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- PDB-4mhg: Crystal structure of ETV6 bound to a specific DNA sequence -

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Basic information

Entry
Database: PDB / ID: 4mhg
TitleCrystal structure of ETV6 bound to a specific DNA sequence
Components
  • Complementary Specific 14 bp DNA
  • Specific 14 bp DNA
  • Transcription factor ETV6
KeywordsTRANSCRIPTION/DNA / ETS domain / Transcription Factor / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / neurogenesis / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity ...mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / neurogenesis / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytosol
Similarity search - Function
SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / ETS family / Ets-domain signature 2. / Ets domain / 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 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 / DNA (> 10) / Transcription factor ETV6
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.199 Å
AuthorsChan, A.C. / De, S. / Coyne III, H.J. / Okon, M. / Murphy, M.E. / Graves, B.J. / McIntosh, L.P.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Steric Mechanism of Auto-Inhibitory Regulation of Specific and Non-Specific DNA Binding by the ETS Transcriptional Repressor ETV6.
Authors: De, S. / Chan, A.C. / Coyne, H.J. / Bhachech, N. / Hermsdorf, U. / Okon, M. / Murphy, M.E. / Graves, B.J. / McIntosh, L.P.
History
DepositionAug 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Jan 30, 2019Group: Data collection / Source and taxonomy / Structure summary
Category: entity / pdbx_entity_src_syn
Item: _entity.pdbx_description / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.4Feb 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

Downloads & links

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Assembly

Deposited unit
B: Specific 14 bp DNA
C: Complementary Specific 14 bp DNA
A: Transcription factor ETV6


Theoretical massNumber of molelcules
Total (without water)21,0123
Polymers21,0123
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-20 kcal/mol
Surface area9370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.582, 57.582, 130.481
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: DNA chain Specific 14 bp DNA


Mass: 4338.844 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Custom oligo / Source: (synth.) synthetic construct (others)
#2: DNA chain Complementary Specific 14 bp DNA


Mass: 4222.740 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: custom oligo / Source: (synth.) synthetic construct (others)
#3: Protein Transcription factor ETV6 / ETS translocation variant 6 / ETS-related protein Tel1 / Tel


