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- PDB-2ypr: Crystal structure of the DNA binding ETS domain of human protein FEV -

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Basic information

Entry
Database: PDB / ID: 2ypr
TitleCrystal structure of the DNA binding ETS domain of human protein FEV
ComponentsPROTEIN FEV
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


neuron fate specification / maternal behavior / neuron maturation / 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 / maternal behavior / neuron maturation / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsAllerston, C.K. / Cooper, C. / Vollmar, M. / Krojer, T. / von Delft, F. / Weigelt, J. / 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
DepositionOct 31, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 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 / 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 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN FEV
B: PROTEIN FEV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7193
Polymers23,6272
Non-polymers921
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-14.4 kcal/mol
Surface area10030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.770, 130.770, 130.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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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.: 2 / Fragment: ETS DOMAIN, RESIDUES 42-141
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-PRARE2 / References: UniProt: Q99581
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.96 Å3/Da / Density % sol: 68.95 % / Description: NONE
Crystal growDetails: 14% PEG3350, 5% GLYCEROL, 100 MM CITRATE PH 5.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.64→75.5 Å / Num. obs: 11808 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 15.9 % / Biso Wilson estimate: 102.82 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.4
Reflection shellResolution: 2.64→2.77 Å / Redundancy: 16.8 % / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FLI

1fli


Resolution: 2.64→75.5 Å / Cor.coef. Fo:Fc: 0.9357 / Cor.coef. Fo:Fc free: 0.9495 / SU R Cruickshank DPI: 0.289 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.296 / SU Rfree Blow DPI: 0.214 / SU Rfree Cruickshank DPI: 0.213
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 559 4.75 %RANDOM
Rwork0.2156 ---
obs0.2162 11771 100 %-
Displacement parametersBiso mean: 87.06 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.449 Å
Refinement stepCycle: LAST / Resolution: 2.64→75.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1484 0 6 9 1499
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081529HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.882062HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d685SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes227HARMONIC5
X-RAY DIFFRACTIONt_it1529HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.19
X-RAY DIFFRACTIONt_other_torsion3.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion178SEMIHARMONIC5
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_contact1645SEMIHARMONIC4
LS refinement shellResolution: 2.64→2.89 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2269 126 4.62 %
Rwork0.237 2604 -
all0.2365 2730 -
obs--100 %
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)
13.8197-0.99860.21646.1834-1.55015.9898-0.1045-0.48250.02430.4318-0.1801-0.2192-0.5986-0.47980.28460.03840.0194-0.07120.085-0.0305-0.1536-8.75227.628720.7694
24.6436-1.5280.47183.6466-1.86564.0629-0.121-0.26630.08790.3860.20850.0071-0.5806-0.7578-0.0874-0.03440.1532-0.06340.016-0.0532-0.24-18.74420.61836.5629
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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