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- PDB-8e66: ETV6 H396Y variant bound to DNA containing the sequence GGAA -

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Basic information

Entry
Database: PDB / ID: 8.0E+66
TitleETV6 H396Y variant bound to DNA containing the sequence GGAA
Components
  • Complementary 15 bp strand
  • GGAA-containing 15 bp DNA
  • Transcription factor ETV6
KeywordsDNA BINDING PROTEIN/DNA / ETS / complex / winged-helix-turn-helix / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
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 ...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 DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
CACODYLATE ION / DNA / DNA (> 10) / Ets variant 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsScheu, K. / Chan, A.C. / Murphy, M.E. / McIntosh, L.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: to be published
Title: The functional role of histidine within the ETV6 ETS domain
Authors: Scheu, K. / Chan, A.C. / Murphy, M.E. / McIntosh, L.P.
History
DepositionAug 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: GGAA-containing 15 bp DNA
C: Complementary 15 bp strand
A: Transcription factor ETV6
D: GGAA-containing 15 bp DNA
E: Complementary 15 bp strand
F: Transcription factor ETV6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8557
Polymers42,7186
Non-polymers1371
Water1,892105
1
B: GGAA-containing 15 bp DNA
C: Complementary 15 bp strand
A: Transcription factor ETV6


  • defined by author&software
  • Evidence: surface plasmon resonance, Binding between the protein and DNA complex was confirmed through NMR, while affinity was determined through SPR. The dimerization of DNA was confirmed through gel filtration.
  • 21.4 kDa, 3 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)21,3593
Polymers21,3593
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-19 kcal/mol
Surface area9920 Å2
MethodPISA
2
D: GGAA-containing 15 bp DNA
E: Complementary 15 bp strand
F: Transcription factor ETV6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4964
Polymers21,3593
Non-polymers1371
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-20 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.841, 94.685, 76.259
Angle α, β, γ (deg.)90.000, 94.760, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain GGAA-containing 15 bp DNA


Mass: 4692.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain Complementary 15 bp strand


Mass: 4486.908 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein Transcription factor ETV6


Mass: 12180.040 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Etv6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9Q8J8
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: 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: 2.51 Å3/Da / Density % sol: 51.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Protein in 50 mM NaCl, 20 mM HEPES, pH 7.5 at ~300 uM incubated 1:1 with 50 mM Sodium cacodylate, 25 mM Ammonium acetate, 10 mM MgCl2, 20% PEG-8000, pH 6.0
PH range: 6.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 17254 / % possible obs: 98 % / Redundancy: 6.7 % / Biso Wilson estimate: 34.13 Å2 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.061 / Rrim(I) all: 0.163 / Χ2: 0.835 / Net I/σ(I): 4.5 / Num. measured all: 115206
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.395.40.6758100.7270.3040.7430.65893.4
2.39-2.435.70.5138190.8090.2270.5630.69693.8
2.43-2.485.90.5128690.8570.2210.5590.6994.4
2.48-2.536.10.4738020.8450.2020.5160.69694.5
2.53-2.596.20.4398100.8790.1860.4780.67495.3
2.59-2.656.10.3998680.9040.1690.4350.68696.6
2.65-2.716.20.3338850.910.1420.3630.68897.5
2.71-2.796.30.338040.9260.1390.3590.69698.7
2.79-2.876.40.2958850.9440.1250.3220.72199.2
2.87-2.966.50.2468900.9630.1020.2670.68299.3
2.96-3.076.60.248570.9650.10.2610.72799.5
3.07-3.196.80.1428800.9950.0580.1540.732100
3.19-3.337.10.1198940.9940.0480.1280.8100
3.33-3.517.20.158620.9860.060.1611.211100
3.51-3.737.20.1538910.9670.0610.1652.073100
3.73-4.027.40.1158660.9870.0450.1241.032100
4.02-4.427.50.18880.990.0390.1070.93100
4.42-5.067.60.0858970.9920.0330.0910.688100
5.06-6.377.60.0858780.9930.0330.0910.685100
6.37-507.40.0558990.9920.0220.0590.60798.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MHG

