[English] 日本語
Yorodumi
- PDB-8e66: ETV6 H396Y variant bound to DNA containing the sequence GGAA -

+
Open data


ID or keywords:

Loading...

-
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-domain signature 2. / Ets domain / ETS family / 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-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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more