[English] 日本語
Yorodumi
- PDB-6dfy: Remodeled crystal structure of DNA-bound DUX4-HD2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dfy
TitleRemodeled crystal structure of DNA-bound DUX4-HD2
Components
  • DNA (5'-D(*AP*AP*GP*AP*TP*TP*AP*GP*AP*TP*TP*AP*GP*T)-3')
  • DNA (5'-D(*TP*TP*CP*TP*AP*AP*TP*CP*TP*AP*AP*TP*CP*A)-3')
  • Double homeobox protein 4
KeywordsDNA BINDING PROTEIN/DNA / DUX4-RESPONSIVE-ELEMENT / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of G0 to G1 transition / Zygotic genome activation (ZGA) / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation ...negative regulation of G0 to G1 transition / Zygotic genome activation (ZGA) / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / apoptotic process / regulation of transcription by RNA polymerase II / nucleolus / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Helix-turn-helix motif / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Double homeobox protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.623 Å
AuthorsAihara, H. / Shi, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
CitationJournal: Leukemia / Year: 2018
Title: Comment on structural basis of DUX4/IGH-driven transactivation.
Authors: Aihara, H. / Shi, K. / Lee, J.K. / Bosnakovski, D. / Kyba, M.
History
DepositionMay 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Double homeobox protein 4
E: DNA (5'-D(*AP*AP*GP*AP*TP*TP*AP*GP*AP*TP*TP*AP*GP*T)-3')
F: DNA (5'-D(*TP*TP*CP*TP*AP*AP*TP*CP*TP*AP*AP*TP*CP*A)-3')
D: Double homeobox protein 4


Theoretical massNumber of molelcules
Total (without water)23,1294
Polymers23,1294
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-26 kcal/mol
Surface area10680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.610, 51.610, 166.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11D-101-

HOH

-
Components

#1: Protein Double homeobox protein 4 / Double homeobox protein 10


Mass: 7286.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: DOUBLE HOMEOBOX PROTEIN 4 / Source: (gene. exp.) Homo sapiens (human) / Gene: DUX4, DUX10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBX2
#2: DNA chain DNA (5'-D(*AP*AP*GP*AP*TP*TP*AP*GP*AP*TP*TP*AP*GP*T)-3')


Mass: 4342.864 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*TP*CP*TP*AP*AP*TP*CP*TP*AP*AP*TP*CP*A)-3')


Mass: 4213.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9747 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9747 Å / Relative weight: 1
ReflectionResolution: 2.62→83.3 Å / Num. obs: 7363 / % possible obs: 99.9 % / Redundancy: 9.5 % / Net I/σ(I): 11.5
Reflection shellResolution: 2.62→2.76 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.5 / Num. unique obs: 1026 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(dev_3139: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5z2t

