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- PDB-9hk0: PNT domain of human ETV7 -

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Basic information

Entry
Database: PDB / ID: 9hk0
TitlePNT domain of human ETV7
ComponentsTranscription factor ETV7
KeywordsTRANSCRIPTION / PNT domain / transcription factor / oligomerization
Function / homology
Function and homology information


animal organ morphogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
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
Transcription factor ETV7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsValer, L. / Binacchi, R. / Ciribilli, Y. / Biasini, E. / Inga, A. / Lolli, G.
Funding support Italy, 1items
OrganizationGrant numberCountry
Other governmentNextGeneration EU PNRR iNEST Italy
CitationJournal: To Be Published
Title: PNT domain of human ETV7
Authors: Binacchi, R. / Valer, L. / Ciribilli, Y. / Biasini, E. / Inga, A. / Lolli, G.
History
DepositionDec 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor ETV7


Theoretical massNumber of molelcules
Total (without water)8,9851
Polymers8,9851
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4690 Å2
Unit cell
Length a, b, c (Å)67.813, 67.813, 29.831
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Transcription factor ETV7 / ETS translocation variant 7 / ETS-related protein Tel2 / Tel-related Ets factor / Transcription factor Tel-2


Mass: 8985.191 Da / Num. of mol.: 1 / Mutation: V105E
Source method: isolated from a genetically manipulated source
Details: First S derives from the expression tag. / Source: (gene. exp.) Homo sapiens (human) / Gene: ETV7, TEL2, TELB, TREF
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9Y603
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.61→58.73 Å / Num. obs: 10339 / % possible obs: 100 % / Redundancy: 18.6 % / CC1/2: 1 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.012 / Rrim(I) all: 0.053 / Χ2: 1 / Net I/σ(I): 28.4 / Num. measured all: 192678
Reflection shellResolution: 1.61→1.64 Å / % possible obs: 100 % / Redundancy: 19.6 % / Rmerge(I) obs: 1.723 / Num. measured all: 9585 / Num. unique obs: 490 / CC1/2: 0.845 / Rpim(I) all: 0.397 / Rrim(I) all: 1.769 / Χ2: 0.97 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→33.907 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.205 494 4.79 %
Rwork0.1838 --
obs0.1847 10317 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.61→33.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms632 0 0 34 666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007694
X-RAY DIFFRACTIONf_angle_d0.792949
X-RAY DIFFRACTIONf_dihedral_angle_d10.855571
X-RAY DIFFRACTIONf_chiral_restr0.05196
X-RAY DIFFRACTIONf_plane_restr0.005126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6103-1.77230.30271240.27242413X-RAY DIFFRACTION100
1.7723-2.02880.2721350.22212415X-RAY DIFFRACTION100
2.0288-2.55590.21771140.20432470X-RAY DIFFRACTION100
2.5559-33.9070.17981210.16512525X-RAY DIFFRACTION100
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)
11.86231.11130.22013.8361-1.20352.57050.44410.85350.1113-0.9591-0.3901-0.53580.28350.8944-0.03410.29940.10360.0910.56960.02260.372228.97183.4493-9.5083
23.6918-1.55320.28827.2224-2.36464.40580.079-0.33460.43360.2968-0.21490.0181-0.29290.46160.10820.2331-0.0235-0.00090.3409-0.03830.267424.91319.2479-2.7023
30.1502-0.68930.40067.9565-4.22232.3045-0.1434-0.52590.34181.42640.65180.0087-0.7239-0.1998-0.39210.4490.02250.02420.4966-0.01880.45519.08348.42782.0281
43.4624-0.8751.38495.178-0.64983.1867-0.04680.1499-0.2263-0.10890.08690.4282-0.1012-0.0412-0.03160.2482-0.02-0.03440.29160.00170.255314.61452.849-6.6025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 55 )
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 70 )
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 83 )
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 116 )

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