[English] 日本語
Yorodumi
- PDB-4lg0: Structure of a ternary FOXO1-ETS1 DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lg0
TitleStructure of a ternary FOXO1-ETS1 DNA complex
Components
  • DNA (5'-D(*DAP*DAP*DAP*DCP*DAP*DAP*DTP*DAP*DAP*DCP*DAP*DGP*DGP*DAP*DAP*DAP*DCP*DCP*DGP*DTP*DG)-3')
  • DNA (5'-D(*DTP*DTP*DCP*DAP*DCP*DGP*DGP*DTP*DTP*DTP*DCP*DCP*DTP*DGP*DTP*DTP*DAP*DTP*DTP*DGP*DT)-3')
  • Forkhead box protein O1
  • Protein C-ets-1
KeywordsTRANSCRIPTION/DNA / DEOXYRIBONUCLEIC ACID / COMPLEX (DNA-BINDING PROTEIN-DNA) / PHOSPHOPROTEIN / PROTO-ONCOGENE / TRANSCRIPTION-DNA COMPLEX / WINGED HELIX / FORKHEAD DOMAIN / ETS BINDING DOMAIN / HELIX-TURN-HELIX / TRANSCRIPTION / TRANSCRIPTION REGULATION / DNA-BINDING / PHOSPHORYLATION / NUCLEUS
Function / homology
Function and homology information


cellular response to hyperoxia / regulation of transcription initiation by RNA polymerase II / AKT-mediated inactivation of FOXO1A / PML body organization / 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 ...cellular response to hyperoxia / regulation of transcription initiation by RNA polymerase II / AKT-mediated inactivation of FOXO1A / PML body organization / 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 / positive regulation of leukocyte adhesion to vascular endothelial cell / temperature homeostasis / negative regulation of fat cell differentiation / FOXO-mediated transcription of cell death genes / protein acetylation / blood vessel development / 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 / negative regulation of cell cycle / canonical Wnt signaling pathway / negative regulation of insulin secretion / cellular response to nitric oxide / positive regulation of blood vessel endothelial cell migration / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / regulation of angiogenesis / positive regulation of autophagy / energy homeostasis / positive regulation of gluconeogenesis / cellular response to starvation / positive regulation of endothelial cell migration / transcription corepressor binding / nuclear receptor coactivator activity / positive regulation of erythrocyte differentiation / protein phosphatase 2A binding / cell motility / promoter-specific chromatin binding / negative regulation of canonical Wnt signaling pathway / MAPK6/MAPK4 signaling / Oncogene Induced Senescence / chromatin DNA binding / beta-catenin binding / autophagy / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of inflammatory response / positive regulation of miRNA transcription / cellular response to insulin stimulus / positive regulation of protein catabolic process / positive regulation of angiogenesis / insulin receptor signaling pathway / gene expression / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / Interleukin-4 and Interleukin-13 signaling / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / nucleic acid binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / immune response / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / response to antibiotic / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / chromatin binding / ubiquitin protein ligase binding / chromatin / positive regulation of gene expression / 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 / DNA binding / nucleoplasm / identical protein binding / 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 / Protein C-ets-1, pointed domain / Transforming protein C-ets / Ets1, N-terminal flanking region of Ets domain / Ets1 N-terminal flanking region of Ets domain / Fork head domain ...: / FOXO protein, KIX-binding domain / KIX-binding domain of forkhead box O, CR2 / FOXO protein, transactivation domain / Transactivation domain of FOXO protein family / Protein C-ets-1, pointed domain / Transforming protein C-ets / Ets1, N-terminal flanking region of Ets domain / Ets1 N-terminal flanking region of Ets domain / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily / 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) / Protein C-ets-1 / Forkhead box protein O1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.19 Å
AuthorsBirrane, G. / Choy, W.C. / Datta, D. / Geiger, C.A. / Grant, M.A.
CitationJournal: To be Published
Title: Structure of a ternary FOXO1-ETS1 DNA complex
Authors: Birrane, G. / Choy, W.C. / Datta, D. / Geiger, C.A. / Grant, M.A.
History
DepositionJun 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Forkhead box protein O1
B: Protein C-ets-1
C: DNA (5'-D(*DTP*DTP*DCP*DAP*DCP*DGP*DGP*DTP*DTP*DTP*DCP*DCP*DTP*DGP*DTP*DTP*DAP*DTP*DTP*DGP*DT)-3')
D: DNA (5'-D(*DAP*DAP*DAP*DCP*DAP*DAP*DTP*DAP*DAP*DCP*DAP*DGP*DGP*DAP*DAP*DAP*DCP*DCP*DGP*DTP*DG)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0806
Polymers40,8464
Non-polymers2342
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-48 kcal/mol
Surface area16410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.658, 114.944, 136.325
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein , 2 types, 2 molecules AB

