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- PDB-4uuv: Structure of the DNA binding ETS domain of human ETV4 in complex ... -

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Basic information

Entry
Database: PDB / ID: 4uuv
TitleStructure of the DNA binding ETS domain of human ETV4 in complex with DNA
Components
  • (5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3') x 2
  • 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
  • ETS TRANSLOCATION VARIANT 4
KeywordsTRANSCRIPTION
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 / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / chromatin ...positive regulation of keratinocyte differentiation / MAPK6/MAPK4 signaling / sequence-specific double-stranded DNA binding / chromosome / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / chromatin / nucleolus / 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-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
DNA / ETS translocation variant 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNewman, J.A. / Cooper, C.D.O. / Kopec, J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / 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
DepositionJul 31, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Jun 10, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: 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 20, 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: ETS TRANSLOCATION VARIANT 4
B: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
C: 5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3'
D: ETS TRANSLOCATION VARIANT 4
E: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
F: 5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3'
G: ETS TRANSLOCATION VARIANT 4
H: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
I: 5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3'
J: ETS TRANSLOCATION VARIANT 4
K: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
L: 5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3'
M: ETS TRANSLOCATION VARIANT 4
N: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
O: 5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3'
P: ETS TRANSLOCATION VARIANT 4
Q: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
R: 5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3'
S: ETS TRANSLOCATION VARIANT 4
T: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
U: 5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3'
V: ETS TRANSLOCATION VARIANT 4
W: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
X: 5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)142,82124
Polymers142,82124
Non-polymers00
Water00
1
J: ETS TRANSLOCATION VARIANT 4
K: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
L: 5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3'
V: ETS TRANSLOCATION VARIANT 4
W: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
X: 5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)35,7356
Polymers35,7356
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-55.6 kcal/mol
Surface area14160 Å2
MethodPISA
2
D: ETS TRANSLOCATION VARIANT 4
E: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
F: 5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3'
G: ETS TRANSLOCATION VARIANT 4
H: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
I: 5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)35,6956
Polymers35,6956
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-57 kcal/mol
Surface area14190 Å2
MethodPISA
3
M: ETS TRANSLOCATION VARIANT 4
N: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
O: 5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3'
S: ETS TRANSLOCATION VARIANT 4
T: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
U: 5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)35,6956
Polymers35,6956
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-55.6 kcal/mol
Surface area14270 Å2
MethodPISA
4
A: ETS TRANSLOCATION VARIANT 4
B: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
C: 5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3'
P: ETS TRANSLOCATION VARIANT 4
Q: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
R: 5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)35,6956
Polymers35,6956
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-51.4 kcal/mol
Surface area14610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.651, 46.133, 171.150
Angle α, β, γ (deg.)90.00, 96.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
ETS TRANSLOCATION VARIANT 4 / ADENOVIRUS E1A ENHANCER-BINDING PROTEIN / E1A-F / POLYOMAVIRUS


Mass: 11757.564 Da / Num. of mol.: 8 / Fragment: ETS DOMAIN, RESIDUES 338-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P43268
#2: DNA chain
5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'


Mass: 3094.042 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain
5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3'


Mass: 2995.967 Da / Num. of mol.: 7 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: DNA chain 5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3'


Mass: 3035.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
Has protein modificationY
Sequence detailsFIRST 2 RESIDUES REMAIN AFTER CLEAVAGE OF 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: 2.43 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growDetails: 25% PEG3350, 0.2M MG CL, 0.1M BIS TRIS

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Data collection

DiffractionMean temperature: 10 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.8→45.26 Å / Num. obs: 32705 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 80.38 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.8 / % possible all: 92.2

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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 4UNO

4uno


Resolution: 2.8→40.97 Å / SU ML: 0.42 / σ(F): 1.34 / Phase error: 29.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 1534 4.7 %
Rwork0.203 --
obs0.2052 32675 94.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.8 Å2
Refinement stepCycle: LAST / Resolution: 2.8→40.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6249 3103 0 0 9352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039904
X-RAY DIFFRACTIONf_angle_d0.52114035
X-RAY DIFFRACTIONf_dihedral_angle_d21.8133822
X-RAY DIFFRACTIONf_chiral_restr0.0221485
X-RAY DIFFRACTIONf_plane_restr0.0021262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.89050.38141140.33572632X-RAY DIFFRACTION88
2.8905-2.99380.36521270.28882885X-RAY DIFFRACTION99
2.9938-3.11360.33831490.28272932X-RAY DIFFRACTION98
3.1136-3.25530.31531710.25482852X-RAY DIFFRACTION97
3.2553-3.42680.3351440.22392826X-RAY DIFFRACTION96
3.4268-3.64140.33931350.22662839X-RAY DIFFRACTION95
3.6414-3.92230.2641470.22762732X-RAY DIFFRACTION92
3.9223-4.31670.2391280.19492809X-RAY DIFFRACTION94
4.3167-4.94040.22981280.18042797X-RAY DIFFRACTION94
4.9404-6.22090.20421450.1832866X-RAY DIFFRACTION95
6.2209-40.97450.18331460.1652971X-RAY DIFFRACTION94

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