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- PDB-5ils: Autoinhibited ETV1 -

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Basic information

Entry
Database: PDB / ID: 5ils
TitleAutoinhibited ETV1
ComponentsETS translocation variant 1
KeywordsDNA BINDING PROTEIN / ETV1 / ETS / transcription factor / autoinhibition transcription / DNA binding
Function / homology
Function and homology information


peripheral nervous system neuron development / mechanosensory behavior / muscle organ development / axon guidance / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...peripheral nervous system neuron development / mechanosensory behavior / muscle organ development / axon guidance / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / 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-domain signature 2. / Ets domain / ETS family / 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-domain signature 2. / Ets domain / ETS family / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.399 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
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ETS translocation variant 1


Theoretical massNumber of molelcules
Total (without water)11,9961
Polymers11,9961
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6750 Å2
2
A: ETS translocation variant 1

A: ETS translocation variant 1


Theoretical massNumber of molelcules
Total (without water)23,9922
Polymers23,9922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area2190 Å2
ΔGint-27 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.186, 50.186, 69.332
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein ETS translocation variant 1 / Ets-related protein 81


Mass: 11995.808 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETV1, ER81 / Production host: Escherichia coli (E. coli) / References: UniProt: P50549
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 5000 MME, 200 mM (NH4)2SO4, 100 mM MES

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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: Feb 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.399→55 Å / Num. obs: 20493 / % possible obs: 100 % / Redundancy: 34.4 % / Biso Wilson estimate: 12.19 Å2 / Rmerge(I) obs: 0.104 / Net I/av σ(I): 39.333 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
1.4-1.4525.51100
1.45-1.5132.811000.969
1.51-1.5834.611000.681
1.58-1.6634.811000.465
1.66-1.7634.811000.352
1.76-1.934.811000.237
1.9-2.0934.711000.137
2.09-2.3934.611000.094
2.39-3.0233.611000.074
3.02-5543.311000.063

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.96 Å36.82 Å
Translation2.96 Å36.82 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.399→27.101 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.36
RfactorNum. reflection% reflectionSelection details
Rfree0.1783 967 4.73 %Random selection
Rwork0.1567 ---
obs0.1577 20457 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.37 Å2 / Biso mean: 17.8159 Å2 / Biso min: 6.98 Å2
Refinement stepCycle: final / Resolution: 1.399→27.101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms845 0 0 114 959
Biso mean---32.22 -
Num. residues----101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006918
X-RAY DIFFRACTIONf_angle_d1.1751247
X-RAY DIFFRACTIONf_chiral_restr0.1123
X-RAY DIFFRACTIONf_plane_restr0.005164
X-RAY DIFFRACTIONf_dihedral_angle_d11.958353
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.3992-1.4730.23721390.216627252864
1.473-1.56520.21151350.172327332868
1.5652-1.68610.17881450.153427572902
1.6861-1.85570.17281250.148827642889
1.8557-2.12410.18311380.151827662904
2.1241-2.67580.16481390.154628142953
2.6758-27.10620.17251460.152429313077
Refinement TLS params.Method: refined / Origin x: -13.3181 Å / Origin y: 18.1221 Å / Origin z: -11.131 Å
111213212223313233
T0.0667 Å2-0.0048 Å2-0.0024 Å2-0.0879 Å20.0005 Å2--0.0797 Å2
L0.3222 °20.0671 °2-0.1343 °2-0.2002 °20.1321 °2--0.2428 °2
S-0.0062 Å °-0.0449 Å °0.0019 Å °0.0027 Å °0.0023 Å °0.0155 Å °0.0359 Å °-0.0003 Å °0.0002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA334 - 434
2X-RAY DIFFRACTION1allS435 - 548

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