[English] 日本語
Yorodumi
- PDB-8anc: 14-3-3 sigma sirtuin-3 phospho-peptide complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8anc
Title14-3-3 sigma sirtuin-3 phospho-peptide complex
Components
  • 14-3-3 protein sigma
  • NAD-dependent protein deacetylase sirtuin-3, mitochondrial
KeywordsPEPTIDE BINDING PROTEIN / Human sirtuin / human 14-3-3 sigma / protein complex / phospho-peptide / NAD / deacetylase
Function / homology
Function and homology information


positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / peptidyl-lysine deacetylation / positive regulation of superoxide dismutase activity / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / protein deacetylation / Regulation of FOXO transcriptional activity by acetylation / regulation of epidermal cell division ...positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / peptidyl-lysine deacetylation / positive regulation of superoxide dismutase activity / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / protein deacetylation / Regulation of FOXO transcriptional activity by acetylation / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / NAD+ binding / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of reactive oxygen species metabolic process / negative regulation of keratinocyte proliferation / establishment of skin barrier / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / aerobic respiration / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / protein export from nucleus / negative regulation of innate immune response / 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 / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Transcriptional activation of mitochondrial biogenesis / negative regulation of ERK1 and ERK2 cascade / positive regulation of insulin secretion / intrinsic apoptotic signaling pathway in response to DNA damage / transferase activity / positive regulation of cell growth / sequence-specific DNA binding / regulation of cell cycle / mitochondrial matrix / cadherin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / 14-3-3 protein sigma / DHS-like NAD/FAD-binding domain superfamily / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. ...Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / 14-3-3 protein sigma / DHS-like NAD/FAD-binding 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 sigma / NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.11 Å
AuthorsWeyand, M. / Steegborn, C. / Debbert, L.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)DFG STE-1701/15 Germany
CitationJournal: To Be Published
Title: 14-3-3 sigma sirtuin-3 phospho-peptide complex
Authors: Weyand, M. / Steegborn, C.
History
DepositionAug 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 protein sigma
P: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9668
Polymers27,7772
Non-polymers1896
Water7,206400
1
A: 14-3-3 protein sigma
P: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules

A: 14-3-3 protein sigma
P: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,93116
Polymers55,5544
Non-polymers37712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5530 Å2
ΔGint-104 kcal/mol
Surface area23760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.600, 112.390, 62.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-302-

MG

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AP

#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 BL21 (bacteria) / References: UniProt: P31947
#2: Protein/peptide NAD-dependent protein deacetylase sirtuin-3, mitochondrial / hSIRT3 / Regulatory protein SIR2 homolog 3 / SIR2-like protein 3 / Sirtuin-3


Mass: 1218.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9NTG7, protein acetyllysine N-acetyltransferase

-
Non-polymers , 4 types, 406 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#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.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes/NaOH pH 7.5, 0.2 M CaCl2, 26% (v/v) PEG 400, 5% (v/v) glycerol, 1 mM TCEP

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.11→45.68 Å / Num. obs: 111528 / % possible obs: 97.6 % / Redundancy: 3.504 % / Biso Wilson estimate: 12.932 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.061 / Χ2: 0.937 / Net I/σ(I): 13.19 / Num. measured all: 390760 / Scaling rejects: 33
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
1.11-1.142.7780.6361.7519502840670200.6330.7883.5
1.14-1.173.2810.4632.5125607815478040.7950.55395.7
1.17-1.213.1470.3972.8124068794976490.8290.47796.2
1.21-1.243.4520.3383.4825845767674880.8760.39997.6
1.24-1.283.4820.2914.0525720753473870.9030.34398
1.28-1.333.4740.2384.9524896723071670.930.2899.1
1.33-1.383.380.25.6923610701769860.9460.23899.6
1.38-1.443.620.1766.7224162670766750.960.20699.5
1.44-1.53.7660.139.124375649264720.980.15199.7
1.5-1.573.7480.10211.2523037617261460.9880.11999.6
1.57-1.663.6360.08413.1621416591058900.990.09899.7
1.66-1.763.4950.06715.4719496559555790.9930.07999.7
1.76-1.883.8780.05819.2320299525452350.9960.06799.6
1.88-2.033.8230.04524.0718732491449000.9970.05399.7
2.03-2.223.740.03530.116821451744980.9980.0499.6
2.22-2.493.4490.0333.4614093411540860.9980.03699.3
2.49-2.873.8440.02838.8413951363536290.9990.03399.8
2.87-3.523.7740.02644.411688311330970.9990.0399.5
3.52-4.973.4130.02346.598283244024270.9990.02799.5
4.97-45.683.7040.02548.085159140713930.9990.02999

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YWT

1ywt


Resolution: 1.11→45.68 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.855 / SU ML: 0.018 / SU R Cruickshank DPI: 0.0289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1456 5111 5.1 %RANDOM
Rwork0.1269 ---
obs0.1278 95338 87.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 242.89 Å2 / Biso mean: 13.818 Å2 / Biso min: 5.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0 Å20 Å2
2---0.62 Å2-0 Å2
3---1.11 Å2
Refinement stepCycle: final / Resolution: 1.11→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 6 405 2304
Biso mean--21.53 32.9 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0122324
X-RAY DIFFRACTIONr_bond_other_d0.0270.0162165
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.6463211
X-RAY DIFFRACTIONr_angle_other_deg1.1461.5545127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7345348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.3691019
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91910453
X-RAY DIFFRACTIONr_chiral_restr0.0960.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022789
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02463
X-RAY DIFFRACTIONr_rigid_bond_restr16.64634489
LS refinement shellResolution: 1.112→1.141 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 171 -
Rwork0.35 3189 -
all-3360 -
obs--39.96 %

+
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