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- PDB-5ybd: X-ray structure of ETS domain of Ergp55 in complex with E74DNA -

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Basic information

Entry
Database: PDB / ID: 5ybd
TitleX-ray structure of ETS domain of Ergp55 in complex with E74DNA
Components
  • DNA (5'-D(P*AP*CP*CP*GP*GP*AP*AP*GP*T)-3')
  • DNA (5'-D(P*CP*AP*CP*TP*TP*CP*CP*GP*GP*T)-3')
  • Transcriptional regulator ERG
KeywordsDNA BINDING PROTEIN / ETS transcription factor / human Ergp55 / ETS-E74DNA complex / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / 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 ...sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / 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
DNA / Transcriptional regulator ERG
Similarity search - Component
Biological speciesHomo sapiens (human)
Drosophila saltans (fry)
Drosophila adunca (fry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.769 Å
AuthorsSaxena, A.K. / Gangwar, S.P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science and TechnologySR/SO/HS-05/2009 India
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Comparative structure analysis of the ETSi domain of ERG3 and its complex with the E74 promoter DNA sequence
Authors: Sharma, R. / Gangwar, S.P. / Saxena, A.K.
History
DepositionSep 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator ERG
B: DNA (5'-D(P*AP*CP*CP*GP*GP*AP*AP*GP*T)-3')
C: DNA (5'-D(P*CP*AP*CP*TP*TP*CP*CP*GP*GP*T)-3')
X: Transcriptional regulator ERG
Y: DNA (5'-D(P*AP*CP*CP*GP*GP*AP*AP*GP*T)-3')
Z: DNA (5'-D(P*CP*AP*CP*TP*TP*CP*CP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)34,8246
Polymers34,8246
Non-polymers00
Water00
1
A: Transcriptional regulator ERG
B: DNA (5'-D(P*AP*CP*CP*GP*GP*AP*AP*GP*T)-3')
C: DNA (5'-D(P*CP*AP*CP*TP*TP*CP*CP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)17,4123
Polymers17,4123
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-19 kcal/mol
Surface area8450 Å2
MethodPISA
2
X: Transcriptional regulator ERG
Y: DNA (5'-D(P*AP*CP*CP*GP*GP*AP*AP*GP*T)-3')
Z: DNA (5'-D(P*CP*AP*CP*TP*TP*CP*CP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)17,4123
Polymers17,4123
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-18 kcal/mol
Surface area8250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.279, 233.871, 80.524
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain X and segid X
12chain B and segid B
22chain Y and segid Y
13chain C and segid C
23chain Z and segid Z

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain X and segid XX0
112chain B and segid BB0
212chain Y and segid YY0
113chain C and segid CC0
213chain Z and segid ZZ0

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Transcriptional regulator ERG / Transforming protein ERG


Mass: 11651.133 Da / Num. of mol.: 2 / Fragment: ETS domain, UNP residues 317-406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERG / Plasmid: pET21a(+) / Cell (production host): Homo sapiens / Production host: Enterobacteria phage L1 (virus) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P11308
#2: DNA chain DNA (5'-D(P*AP*CP*CP*GP*GP*AP*AP*GP*T)-3')


Mass: 2764.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila saltans (fry)
#3: DNA chain DNA (5'-D(P*CP*AP*CP*TP*TP*CP*CP*GP*GP*T)-3')


Mass: 2995.967 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila adunca (fry)

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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: 2.68 Å3/Da / Density % sol: 54.04 % / Description: rectangular plate
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20%(w/v) PEG4000, 200mM MgCl2 as precipitant solution
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 10, 2013 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si(111)monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionRedundancy: 6.4 % / Number: 63032 / Rmerge(I) obs: 0.078 / Χ2: 1.68 / D res high: 2.77 Å / D res low: 50 Å / Num. obs: 9898 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
7.515010.0584.4695.4
5.967.5110.0613.1246.1
5.215.9610.0663.1096.2
4.745.2110.0632.336.4
4.44.7410.0592.1936.4
4.144.410.061.9256.5
3.934.1410.0641.8926.5
3.763.9310.0761.8346.5
3.613.7610.0761.4546.5
3.493.6110.0791.3496.5
3.383.4910.0771.3446.5
3.283.3810.0861.3226.5
3.23.2810.0881.1656.5
3.123.210.1161.0626.5
3.053.1210.1721.0096.5
2.983.0510.2640.8536.4
2.922.9810.3040.8286.6
2.872.9210.3550.8746.5
2.822.8710.4150.7966.4
2.772.8210.4560.7966.2
ReflectionResolution: 2.769→50 Å / Num. obs: 9898 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 54.12 Å2 / Rmerge(I) obs: 0.078 / Χ2: 1.681 / Net I/av σ(I): 33.548 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
2.77-2.826.20.4560.7961100
2.82-2.876.40.4150.7961100
2.87-2.926.50.3550.8741100
2.92-2.986.60.3040.8281100
2.98-3.056.40.2640.8531100
3.05-3.126.50.1721.0091100
3.12-3.26.50.1161.0621100
3.2-3.286.50.0881.1651100
3.28-3.386.50.0861.322199.6
3.38-3.496.50.0771.3441100
3.49-3.616.50.0791.3491100
3.61-3.766.50.0761.4541100
3.76-3.936.50.0761.8341100
3.93-4.146.50.0641.8921100
4.14-4.46.50.061.9251100
4.4-4.746.40.0592.1931100
4.74-5.216.40.0632.331100
5.21-5.966.20.0663.1091100
5.96-7.516.10.0613.1241100
7.51-505.40.0584.469198.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.769→38.978 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.91
RfactorNum. reflection% reflection
Rfree0.2816 471 4.78 %
Rwork0.2044 --
obs0.2081 9861 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 170.91 Å2 / Biso mean: 37.09 Å2 / Biso min: 14.94 Å2
Refinement stepCycle: final / Resolution: 2.769→38.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1603 776 0 0 2379
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072514
X-RAY DIFFRACTIONf_angle_d1.2653543
X-RAY DIFFRACTIONf_chiral_restr0.052370
X-RAY DIFFRACTIONf_plane_restr0.005320
X-RAY DIFFRACTIONf_dihedral_angle_d22.719977
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A903X-RAY DIFFRACTION7.975TORSIONAL
12X903X-RAY DIFFRACTION7.975TORSIONAL
21B174X-RAY DIFFRACTION7.975TORSIONAL
22Y174X-RAY DIFFRACTION7.975TORSIONAL
31C194X-RAY DIFFRACTION7.975TORSIONAL
32Z194X-RAY DIFFRACTION7.975TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7685-3.1690.33851680.24163018318699
3.169-3.9920.29141480.19873113326199
3.992-38.98230.25981550.19832593414100
Refinement TLS params.Method: refined / Origin x: 10.3564 Å / Origin y: 30.8682 Å / Origin z: 0.1159 Å
111213212223313233
T0.1542 Å2-0.0396 Å2-0.0322 Å2-0.2107 Å20.0043 Å2--0.2056 Å2
L0.5964 °2-0.7315 °20.0206 °2-2.2711 °2-0.801 °2--1.992 °2
S0.0832 Å °-0.0497 Å °-0.1115 Å °-0.0215 Å °-0.0178 Å °0.0396 Å °-0.008 Å °0.0355 Å °-0.0651 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA311 - 406
2X-RAY DIFFRACTION1allB2 - 10
3X-RAY DIFFRACTION1allC14 - 23
4X-RAY DIFFRACTION1allX310 - 403
5X-RAY DIFFRACTION1allY2 - 10
6X-RAY DIFFRACTION1allZ14 - 23

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