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- PDB-4bnc: Crystal structure of the DNA-binding domain of human ETV1 complex... -

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Basic information

Entry
Database: PDB / ID: 4bnc
TitleCrystal structure of the DNA-binding domain of human ETV1 complexed 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'
  • HUMAN ETV1
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN
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 / cell differentiation / 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 / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / chromatin / 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
DNA / ETS translocation variant 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.9 Å
AuthorsAllerston, C.K. / Cooper, C.D.O. / Krojer, T. / Chaikuad, A. / Vollmar, M. / Froese, D.S. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / 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
DepositionMay 14, 2013Deposition site: PDBE / Processing site: PDBE
SupersessionJul 3, 2013ID: 4B06
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Jun 10, 2015Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN ETV1
B: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
C: 5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP)-3'


Theoretical massNumber of molelcules
Total (without water)18,5273
Polymers18,5273
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-14.9 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.883, 64.883, 129.587
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein HUMAN ETV1


Mass: 12437.209 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 / References: UniProt: P50549
#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.) HOMO SAPIENS (human)
#3: 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.) HOMO SAPIENS (human)

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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: 7.18 Å3/Da / Density % sol: 82.87 % / Description: NONE
Crystal growDetails: SEMET PROTEIN/DNA WAS CRYSTALLISED IN 20%(W/V) PEG 3350 0.2M POTASSIUM CITRATE. NATIVE PROTEIN/DNA WAS CRYSTALLISED IN 28% LMW PEG SMEAR, 100MM TRIS, PH 8.5, 200MM NACL, 5% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.9→129.8 Å / Num. obs: 6594 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 127.18 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.6
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 9.3 % / Rmerge(I) obs: 1.27 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.9→58.02 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.9586 / SU R Cruickshank DPI: 0.442 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.508 / SU Rfree Blow DPI: 0.274 / SU Rfree Cruickshank DPI: 0.266
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 310 4.7 %RANDOM
Rwork0.2062 ---
obs0.207 6594 99.64 %-
Displacement parametersBiso mean: 123.75 Å2
Baniso -1Baniso -2Baniso -3
1--7.9306 Å20 Å20 Å2
2---7.9306 Å20 Å2
3---15.8611 Å2
Refine analyzeLuzzati coordinate error obs: 0.899 Å
Refinement stepCycle: LAST / Resolution: 2.9→58.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms734 404 0 0 1138
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011207HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.061716HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d433SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes14HARMONIC2
X-RAY DIFFRACTIONt_gen_planes133HARMONIC5
X-RAY DIFFRACTIONt_it1207HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion4.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion153SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1260SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.24 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2409 87 4.81 %
Rwork0.229 1722 -
all0.2296 1809 -
obs--99.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.02112.4041-0.61072.3461-2.54299.0114-0.40730.3415-0.1994-0.90040.44050.0292-0.1799-0.727-0.0332-0.2842-0.04450.21950.3587-0.0334-0.297349.535561.1851.2881
215.353-4.3976-1.46656.8905-1.74613.9932-0.4325-0.8267-0.64860.12170.0463-0.54420.3295-0.47320.3862-0.6079-0.03920.18030.60790.1539-0.022448.569755.3966.636
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B AND C

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