4mhg


Resolution: 2.35→25.92 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2547 1649 9.99 %
Rwork0.2165 14860 -
obs0.2203 16509 93.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.62 Å2 / Biso mean: 33.3706 Å2 / Biso min: 18.84 Å2
Refinement stepCycle: final / Resolution: 2.35→25.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1608 1218 5 105 2936
Biso mean--60.92 29.48 -
Num. residues----244
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.420.32211110.27291005111676
2.42-2.50.321210.28651085120682
2.5-2.590.34551220.29181084120685
2.59-2.690.33361280.27451209133791
2.69-2.820.31121410.27251260140196
2.82-2.960.33511540.27251298145299
2.96-3.150.31971400.27312771417100
3.15-3.390.26241460.230113281474100
3.39-3.730.26461470.21813331480100
3.73-4.270.21381460.182313151461100
4.27-5.370.18691420.163613151457100
5.37-25.920.18341510.154513511502100
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)
10.75240.05250.83550.3111-0.62241.26270.19960.19810.05940.1683-0.4263-0.48820.02510.1018-0.01110.37670.03960.02320.306-0.05830.25951.93423.9042-1.6025
21.09460.14220.33620.2495-0.20261.64250.21580.42360.0239-0.4793-0.3697-0.2376-0.03980.0311-0.01440.32310.0040.05360.34410.04510.32523.69996.8365-1.8067
30.35930.22150.14250.163-0.05310.23670.06350.23820.63830.24350.49710.3726-0.5585-0.46140.02120.28220.0166-0.01790.33710.00440.2586-4.387111.093516.419
40.0979-0.1228-0.19370.1168-0.18440.215-0.0880.24220.01120.0856-0.01210.20680.0395-0.02310.00010.22430.00260.0020.29470.0040.2733-4.1314-0.522421.5124
50.36750.28720.11710.49630.07320.0256-0.33170.20780.3079-0.50730.12240.30530.2004-0.704-0.01390.3114-0.03320.04650.2625-0.02550.2605-10.02753.7258.8144
61.1687-0.1136-0.12-0.0725-1.04060.5208-0.06750.16940.2205-0.047-0.138-0.02770.09710.1962-0.00870.21690.0014-0.0360.21910.04230.24622.80795.019911.3758
70.75280.52-0.33970.2575-0.65491.72630.2066-0.0692-0.0790.1122-0.463-0.15850.02530.3953-0.12640.251-0.0112-0.02740.16010.00130.218-0.7964-23.804640.2889
80.3382-0.0733-0.40360.128-0.08171.19050.07070.0392-0.02960.0429-0.1368-0.3520.19060.027100.2856-0.00910.0160.28770.00240.4130.9086-26.965740.429
92.15510.0942-0.7690.3315-0.47110.5436-0.49220.6996-1.6031-0.42860.4153-0.2931.0946-0.4448-0.02340.3126-0.03760.07240.21430.03410.3129-7.0976-30.160222.5117
103.15691.0792-0.7281.180.31350.7970.26620.76781.0167-0.5641-0.0850.3978-0.543-0.3142-0.07290.2234-0.0197-0.01660.34930.13490.1448-10.1877-19.421317.1478
110.85230.04240.02280.76280.19581.8197-0.2827-0.14760.0946-0.10310.0307-0.0280.61680.4145-0.45120.15840.07440.02720.33850.04960.216-7.6348-21.60424.4592
120.17680.0439-0.1451-0.2064-0.0754-0.08390.11690.0120.0206-0.002-0.19190.1131-0.13570.01190.00010.2355-0.0001-0.00720.22540.00480.3074-3.4015-25.158534.0108
130.29190.28610.17610.18010.05020.1624-0.0054-0.1897-0.19040.2243-0.33670.32270.10010.1947-0.00040.1917-0.00890.00820.26930.01580.24564.6697-17.516824.5457
141.1652-0.71550.48650.407-0.31870.2956-0.32912.08360.1611-0.7157-0.08880.576-0.7582-0.1127-0.4801-0.86750.6017-0.49460.13280.34660.19733.8667-23.580720.101
150.0370.0126-0.03790.04670.0228-0.00190.14080.7375-0.5367-0.64670.0237-0.0175-0.07510.1560.00010.50930.1040.02050.3967-0.1030.46753.5704-36.254718.5814
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 15 )B1 - 15
2X-RAY DIFFRACTION2chain 'C' and (resid 1 through 15 )C1 - 15
3X-RAY DIFFRACTION3chain 'A' and (resid 333 through 346 )A333 - 346
4X-RAY DIFFRACTION4chain 'A' and (resid 347 through 368 )A347 - 368
5X-RAY DIFFRACTION5chain 'A' and (resid 369 through 379 )A369 - 379
6X-RAY DIFFRACTION6chain 'A' and (resid 380 through 424 )A380 - 424
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 15 )D1 - 15
8X-RAY DIFFRACTION8chain 'E' and (resid 1 through 15 )E1 - 15
9X-RAY DIFFRACTION9chain 'F' and (resid 334 through 345 )F334 - 345
10X-RAY DIFFRACTION10chain 'F' and (resid 346 through 358 )F346 - 358
11X-RAY DIFFRACTION11chain 'F' and (resid 359 through 380 )F359 - 380
12X-RAY DIFFRACTION12chain 'F' and (resid 381 through 400 )F381 - 400
13X-RAY DIFFRACTION13chain 'F' and (resid 401 through 411 )F401 - 411
14X-RAY DIFFRACTION14chain 'F' and (resid 412 through 418 )F412 - 418
15X-RAY DIFFRACTION15chain 'F' and (resid 419 through 425 )F419 - 425

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