal transduction / TRAF6 mediated NF-kB activation / cellular response to lipoteichoic acid / response to muramyl dipeptide / The NLRP3 inflammasome / Regulation of localization of FOXO transcription factors / general transcription initiation factor binding / keratinocyte proliferation / Transcriptional Regulation by VENTX / NF-kappaB binding / hair follicle development / phosphoserine residue binding / neuropeptide signaling pathway / positive regulation of vascular endothelial growth factor production / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / RNA polymerase II core promoter sequence-specific DNA binding / canonical NF-kappaB signal transduction / establishment of skin barrier / response to amino acid / cellular response to interleukin-1 / cellular defense response / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Purinergic signaling in leishmaniasis infection / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of insulin receptor signaling pathway / response to cAMP / tumor necrosis factor-mediated signaling pathway / response to muscle stretch / protein export from nucleus / negative regulation of innate immune response / NF-kB is activated and signals survival / positive regulation of interleukin-12 production / CD209 (DC-SIGN) signaling / response to interleukin-1 / negative regulation of angiogenesis / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / negative regulation of miRNA transcription / response to progesterone / liver development / response to organic substance / positive regulation of interleukin-1 beta production / stem cell proliferation / response to cytokine / response to ischemia / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of interleukin-8 production / Dectin-1 mediated noncanonical NF-kB signaling / negative regulation of extrinsic apoptotic signaling pathway / TP53 Regulates Metabolic Genes / Activation of NF-kappaB in B cells / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / animal organ morphogenesis
Similarity search - Function
Transcription factor RelA (p65) / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. ...Transcription factor RelA (p65) / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / ig-like, plexins, transcription factors / 14-3-3 protein sigma / IPT domain / 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 / p53-like transcription factor, DNA-binding / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
1-(4-methylphenyl)imidazole / 14-3-3 protein sigma / Transcription factor p65
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsWolter, M. / Ottmann, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission675179European Union
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Fragment-Based Stabilizers of Protein-Protein Interactions through Imine-Based Tethering.
Authors: Wolter, M. / Valenti, D. / Cossar, P.J. / Levy, L.M. / Hristeva, S. / Genski, T. / Hoffmann, T. / Brunsveld, L. / Tzalis, D. / Ottmann, C.
History
DepositionApr 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Dec 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 protein sigma
P: p65pS45
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1794
Polymers27,9712
Non-polymers2082
Water6,125340
1
A: 14-3-3 protein sigma
P: p65pS45
hetero molecules

A: 14-3-3 protein sigma
P: p65pS45
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3588
Polymers55,9434
Non-polymers4154
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4580 Å2
ΔGint-48 kcal/mol
Surface area23430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.384, 112.219, 62.556
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 26558.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide p65pS45


Mass: 1412.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q04206*PLUS
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-P5N / 1-(4-methylphenyl)imidazole


Mass: 172.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8N2O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.095 M HEPES Na pH 7.1, 27% PEG400, 0.19M Calcium chloride, 5% Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.8→41.77 Å / Num. obs: 26657 / % possible obs: 98.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 11.45 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.04 / Rrim(I) all: 0.076 / Net I/σ(I): 13.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.842.40.249348414500.9140.180.312.690.4
9-41.772.70.01663323210.010.01958.291.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.372
Highest resolutionLowest resolution
Rotation34.43 Å1.9 Å

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QHL

6qhl


Resolution: 1.8→41.769 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 21.18
RfactorNum. reflection% reflectionSelection details
Rfree0.2196 2425 5.04 %RANDOM
Rwork0.1757 ---
obs0.1779 26657 92.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.75 Å2 / Biso mean: 15.9511 Å2 / Biso min: 0.25 Å2
Refinement stepCycle: final / Resolution: 1.8→41.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1892 0 13 340 2245
Biso mean--43.04 25.62 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091971
X-RAY DIFFRACTIONf_angle_d0.8752660
X-RAY DIFFRACTIONf_chiral_restr0.049290
X-RAY DIFFRACTIONf_plane_restr0.005351
X-RAY DIFFRACTIONf_dihedral_angle_d5.351642
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.83650.30221190.241233579
1.8365-1.87640.30711240.2286252688
1.8764-1.92010.21731520.2127267292
1.9201-1.96810.25951480.1918268593
1.9681-2.02130.20511390.1862276295
2.0213-2.08080.2371570.1694279496
2.0808-2.14790.21981400.1713282097
2.1479-2.22470.21481430.1717289798
2.2247-2.31380.21761780.1617277298
2.3138-2.4190.22291270.1676282797
2.419-2.54660.19621510.1793278696
2.5466-2.70610.24231500.1755276995
2.7061-2.9150.26961640.1848270694
2.915-3.20820.24241370.1736267492
3.2082-3.67220.18921260.1581265990
3.6722-4.62570.16941490.1522251487
4.6257-41.7690.2061210.1801250486

+
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