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- PDB-5ilu: Autoinhibited ETV4 -

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Basic information

Entry
Database: PDB / ID: 5ilu
TitleAutoinhibited ETV4
ComponentsETS translocation variant 4
KeywordsDNA BINDING PROTEIN / ETV4 / ETS / transcription factor / autoinhibition transcription / DNA binding
Function / homology
Function and homology information


positive regulation of keratinocyte differentiation / MAPK6/MAPK4 signaling / sequence-specific double-stranded DNA binding / chromosome / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / nucleolus / regulation of transcription by RNA polymerase II ...positive regulation of keratinocyte differentiation / MAPK6/MAPK4 signaling / sequence-specific double-stranded DNA binding / chromosome / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
PEA3-type ETS-domain transcription factor, N-terminal / PEA3 subfamily ETS-domain transcription factor N terminal domain / Ets-domain signature 1. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...PEA3-type ETS-domain transcription factor, N-terminal / PEA3 subfamily ETS-domain transcription factor N terminal domain / Ets-domain signature 1. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / 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
ETS translocation variant 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.101 Å
AuthorsWhitby, F.G. / Currie, S.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM38663 United States
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structured and disordered regions cooperatively mediate DNA-binding autoinhibition of ETS factors ETV1, ETV4 and ETV5.
Authors: Currie, S.L. / Lau, D.K.W. / Doane, J.J. / Whitby, F.G. / Okon, M. / McIntosh, L.P. / Graves, B.J.
History
DepositionMar 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ETS translocation variant 4


Theoretical massNumber of molelcules
Total (without water)11,4491
Polymers11,4491
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6270 Å2
2
A: ETS translocation variant 4

A: ETS translocation variant 4


Theoretical massNumber of molelcules
Total (without water)22,8982
Polymers22,8982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area1610 Å2
ΔGint-22 kcal/mol
Surface area10930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.866, 50.866, 68.621
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-563-

HOH

21A-605-

HOH

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Components

#1: Protein ETS translocation variant 4 / Adenovirus E1A enhancer-binding protein / E1A-F / Polyomavirus enhancer activator 3 homolog / Protein PEA3


Mass: 11449.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETV4, E1AF, PEA3 / Production host: Escherichia coli (E. coli) / References: UniProt: P43268
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.3 / Details: 1000 mM (NH4)2HPO4, 100 mM C2H3NaO2, pH 4.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 42215 / % possible obs: 100 % / Redundancy: 37.4 % / Biso Wilson estimate: 10.34 Å2 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.02 / Rrim(I) all: 0.099 / Χ2: 1.024 / Net I/av σ(I): 29.167 / Net I/σ(I): 5.9 / Num. measured all: 1577832
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
1.1-1.1415.61100
1.14-1.1824.41100
1.18-1.2433.71100
1.24-1.339.91100
1.3-1.3941.711000.924
1.39-1.4941.911000.596
1.49-1.6441.911000.349
1.64-1.8841.811000.192
1.88-2.3740.1199.90.097
2.37-5051.611000.06

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.101→44.051 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.62
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 1988 4.72 %Random selection
Rwork0.1729 ---
obs0.1739 42111 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.05 Å2 / Biso mean: 17.0204 Å2 / Biso min: 7.39 Å2
Refinement stepCycle: final / Resolution: 1.101→44.051 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms808 0 0 125 933
Biso mean---31.85 -
Num. residues----97
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005922
X-RAY DIFFRACTIONf_angle_d0.8231261
X-RAY DIFFRACTIONf_chiral_restr0.083126
X-RAY DIFFRACTIONf_plane_restr0.005169
X-RAY DIFFRACTIONf_dihedral_angle_d13.081353
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1006-1.12820.40021380.35862801293998
1.1282-1.15870.31881420.299628232965100
1.1587-1.19280.28071430.274927922935100
1.1928-1.23130.23761390.25528372976100
1.2313-1.27530.30711420.224328492991100
1.2753-1.32630.21941400.194828092949100
1.3263-1.38670.20571420.17628442986100
1.3867-1.45980.18351430.16628633006100
1.4598-1.55130.15781420.157528803022100
1.5513-1.67110.17311400.152328633003100
1.6711-1.83920.17291360.150828763012100
1.8392-2.10540.16121420.151229103052100
2.1054-2.65250.18031450.160829263071100
2.6525-44.08660.18641540.159130503204100
Refinement TLS params.Method: refined / Origin x: -13.2417 Å / Origin y: 17.834 Å / Origin z: -9.954 Å
111213212223313233
T0.0768 Å2-0.0022 Å2-0.0007 Å2-0.0839 Å20.0077 Å2--0.0911 Å2
L0.9669 °20.0963 °2-0.0571 °2-0.4661 °20.3444 °2--1.2184 °2
S-0.0104 Å °-0.06 Å °-0.033 Å °0.0222 Å °-0.0016 Å °0.0164 Å °0.0747 Å °0.0095 Å °0.0132 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA340 - 436
2X-RAY DIFFRACTION1allS437 - 575

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