Mass: 12450.353 Da / Num. of mol.: 1 / Fragment: ETV6 ETS domain, UNP residues 329-426 / Mutation: C334S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Etv6, Tel, Tel1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P97360
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.97 Å3/Da / Density % sol: 58.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 22% PEG 8000, 50 mM Sodium Cacodylate, 100 mM NH4Ac, 10 mM MgCl2, pH 6.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9753 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9753 Å / Relative weight: 1
ReflectionResolution: 2.199→50 Å / Num. all: 13342 / Num. obs: 13307 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 38.02 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.199-2.248.10.7111100
2.24-2.288.10.6561100
2.28-2.328.20.6211100
2.32-2.378.10.4991100
2.37-2.428.10.4511100
2.42-2.488.20.4041100
2.48-2.5480.3371100
2.54-2.618.10.2731100
2.61-2.6980.2411100
2.69-2.778.10.1821100
2.77-2.878.10.1771100
2.87-2.997.90.1391100
2.99-3.1280.099199.8
3.12-3.2980.0781100
3.29-3.497.90.0821100
3.49-3.767.80.0731100
3.76-4.147.80.056199.9
4.14-4.747.30.0411100
4.74-5.977.70.0381100
5.97-506.80.036193.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.199→26.34 Å / Occupancy max: 1 / Occupancy min: 0.45 / SU ML: 0.16 / σ(F): 1.35 / Phase error: 21.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2214 666 5.01 %
Rwork0.1751 --
obs0.1773 13290 99.61 %
all-13342 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.4764 Å2
Refinement stepCycle: LAST / Resolution: 2.199→26.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms790 568 0 124 1482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061498
X-RAY DIFFRACTIONf_angle_d1.3252148
X-RAY DIFFRACTIONf_dihedral_angle_d25.626616
X-RAY DIFFRACTIONf_chiral_restr0.075225
X-RAY DIFFRACTIONf_plane_restr0.005174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1992-2.36890.24981340.212476X-RAY DIFFRACTION100
2.3689-2.60710.24711300.20432504X-RAY DIFFRACTION100
2.6071-2.98390.2821360.21642489X-RAY DIFFRACTION100
2.9839-3.75770.221360.17082508X-RAY DIFFRACTION99
3.7577-26.3420.18621300.15232647X-RAY DIFFRACTION99
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)
19.6224-3.31424.43947.344-3.54147.1714-0.0526-0.7459-0.32950.7936-0.08230.2948-0.0962-0.7560.15590.4901-0.11720.05040.3646-0.04940.321616.1786-9.28049.7043
27.1943.187-3.72967.07-4.84013.7909-0.5281-0.35791.1348-0.06350.22681.8371-0.5141-0.27930.15150.5583-0.1415-0.04870.4103-0.02870.662613.0328-0.29051.9857
37.10884.04870.23087.39420.96128.80640.0260.26750.6595-0.14040.16711.6576-0.1447-0.8093-0.20760.4357-0.1352-0.08280.32170.02910.64938.9872-9.1765-1.7784
41.4449-0.12080.24542.2455-0.40981.9263-0.16770.130.3764-0.2766-0.2371-0.35860.16870.00550.40510.4396-0.1721-0.03420.25990.04460.407723.5545-6.8827-0.3894
54.99262.33180.60734.4428-2.88023.03010.2233-0.24340.27010.8156-0.0761-0.1626-0.40040.1459-0.03420.6527-0.2171-0.16780.4016-0.0050.450528.3718-6.56089.2744
69.6409-1.55530.90632.06990.10136.47210.3408-0.21330.0506-0.1508-0.1351-0.22830.11640.3244-0.21740.5081-0.1613-0.05820.28080.06840.324928.6831-13.06510.364
76.74770.05292.86372.61182.97095.8869-0.157-0.0918-0.2257-0.42810.17080.24060.0431-0.0987-0.01060.4202-0.1582-0.02260.21630.02310.279516.1277-21.81732.1598
89.83381.5082-3.4457.54290.60028.7365-0.2807-0.5803-0.03420.35010.07020.9870.8051-0.78450.26740.3665-0.07810.02080.2957-0.01570.486310.0193-16.75724.6596
94.5995-2.2909-1.19814.0076-3.53166.88230.4262-0.16460.4077-0.995-0.188-0.19670.20010.7221-0.13690.6407-0.1140.02470.3377-0.04040.270123.7461-18.4146-10.5422
107.329-0.55062.97763.3485-0.96417.62410.3811-0.4732-0.93380.13490.0635-0.64790.4602-0.0362-0.72270.4836-0.13150.01320.26490.01920.402127.1895-29.08272.1249
112.4123-0.6522-0.73783.40314.35515.55840.1619-0.72390.430.99230.4138-1.251-0.37360.5459-0.5880.6671-0.2343-0.05680.63760.00030.387533.2362-17.698915.5316
128.6246-4.72026.60955.5609-4.31567.20870.4124-0.2851-0.7689-0.71530.55840.22841.01490.2196-0.82920.5061-0.1688-0.01350.5325-0.00470.255729.1674-22.965220.92
131.85770.64982.08242.38111.74512.7672-0.05470.1560.0006-0.52210.3125-0.4757-0.29880.5253-0.18990.4892-0.20440.05210.34320.04120.371731.2643-20.5053.8662
145.9349-3.74214.20893.3319-4.00074.86761.72141.8602-2.7563-1.98440.48210.55480.17281.737-1.89250.8616-0.0375-0.10230.5771-0.22110.603626.9956-27.6291-10.6751
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 335:344)
2X-RAY DIFFRACTION2(chain A and resid 345:351)
3X-RAY DIFFRACTION3(chain A and resid 352:366)
4X-RAY DIFFRACTION4(chain A and resid 367:377)
5X-RAY DIFFRACTION5(chain A and resid 378:382)
6X-RAY DIFFRACTION6(chain A and resid 383:390)
7X-RAY DIFFRACTION7(chain A and resid 391:408)
8X-RAY DIFFRACTION8(chain A and resid 409:424)
9X-RAY DIFFRACTION9(chain B and resid 1:5)
10X-RAY DIFFRACTION10(chain B and resid 6:9)
11X-RAY DIFFRACTION11(chain B and resid 10:14)
12X-RAY DIFFRACTION12(chain C and resid 1:5)
13X-RAY DIFFRACTION13(chain C and resid 6:10)
14X-RAY DIFFRACTION14(chain C and resid 11:14)

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