[English] 日本語
Yorodumi
- PDB-5dui: Identification of a new FoxO1 binding site that precludes CREB bi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dui
TitleIdentification of a new FoxO1 binding site that precludes CREB binding at the glucose-6-phosphatase catalytic subunit gene promoter
Components
  • DNA (5'-D(*AP*TP*GP*AP*TP*TP*TP*AP*CP*GP*TP*AP*AP*AP*AP*TP*AP*GP*AP*AP*A)-3')
  • DNA (5'-D(*TP*TP*TP*TP*CP*TP*AP*TP*TP*TP*TP*AP*CP*GP*TP*AP*AP*AP*TP*CP*A)-3')
  • Forkhead box protein O1
KeywordsTRANSCRIPTION/dna / transcription factor / winged helix / DNA binding / protein-DNA complex / diabetes / 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 / response to fatty acid / cellular response to cold / negative regulation of stress-activated MAPK cascade / protein acetylation ...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 / response to fatty acid / cellular response to cold / negative regulation of stress-activated MAPK cascade / protein acetylation / Regulation of FOXO transcriptional activity by acetylation / negative regulation of fat cell differentiation / negative regulation of cardiac muscle hypertrophy in response to stress / FOXO-mediated transcription of cell death genes / temperature homeostasis / Constitutive Signaling by AKT1 E17K in Cancer / energy homeostasis / Regulation of gene expression in beta cells / Regulation of localization of FOXO transcription factors / negative regulation of insulin secretion / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / fat cell differentiation / positive regulation of gluconeogenesis / cellular response to nitric oxide / positive regulation of autophagy / protein phosphatase 2A binding / intracellular glucose homeostasis / cellular response to starvation / promoter-specific chromatin binding / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / beta-catenin binding / MAPK6/MAPK4 signaling / insulin receptor signaling pathway / positive regulation of protein catabolic process / cellular response to insulin stimulus / Interleukin-4 and Interleukin-13 signaling / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nucleic acid binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of apoptotic process / apoptotic process / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin binding / regulation of transcription by RNA polymerase II / DNA damage response / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / chromatin / 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: 2.306 Å
AuthorsSingh, P. / Endrizzi, J.A. / Chi, Y.-I.
CitationJournal: J. Struct. Biol. / Year: 2017
Title: Crystal structures reveal a new and novel FoxO1 binding site within the human glucose-6-phosphatase catalytic subunit 1 gene promoter.
Authors: Singh, P. / Han, E.H. / Endrizzi, J.A. / O'Brien, R.M. / Chi, Y.I.
History
DepositionSep 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: 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: Forkhead box protein O1
B: Forkhead box protein O1
C: DNA (5'-D(*TP*TP*TP*TP*CP*TP*AP*TP*TP*TP*TP*AP*CP*GP*TP*AP*AP*AP*TP*CP*A)-3')
D: DNA (5'-D(*AP*TP*GP*AP*TP*TP*TP*AP*CP*GP*TP*AP*AP*AP*AP*TP*AP*GP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)37,7714
Polymers37,7714
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-33 kcal/mol
Surface area16610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.610, 79.026, 48.266
Angle α, β, γ (deg.)90.000, 90.790, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Forkhead box protein O1 / Forkhead box protein O1A / Forkhead in rhabdomyosarcoma


Mass: 12445.928 Da / Num. of mol.: 2 / Fragment: unp residues 151-259
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
#2: DNA chain DNA (5'-D(*TP*TP*TP*TP*CP*TP*AP*TP*TP*TP*TP*AP*CP*GP*TP*AP*AP*AP*TP*CP*A)-3')


Mass: 6377.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*AP*TP*GP*AP*TP*TP*TP*AP*CP*GP*TP*AP*AP*AP*AP*TP*AP*GP*AP*AP*A)-3')


Mass: 6502.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 14-18% PEG 8000 0.1M Ammonium sulfate 20mM Magnesium chloride 50mM MES pH 5.6 10% glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 14596 / % possible obs: 94.5 % / Redundancy: 4.5 % / Biso Wilson estimate: 41.13 Å2 / Rmerge(I) obs: 0.08 / Χ2: 1.007 / Net I/av σ(I): 16.574 / Net I/σ(I): 22.2 / Num. measured all: 65246
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.342.60.4656620.81785.5
2.34-2.382.70.4256550.7887.4
2.38-2.432.80.416830.81989.9
2.43-2.482.90.4047150.85591.9
2.48-2.533.20.3347300.84593.6
2.53-2.593.40.2927160.87694
2.59-2.663.50.2777140.93293.8
2.66-2.733.80.2297270.94194.7
2.73-2.813.90.1987411.01896
2.81-2.94.10.177371.00496.6
2.9-34.50.1427470.95497
3-3.124.80.1297581.1397.9
3.12-3.2650.1087341.05295
3.26-3.445.40.0937371.03896.2
3.44-3.655.70.0857641.0897.4
3.65-3.9360.0897561.24198.4
3.93-4.336.20.0867641.24798.1
4.33-4.956.10.0767621.05898.8
4.95-6.246.20.0697720.93299
6.24-505.80.0677220.77988.7

-
Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CO6

3co6


Resolution: 2.306→40.144 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 28.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2452 605 4.96 %
Rwork0.2083 11586 -
obs0.2102 12191 78.68 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.576 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso max: 189.95 Å2 / Biso mean: 69.4285 Å2 / Biso min: 23.49 Å2
Baniso -1Baniso -2Baniso -3
1-1.9587 Å20 Å2-3.9023 Å2
2---1.4792 Å20 Å2
3----0.4796 Å2
Refinement stepCycle: final / Resolution: 2.306→40.144 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1368 855 0 51 2274
Biso mean---45.24 -
Num. residues----213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022360
X-RAY DIFFRACTIONf_angle_d0.7583362
X-RAY DIFFRACTIONf_chiral_restr0.045359
X-RAY DIFFRACTIONf_plane_restr0.001276
X-RAY DIFFRACTIONf_dihedral_angle_d21.452923
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3061-2.53820.2849650.25911448151339
2.5382-2.90540.35331500.2783009315982
2.9054-3.66010.25931900.21743537372796
3.6601-40.15040.21162000.1823592379297
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2232-0.03680.47477.95951.00474.92150.0483-0.1826-0.12520.40480.1915-0.70970.46510.4976-0.16620.34470.10670.18530.07890.02190.5235-9.255-14.2928.101
23.8506-2.2481-0.18776.67480.04741.8956-0.1012-0.44620.46470.44850.1193-0.3328-0.15970.1019-0.06530.5141-0.01090.28020.1694-0.12340.455626.75115.14-9.566
32.3423-0.3231-2.7130.04810.3893.2017-0.0633-0.18180.0649-0.24420.0194-0.16090.12390.5239-0.10920.4767-0.05850.56240.4223-0.10160.56496.5390.3916.869
45.97550.6318-4.32420.063-0.46323.1756-0.1736-0.0691-0.0788-0.24480.1311-0.26260.22750.47170.30590.6546-0.03220.54370.4634-0.05580.72774.4950.4318.655
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 160:245 )A160 - 245
2X-RAY DIFFRACTION2( CHAIN B AND RESID 161:245 )B161 - 245
3X-RAY DIFFRACTION3( CHAIN C AND RESID 1:21 )C1 - 21
4X-RAY DIFFRACTION4( CHAIN D AND RESID 1:21 )D1 - 21

+
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