[English] 日本語
Yorodumi
- PDB-3co7: Crystal Structure of FoxO1 DBD Bound to DBE2 DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3co7
TitleCrystal Structure of FoxO1 DBD Bound to DBE2 DNA
Components
  • DNA (5'-D(*DCP*DAP*DAP*DAP*DAP*DTP*DGP*DTP*DAP*DAP*DAP*DCP*DAP*DAP*DGP*DA)-3')
  • DNA (5'-D(*DTP*DCP*DTP*DTP*DGP*DTP*DTP*DTP*DAP*DCP*DAP*DTP*DTP*DTP*DTP*DG)-3')
  • Forkhead box protein O1
KeywordsTranscription/DNA / winged helix / forkhead domain / Chromosomal rearrangement / Cytoplasm / DNA-binding / Nucleus / Phosphoprotein / Proto-oncogene / Transcription / Transcription regulation / Transcription-DNA COMPLEX
Function / homology
Function and homology information


cellular response to hyperoxia / regulation of transcription initiation by RNA polymerase II / AKT-mediated inactivation of FOXO1A / FOXO-mediated transcription of cell cycle genes / AKT phosphorylates targets in the nucleus / positive regulation of smooth muscle cell apoptotic process / neuronal stem cell population maintenance / regulation of neural precursor cell proliferation / response to fatty acid / negative regulation of stress-activated MAPK cascade ...cellular response to hyperoxia / regulation of transcription initiation by RNA polymerase II / AKT-mediated inactivation of FOXO1A / FOXO-mediated transcription of cell cycle genes / AKT phosphorylates targets in the nucleus / positive regulation of smooth muscle cell apoptotic process / neuronal stem cell population maintenance / regulation of neural precursor cell proliferation / response to fatty acid / negative regulation of stress-activated MAPK cascade / Regulation of FOXO transcriptional activity by acetylation / regulation of reactive oxygen species metabolic process / negative regulation of cardiac muscle hypertrophy in response to stress / cellular response to cold / temperature homeostasis / negative regulation of fat cell differentiation / FOXO-mediated transcription of cell death genes / blood vessel development / protein acetylation / fat cell differentiation / Constitutive Signaling by AKT1 E17K in Cancer / intracellular glucose homeostasis / Regulation of gene expression in beta cells / Regulation of localization of FOXO transcription factors / canonical Wnt signaling pathway / negative regulation of insulin secretion / cellular response to nitric oxide / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of autophagy / energy homeostasis / positive regulation of gluconeogenesis / cellular response to starvation / protein phosphatase 2A binding / promoter-specific chromatin binding / negative regulation of canonical Wnt signaling pathway / MAPK6/MAPK4 signaling / chromatin DNA binding / beta-catenin binding / autophagy / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to insulin stimulus / positive regulation of protein catabolic process / insulin receptor signaling pathway / cellular response to oxidative stress / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / sequence-specific DNA binding / nucleic acid binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / chromatin binding / ubiquitin protein ligase binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / FOXO protein, KIX-binding domain / KIX-binding domain of forkhead box O, CR2 / FOXO protein, transactivation domain / Transactivation domain of FOXO protein family / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 ...: / FOXO protein, KIX-binding domain / KIX-binding domain of forkhead box O, CR2 / FOXO protein, transactivation domain / Transactivation domain of FOXO protein family / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Forkhead box protein O1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsBrent, M.M. / Anand, R. / Marmorstein, R.
CitationJournal: Structure / Year: 2008
Title: Structural Basis for DNA Recognition by FoxO1 and Its Regulation by Posttranslational Modification.
Authors: Brent, M.M. / Anand, R. / Marmorstein, R.
History
DepositionMar 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*DTP*DCP*DTP*DTP*DGP*DTP*DTP*DTP*DAP*DCP*DAP*DTP*DTP*DTP*DTP*DG)-3')
B: DNA (5'-D(*DCP*DAP*DAP*DAP*DAP*DTP*DGP*DTP*DAP*DAP*DAP*DCP*DAP*DAP*DGP*DA)-3')
D: DNA (5'-D(*DTP*DCP*DTP*DTP*DGP*DTP*DTP*DTP*DAP*DCP*DAP*DTP*DTP*DTP*DTP*DG)-3')
E: DNA (5'-D(*DCP*DAP*DAP*DAP*DAP*DTP*DGP*DTP*DAP*DAP*DAP*DCP*DAP*DAP*DGP*DA)-3')
C: Forkhead box protein O1
F: Forkhead box protein O1


