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- PDB-7ju2: Crystal structure of the monomeric ETV6 PNT domain -

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Basic information

Entry
Database: PDB / ID: 7ju2
TitleCrystal structure of the monomeric ETV6 PNT domain
ComponentsTranscription factor ETV6
KeywordsONCOPROTEIN / PNT domain / ETS transcription factor / chromosomal translocation / kinase fusion
Function / homology
Function and homology information


Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / neurogenesis / Signaling by FLT3 fusion proteins / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific ...Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / neurogenesis / Signaling by FLT3 fusion proteins / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / 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 / protein domain specific binding / regulation of transcription by RNA polymerase II / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / nucleus / plasma membrane / cytosol
Similarity search - Function
SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain ...SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
FORMIC ACID / Transcription factor ETV6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85002183464 Å
AuthorsGerak, C.A.N. / Kolesnikov, M. / Murphy, M.E.P. / McIntosh, L.P.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Biophysical characterization of the ETV6 PNT domain polymerization interfaces.
Authors: Gerak, C.A.N. / Cho, S.Y. / Kolesnikov, M. / Okon, M. / Murphy, M.E.P. / Sessions, R.B. / Roberge, M. / McIntosh, L.P.
History
DepositionAug 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Transcription factor ETV6
B: Transcription factor ETV6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2674
Polymers20,1752
Non-polymers922
Water1,892105
1
A: Transcription factor ETV6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1332
Polymers10,0871
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transcription factor ETV6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1332
Polymers10,0871
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.860, 59.860, 169.380
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-203-

HOH

21B-235-

HOH

31B-241-

HOH

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Components

#1: Protein Transcription factor ETV6 / ETS translocation variant 6 / ETS-related protein Tel1 / Tel


Mass: 10087.406 Da / Num. of mol.: 2 / Fragment: PNT domain / Mutation: A93D,V112E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TEL, TEL1 / Production host: Escherichia coli (E. coli) / References: UniProt: P41212
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.17 Å3/Da / Density % sol: 43.35 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.8 M Sodium Acetate / Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→44.2145476704 Å / Num. obs: 16167 / % possible obs: 100 % / Redundancy: 22.966 % / Biso Wilson estimate: 30.232 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.077 / Χ2: 1.063 / Net I/σ(I): 28.24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.923.6361.2662.7911500.9011.293100
1.9-1.9523.5910.8784.211240.9370.89799.9
1.95-2.0123.6370.6725.4111120.9560.686100
2.01-2.0723.6410.5077.2210770.9770.518100
2.07-2.1423.4930.49.4810560.9820.408100
2.14-2.2123.6590.29512.419970.9910.302100
2.21-2.2923.3080.23915.759840.9950.245100
2.29-2.3923.5420.18719.649410.9960.191100
2.39-2.4923.2580.15223.829190.9980.155100
2.49-2.6223.3540.12827.558500.9980.131100
2.62-2.7623.1510.10732.378370.9990.109100
2.76-2.9323.0370.08538.137890.9990.087100
2.93-3.1322.8630.06747.057460.9990.069100
3.13-3.3822.4120.05456.847060.9990.055100
3.38-3.722.1340.04563.2166310.046100
3.7-4.1421.8560.03671.315920.9990.037100
4.14-4.7821.4390.03574.3553710.035100
4.78-5.8521.1640.03470.9347010.035100
5.85-8.2720.2270.03369.9937910.033100
8.27-44.214547670416.6470.03370.662380.9980.03599.2

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575refinement
PHASERphasing
Cootmodel building
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1lky

1lky


Resolution: 1.85002183464→44.2145476704 Å / SU ML: 0.178347916047 / Cross valid method: FREE R-VALUE / σ(F): 1.37855322817 / Phase error: 23.7786269711
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.233909689005 809 5.00463965357 %
Rwork0.199621733223 15356 -
obs0.201380319359 16165 99.9814448293 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.7731599543 Å2
Refinement stepCycle: LAST / Resolution: 1.85002183464→44.2145476704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1313 0 6 105 1424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005537127847761371
X-RAY DIFFRACTIONf_angle_d0.7306798189311856
X-RAY DIFFRACTIONf_chiral_restr0.0438273535197192
X-RAY DIFFRACTIONf_plane_restr0.00490252957529238
X-RAY DIFFRACTIONf_dihedral_angle_d10.6213952537824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85002183464-1.96590.2843565527041310.219533914532475X-RAY DIFFRACTION99.9616417338
1.9659-2.11770.236025381231310.2014670030272489X-RAY DIFFRACTION100
2.1177-2.33080.2309873278971320.2050701136142513X-RAY DIFFRACTION100
2.3308-2.66810.2458062842381330.200293450062524X-RAY DIFFRACTION100
2.6681-3.36130.2486303158041360.2136103490442590X-RAY DIFFRACTION100
3.3613-44.21454767040.2186881260821460.1891936581942765X-RAY DIFFRACTION99.9656593407

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