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


Mass: 14788.608 Da / Num. of mol.: 1 / Fragment: DNA Binding Domain, UNP residues 143-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKHR, FOXO1, FOXO1A / Plasmid: pET-50b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12778
#2: Protein Protein C-ets-1 / p54


Mass: 13174.081 Da / Num. of mol.: 1 / Fragment: DNA binding domain, UNP residues 331-440
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C-ets-1, ETS1, EWSR2 / Plasmid: pET-19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14921

-
DNA chain , 2 types, 2 molecules CD

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


Mass: 6401.128 Da / Num. of mol.: 1 / Fragment: FOX-ETS site from ve-Cadherin / Source method: obtained synthetically / Details: This sequence occurs naturally in humans.
#4: DNA chain DNA (5'-D(*DAP*DAP*DAP*DCP*DAP*DAP*DTP*DAP*DAP*DCP*DAP*DGP*DGP*DAP*DAP*DAP*DCP*DCP*DGP*DTP*DG)-3')


Mass: 6482.253 Da / Num. of mol.: 1 / Fragment: FOX-ETS site from ve-Cadherin / Source method: obtained synthetically / Details: This sequence occurs naturally in humans.

-
Non-polymers , 3 types, 72 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 3.29 Å3/Da / Density % sol: 62.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 400, 0.05M 2-Amino-2-hydroxymethyl-propane-1,3-diol, 0.1M potassium chloride, 0.01M magnesium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075,0.9793,0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2012
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0751
20.97931
30.9791
ReflectionResolution: 2.19→100 Å / Num. all: 27722 / Num. obs: 27722 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 49.7 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.11 / Net I/σ(I): 24.1
Reflection shellResolution: 2.2→2.28 Å / % possible all: 95.4

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.8.0047refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.19→43.938 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.927 / SU B: 12.355 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1407 5.2 %RANDOM
Rwork0.19445 ---
all0.1968 25814 --
obs0.1968 25814 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å2-0 Å20 Å2
2---3.85 Å20 Å2
3---5.54 Å2
Refinement stepCycle: LAST / Resolution: 2.19→43.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1609 855 14 70 2548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0162695
X-RAY DIFFRACTIONr_bond_other_d0.0010.022106
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.6463812
X-RAY DIFFRACTIONr_angle_other_deg1.07934891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5025204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70223.41582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53515311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1521512
X-RAY DIFFRACTIONr_chiral_restr0.090.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022432
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02623
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6285.282819
X-RAY DIFFRACTIONr_mcbond_other4.6265.273818
X-RAY DIFFRACTIONr_mcangle_it6.7327.8741022
X-RAY DIFFRACTIONr_mcangle_other6.7297.8861023
X-RAY DIFFRACTIONr_scbond_it4.4144.9881876
X-RAY DIFFRACTIONr_scbond_other4.4144.9871876
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5897.3762791
X-RAY DIFFRACTIONr_long_range_B_refined10.12740.9353337
X-RAY DIFFRACTIONr_long_range_B_other10.12540.9543338
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.194→2.251 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 76 -
Rwork0.306 1460 -
obs--74.89 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.29990.101-0.02060.3195-0.9493.9836-0.1278-0.3204-0.0605-0.16770.2017-0.01660.1658-0.7185-0.07390.21070.03950.03830.64930.04210.109332.76423.22718.297
22.53321.15740.07271.80940.09510.7639-0.12390.0255-0.0808-0.0554-0.1045-0.2970.09580.27650.22840.02870.09320.04630.50050.10630.276469.5724.9612.231
31.6654-1.01660.25311.03650.41660.88190.04540.1004-0.05250.0398-0.1233-0.00470.1366-0.02610.07780.08960.14680.06520.34470.07170.317654.14316.75815.344
42.1521-0.0486-1.32570.0626-0.10431.4295-0.04660.1913-0.18350.0515-0.16570.0626-0.17440.2840.21230.25130.03890.05660.48340.0220.305650.94521.55815.203
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A156 - 244
2X-RAY DIFFRACTION2B333 - 438
3X-RAY DIFFRACTION3C1 - 21
4X-RAY DIFFRACTION4D1 - 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