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- PDB-4uno: Crystal structure of the ETS domain of human ETV5 in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 4uno
TitleCrystal structure of the ETS domain of human ETV5 in complex with DNA
Components
  • 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
  • 5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3'
  • ETS TRANSLOCATION VARIANT 5
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


male germ-line stem cell asymmetric division / positive regulation of glial cell proliferation / positive regulation of neuron differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity ...male germ-line stem cell asymmetric division / positive regulation of glial cell proliferation / positive regulation of neuron differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / 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
DNA / ETS translocation variant 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsNewman, J.A. / Aitkenhead, H. / Cooper, C.D.O. / Pinkas, D.M. / Shrestha, L. / Burgess-Brown, N. / Kopec, J. / Fitzpatrick, F. / Tallant, C. / von Delft, F. ...Newman, J.A. / Aitkenhead, H. / Cooper, C.D.O. / Pinkas, D.M. / Shrestha, L. / Burgess-Brown, N. / Kopec, J. / Fitzpatrick, F. / Tallant, C. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / 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
DepositionMay 29, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 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 / 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ETS TRANSLOCATION VARIANT 5
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'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9745
Polymers17,8943
Non-polymers802
Water1,802100
1
A: ETS TRANSLOCATION VARIANT 5
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'
hetero molecules

A: ETS TRANSLOCATION VARIANT 5
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'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,94710
Polymers35,7876
Non-polymers1604
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-y+1,-x+1,-z+1/31
Buried area6960 Å2
ΔGint-58.8 kcal/mol
Surface area15480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.022, 58.022, 84.711
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein ETS TRANSLOCATION VARIANT 5 / ETS-RELATED PROTEIN ERM


Mass: 11803.574 Da / Num. of mol.: 1 / Fragment: ETS DOMAIN, RESIDUES 365-462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P41161
#2: 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)
#3: DNA chain 5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3'


Mass: 2995.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST 2 RESIDUES REMAIN AFTER TAG CLEAVAGE

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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: 2.3 Å3/Da / Density % sol: 46.53 % / Description: NONE
Crystal growDetails: 40% PEG 300, 0.2M CALCIUM ACETATE, 0.1M CACODYLATE PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.95→19.52 Å / Num. obs: 12146 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.4
Reflection shellResolution: 1.95→2 Å / Redundancy: 9 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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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 4BNC

4bnc


Resolution: 1.95→19.515 Å / SU ML: 0.15 / σ(F): 1.35 / Phase error: 22.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2031 598 4.9 %
Rwork0.1729 --
obs0.1746 12119 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.8 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms793 404 2 100 1299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081287
X-RAY DIFFRACTIONf_angle_d1.1261824
X-RAY DIFFRACTIONf_dihedral_angle_d21.728504
X-RAY DIFFRACTIONf_chiral_restr0.046190
X-RAY DIFFRACTIONf_plane_restr0.006165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.1460.25231430.21262857X-RAY DIFFRACTION100
2.146-2.4560.22651480.19632849X-RAY DIFFRACTION100
2.456-3.09240.28561410.19962883X-RAY DIFFRACTION100
3.0924-19.51630.16711660.14992932X-RAY DIFFRACTION100

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