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- PDB-4irg: Uninhibited DNA-binding domain of the Ets transcription factor ERG -

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Basic information

Entry
Database: PDB / ID: 4irg
TitleUninhibited DNA-binding domain of the Ets transcription factor ERG
ComponentsTranscriptional regulator ERGERG (gene)
KeywordsDNA BINDING PROTEIN / winged Helix-Turn-Helix / Ets domain
Function / homology
Function and homology information


sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein phosphorylation / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / signal transduction ...sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein phosphorylation / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. ...SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily / 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
Transcriptional regulator ERG
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRegan, M.C. / Horanyi, P.S. / Pryor, E.E. / Sarver, J.L. / Cafiso, D.S. / Bushweller, J.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural and dynamic studies of the transcription factor ERG reveal DNA binding is allosterically autoinhibited.
Authors: Regan, M.C. / Horanyi, P.S. / Pryor, E.E. / Sarver, J.L. / Cafiso, D.S. / Bushweller, J.H.
History
DepositionJan 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Aug 28, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator ERG


Theoretical massNumber of molelcules
Total (without water)12,5621
Polymers12,5621
Non-polymers00
Water82946
1
A: Transcriptional regulator ERG

A: Transcriptional regulator ERG


Theoretical massNumber of molelcules
Total (without water)25,1242
Polymers25,1242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area1930 Å2
ΔGint-16 kcal/mol
Surface area10440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.699, 44.699, 175.112
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

21A-410-

HOH

31A-411-

HOH

41A-426-

HOH

51A-446-

HOH

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Components

#1: Protein Transcriptional regulator ERG / ERG (gene) / Transforming protein ERG


Mass: 12562.145 Da / Num. of mol.: 1 / Fragment: Ets Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERG / Production host: Escherichia coli (E. coli) / References: UniProt: P11308
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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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: 2.01 Å3/Da / Density % sol: 38.81 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.4M Sodium Citrate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 1, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→35.43 Å / Num. all: 12118 / Num. obs: 11537
Reflection shellResolution: 1.7→1.73 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→35.43 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.229 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22756 580 4.8 %RANDOM
Rwork0.18809 ---
obs0.1899 11537 99.25 %-
all-12118 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.615 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.26 Å20 Å2
2--0.26 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms807 0 0 46 853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.019827
X-RAY DIFFRACTIONr_bond_other_d0.0010.02760
X-RAY DIFFRACTIONr_angle_refined_deg2.0011.9321113
X-RAY DIFFRACTIONr_angle_other_deg0.99731743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.27597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96623.40944
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73615146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.365157
X-RAY DIFFRACTIONr_chiral_restr0.1390.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02945
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02214
LS refinement shellResolution: 1.7→1.747 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 50 -
Rwork0.23 784 -
obs--96.42 %
Refinement TLS params.Method: refined / Origin x: 3.2028 Å / Origin y: 12.9128 Å / Origin z: -6.1583 Å
111213212223313233
T0.0133 Å2-0.0023 Å2-0.0123 Å2-0.0195 Å20.0176 Å2--0.0257 Å2
L1.5693 °2-0.4856 °2-0.2954 °2-1.7385 °20.5814 °2--2.1591 °2
S-0.0137 Å °0.1367 Å °0.1453 Å °-0.1254 Å °0.0079 Å °0.0944 Å °-0.0959 Å °-0.1184 Å °0.0058 Å °

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