Theoretical massNumber of molelcules
Total (without water)45,8926
Polymers45,8926
Non-polymers00
Water724
1
A: DNA (5'-D(*DTP*DCP*DTP*DTP*DGP*DTP*DTP*DTP*DAP*DCP*DAP*DTP*DTP*DTP*DTP*DG)-3')
B: DNA (5'-D(*DCP*DAP*DAP*DAP*DAP*DTP*DGP*DTP*DAP*DAP*DAP*DCP*DAP*DAP*DGP*DA)-3')
C: Forkhead box protein O1


Theoretical massNumber of molelcules
Total (without water)22,9463
Polymers22,9463
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-25.4 kcal/mol
Surface area9580 Å2
MethodPISA
2
D: DNA (5'-D(*DTP*DCP*DTP*DTP*DGP*DTP*DTP*DTP*DAP*DCP*DAP*DTP*DTP*DTP*DTP*DG)-3')
E: DNA (5'-D(*DCP*DAP*DAP*DAP*DAP*DTP*DGP*DTP*DAP*DAP*DAP*DCP*DAP*DAP*DGP*DA)-3')
F: Forkhead box protein O1


Theoretical massNumber of molelcules
Total (without water)22,9463
Polymers22,9463
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-25.5 kcal/mol
Surface area9580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.641, 99.641, 98.468
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain C,F, using restrain
22chain A,D, using restrain
33chain B,E, using restrain

NCS ensembles :
ID
1
2
3

-
Components

#1: DNA chain DNA (5'-D(*DTP*DCP*DTP*DTP*DGP*DTP*DTP*DTP*DAP*DCP*DAP*DTP*DTP*DTP*DTP*DG)-3')


Mass: 4860.159 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*DCP*DAP*DAP*DAP*DAP*DTP*DGP*DTP*DAP*DAP*DAP*DCP*DAP*DAP*DGP*DA)-3')


Mass: 4932.272 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein Forkhead box protein O1 / / Forkhead box protein O1A / Forkhead in rhabdomyosarcoma


Mass: 13153.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXO1, FKHR, FOXO1A / Production host: Escherichia coli (E. coli) / References: UniProt: Q12778
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 21% PEG 4000, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2PEG 400012

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 6, 2007
RadiationMonochromator: Cryo-Cooled Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 59464 / Num. obs: 58591 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.088 / Χ2: 1.058 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.7-2.84.20.66558621.0499.9
2.8-2.914.20.49558661.07399.8
2.91-3.044.30.32458231.08899.8
3.04-3.24.30.16258781.05399.6
3.2-3.44.30.10858251.07199.8
3.4-3.664.30.159051.03999.9
3.66-4.034.30.09358541.07299.9
4.03-4.614.30.08359341.045100
4.61-5.84.30.07459131.03499.8
5.8-304.30.06957311.06297

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→30 Å / FOM work R set: 0.754 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.276 4503 9.4 %
Rwork0.267 --
all-46290 -
obs-46237 96.5 %
Solvent computationBsol: 48.743 Å2
Displacement parametersBiso mean: 68.977 Å2
Baniso -1Baniso -2Baniso -3
1-11.492 Å20 Å20 Å2
2--11.492 Å20 Å2
3----22.984 Å2
Refinement stepCycle: LAST / Resolution: 2.91→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 1300 0 4 2656
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.0991.5
X-RAY DIFFRACTIONc_scbond_it2.0592
X-RAY DIFFRACTIONc_mcangle_it1.9152
X-RAY DIFFRACTIONc_scangle_it3.4362.5
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDRmsTypeWeight
11FX-RAY DIFFRACTION0.025restrain70
22DX-RAY DIFFRACTION0.021restrain70
33EX-RAY DIFFRACTION0.021restrain70
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param

+
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