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- PDB-4co8: Structure of the DNA binding ETS domain of human ETV4 -

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Basic information

Entry
Database: PDB / ID: 4co8
TitleStructure of the DNA binding ETS domain of human ETV4
ComponentsETS 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / 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
ETS translocation variant 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsNewman, J.A. / Cooper, C.D.O. / Shrestha, L. / Burgess-Brown, N. / 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
DepositionJan 27, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2014Provider: 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 / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: ETS TRANSLOCATION VARIANT 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8474
Polymers15,6611
Non-polymers1863
Water2,108117
1
A: ETS TRANSLOCATION VARIANT 4
hetero molecules

A: ETS TRANSLOCATION VARIANT 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6948
Polymers31,3222
Non-polymers3726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area2600 Å2
ΔGint-12.7 kcal/mol
Surface area10660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.801, 50.801, 67.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2111-

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: 15660.855 Da / Num. of mol.: 1 / Fragment: ETS DOMAIN, RESIDUES 338-470
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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsFIRST TWO RESIDUES ARE REMAINING FROM CLEAVAGE OF N- TERMINAL HIS 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: 1.61 Å3/Da / Density % sol: 23.57 % / Description: NONE
Crystal growDetails: 0.8 M SODIUM CITRATE TRIBASIC, 0.1 M CACODYLATE PH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.05→26.8 Å / Num. obs: 46056 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.1
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.1 / % possible all: 67.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BNC

4bnc


Resolution: 1.05→43.99 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.547 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.13201 2245 4.9 %RANDOM
Rwork0.11654 ---
obs0.11727 43771 96.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.559 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.05→43.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms800 0 12 117 929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02936
X-RAY DIFFRACTIONr_bond_other_d0.0010.02880
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.9731276
X-RAY DIFFRACTIONr_angle_other_deg0.81432031
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4625117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05623.8347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11715160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.917156
X-RAY DIFFRACTIONr_chiral_restr0.0890.2129
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211074
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02226
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_it1.3231.342435
X-RAY DIFFRACTIONr_mcbond_other1.3211.333433
X-RAY DIFFRACTIONr_mcangle_it1.9272.013549
X-RAY DIFFRACTIONr_mcangle_other1.9332.015550
X-RAY DIFFRACTIONr_scbond_it1.8061.5501
X-RAY DIFFRACTIONr_scbond_other1.7931.499501
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2572.175721
X-RAY DIFFRACTIONr_long_range_B_refined3.54511.8821150
X-RAY DIFFRACTIONr_long_range_B_other3.54411.8941151
X-RAY DIFFRACTIONr_rigid_bond_restr1.3431816
X-RAY DIFFRACTIONr_sphericity_free32.534534
X-RAY DIFFRACTIONr_sphericity_bonded8.66351870
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 112 -
Rwork0.227 2316 -
obs--69.61 %

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