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- PDB-3zp5: Crystal structure of the DNA binding ETS domain of the human prot... -

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Basic information

Entry
Database: PDB / ID: 3zp5
TitleCrystal structure of the DNA binding ETS domain of the human protein FEV in complex with DNA
Components
  • 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
  • 5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP)-3'
  • PROTEIN FEV
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


neuron fate specification / neuron maturation / maternal behavior / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of gene expression ...neuron fate specification / neuron maturation / maternal behavior / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / chromatin / nucleus
Similarity search - Function
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 ...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
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNewman, J.A. / Cooper, C.D.O. / Krojer, T. / Shrestha, L. / Allerston, C.K. / Vollmar, M. / Arrowsmith, C.H. / Burgess-Brown, N. / Edwards, A. / von Delft, F. / Gileadi, O.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structures of the Ets Domains of Transcription Factors Etv1, Etv4, Etv5 and Fev: Determinants of DNA Binding and Redox Regulation by Disulfide Bond Formation.
Authors: Cooper, C.D.O. / Newman, J.A. / Aitkenhead, H. / Allerston, C.K. / Gileadi, O.
History
DepositionFeb 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Jun 10, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN FEV
C: 5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP)-3'
G: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'


Theoretical massNumber of molelcules
Total (without water)17,9033
Polymers17,9033
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-17.5 kcal/mol
Surface area7610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.224, 64.554, 110.214
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PROTEIN FEV / FIFTH EWING VARIANT PROTEIN / PC12 ETS DOMAIN-CONTAINING TRANSCRIPTION FACTOR 1 / PC12 ETS FACTOR 1 / PET-1


Mass: 11813.431 Da / Num. of mol.: 1 / Fragment: ETS DOMAIN, RESIDUES 42-141
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q99581
#2: DNA chain 5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP)-3'


Mass: 2995.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'


Mass: 3094.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsFIRST TWO RESIDUES ARE FROM PURIFICATION TAG

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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: 2.4 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growDetails: 25% PEG 3350, 0.1M BIS TRIS PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→110 Å / Num. obs: 12431 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 38.52 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 23.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YPR

2ypr


Resolution: 2→30.976 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 31.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2539 598 4.8 %
Rwork0.2097 --
obs0.2118 12387 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.75 Å2
Refinement stepCycle: LAST / Resolution: 2→30.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms745 404 0 36 1185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021235
X-RAY DIFFRACTIONf_angle_d0.6961748
X-RAY DIFFRACTIONf_dihedral_angle_d21.76482
X-RAY DIFFRACTIONf_chiral_restr0.035179
X-RAY DIFFRACTIONf_plane_restr0.001156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.20140.33341530.29272895X-RAY DIFFRACTION100
2.2014-2.51980.28691490.26182927X-RAY DIFFRACTION100
2.5198-3.17420.29351440.24482957X-RAY DIFFRACTION100
3.1742-30.97970.22071520.17593010X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -11.1284 Å / Origin y: -7.6218 Å / Origin z: -15.7403 Å
111213212223313233
T0.5068 Å20.0268 Å2-0.0308 Å2-0.374 Å2-0.1032 Å2--0.3625 Å2
L3.7419 °2-0.7152 °2-3.8808 °2-2.3349 °21.9128 °2--9.2899 °2
S0.2216 Å °0.47 Å °-0.2159 Å °0.112 Å °-0.6011 Å °0.2148 Å °-0.5889 Å °-1.0711 Å °0.2112 Å °
Refinement TLS groupSelection details: ALL

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