5z2t


Resolution: 2.623→49.297 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2794 341 4.69 %
Rwork0.2457 --
obs0.2475 7266 99.25 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.623→49.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms857 551 0 12 1420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061489
X-RAY DIFFRACTIONf_angle_d0.9732123
X-RAY DIFFRACTIONf_dihedral_angle_d22.661799
X-RAY DIFFRACTIONf_chiral_restr0.05232
X-RAY DIFFRACTIONf_plane_restr0.006184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6231-3.30470.41731650.34653360X-RAY DIFFRACTION99
3.3047-49.30610.24631760.21943565X-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)
13.8398-1.52514.28993.95450.69337.6819-0.47760.45061.23.1748-0.31150.7520.50880.0011.61861.47050.09660.07771.73780.08010.97537.7353-0.4962183.9563
26.6055-4.43571.65816.245-0.75890.45350.0701-3.3314-0.68230.16730.27721.90450.0908-0.2847-0.10860.5596-0.3221-0.11751.45530.22540.9159.1616-10.9352180.5434
38.7515-1.3061-3.26393.21564.92448.23920.42660.1904-1.5944-0.2633-1.5948-0.0414-0.2562-0.51240.86220.58990.0091-0.14080.89490.19670.828714.2067-15.0056176.4424
44.79654.9733-5.59725.695-6.00436.7118-1.6493-1.2153-1.78130.4658-0.221-0.38091.97820.54222.09231.4982-0.0286-0.02141.1588-0.11780.99617.9654-16.1389171.866
52.83411.8763-1.4443.58552.66976.3417-1.48771.79830.7725-1.64590.75690.1755-0.7499-1.21850.40591.5214-0.5805-0.04951.13260.01580.499316.8357-8.6582165.8944
60.8435-0.564-2.63752.31462.02628.2871-0.01940.0427-0.0113-0.2006-0.15950.1064-0.5998-0.72820.03341.3458-0.5693-0.65751.50430.57920.808810.1877-6.4665166.0077
75.97682.8413.07671.99972.74419.5872-0.98731.55780.7274-2.3013-0.83361.3690.9484-1.46940.58871.6797-0.639-0.63551.29190.30481.28684.8143-8.9571170.6362
85.3607-1.8763-0.16053.0336-1.84481.5237-0.5323-0.22340.7142-0.66050.05150.5084-0.4788-0.71670.27850.7847-0.0833-0.48941.5544-0.12891.57087.5278-2.5216173.9413
95.2368-3.17922.95478.10692.99065.37180.7545-1.22570.9091-0.442-0.772-0.0871-0.1628-0.2869-0.43271.1236-0.6-0.01880.98460.0860.500613.3927-1.3063173.6016
104.59073.20734.10512.62652.99433.725-0.0286-0.6544-0.5023-0.79950.0617-0.29040.456-0.723-0.070.3868-0.0157-0.06270.5376-0.07930.576618.9778-5.9096176.028
111.9998-6.803-6.73476.53780.5337.24210.1118-3.6159-0.97940.7160.6472-2.04970.6458-0.2834-0.60970.6599-0.1673-0.06890.74550.08830.840625.05-9.0736177.7427
121.2143-0.09230.61523.91371.20183.22720.193-0.0675-0.011-0.45450.94090.23922.5035-0.42430.35761.39710.3544-0.01812.10860.25160.583737.44680.9204203.3329
138.9062-5.69426.71063.9463-4.27065.05780.1815-1.2367-0.55010.2336-0.48-0.3054-0.09890.1183-0.08710.72040.2689-0.25692.0898-0.58861.314940.33518.1255203.3712
147.1555-4.9076-3.65714.09324.74978.9846-0.11652.98311.018-0.97662.0544-2.2454-0.03184.0233-2.07330.8458-0.0941-0.07231.7067-0.31991.278238.806812.9557199.4973
156.26-5.9431.88336.4786-4.25578.8782-1.5224-0.69682.59580.0880.4563-1.5303-1.7410.10050.99011.4443-0.35730.2071.4007-0.4091.550936.641617.3187196.5931
167.45793.1625-7.07221.3695-3.26939.24470.56520.93942.3669-0.250.8875-0.35510.054-1.184-1.12981.3569-0.7565-0.43521.53860.20081.761433.716916.9557189.9065
178.3115-0.3133-4.09322.0724-0.48032.2107-0.46120.9054-0.0546-0.74690.85040.140.502-0.8449-0.07611.096-0.64620.29861.8667-0.20320.793239.612510.1945185.2144
185.824-4.0441-2.95172.80812.04991.4955-0.38041.4381-0.9384-0.498-0.4177-0.63870.4103-0.208-0.10680.6541-0.54290.32621.7743-0.22141.253742.50738.2042189.0099
197.3237.9343-0.5371.99952.85157.1751-1.32033.0808-0.4935-1.8842-0.366-2.3085-0.7871-0.06290.99590.77050.08720.13882.38420.61851.373946.57457.3178194.4321
201.0242-1.33391.72743.3368-2.84583.7241-0.4405-1.02190.0881-0.58140.0315-2.5022-0.25880.40420.19060.67240.01760.05391.44690.16621.236941.13431.6275192.8954
214.77470.2007-5.1829.37523.11636.81130.2358-0.9894-2.221-0.59241.7303-1.34061.07382.5977-1.80110.7488-0.0999-0.24051.282-0.03970.932236.00592.52191.9931
223.45162.2976-2.25442.50361.08078.3386-0.4678-0.17020.0458-1.25031.25990.9422-0.9231-0.5552-0.59470.6972-0.1309-0.34070.53890.16311.063431.87867.0103193.3367
232.84482.6162-3.66357.3418-1.65545.864-0.41270.11242.0299-0.45280.3917-0.0717-0.44391.64240.25990.6258-0.205-0.33380.9448-0.00360.825327.467910.1471194.6933
244.35881.4425-2.13061.92730.2681.69470.52790.02261.8453-0.23070.0486-0.8569-0.04240.0311.82170.60310.50460.03641.7355-0.10640.986624.989712.1301198.0308
256.42325.59834.94835.42143.27138.0745-0.1714-0.1136-1.17310.11651.1204-0.5211-1.08240.1104-0.6220.9479-0.10140.00410.9540.09190.781127.65141.7359200.7634
262.4134-1.6921-1.17696.9081-3.81544.52510.60650.0591-1.5234-0.02690.9211-0.25541.8378-0.4699-1.71411.1863-0.3109-0.30870.9668-0.11250.825821.7861-2.8494186.9808
276.41692.8162-7.11225.3786-5.92459.81580.95191.37411.1969-1.48840.44370.0476-1.703-0.0487-1.2921.2576-0.37340.32631.159-0.15790.862826.22856.4204171.416
283.9328-2.9892.27373.9099-0.35642.97891.3718-0.6855-0.3221-1.25980.0030.8238-1.0685-1.0056-1.36711.031-0.00290.24090.89050.20520.914423.2099-0.9299165.4274
295.42455.66575.83695.99456.07146.36890.68420.2819-1.20790.409-0.0666-2.1852-0.22180.7101-0.53880.8478-0.1527-0.05631.0646-0.13210.963829.90472.9816178.7718
307.3196-5.89554.81797.5363-7.25077.38470.1892-1.5741-0.72660.79930.96111.3491-0.5786-2.3269-1.17440.8336-0.1783-0.08261.57860.11980.849419.11162.3689192.131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain C and resid 9:13)
2X-RAY DIFFRACTION2(chain C and resid 14:20)
3X-RAY DIFFRACTION3(chain C and resid 21:24)
4X-RAY DIFFRACTION4(chain C and resid 25:28)
5X-RAY DIFFRACTION5(chain C and resid 29:32)
6X-RAY DIFFRACTION6(chain C and resid 33:36)
7X-RAY DIFFRACTION7(chain C and resid 37:41)
8X-RAY DIFFRACTION8(chain C and resid 42:46)
9X-RAY DIFFRACTION9(chain C and resid 47:50)
10X-RAY DIFFRACTION10(chain C and resid 51:56)
11X-RAY DIFFRACTION11(chain C and resid 57:61)
12X-RAY DIFFRACTION12(chain D and resid 10:13)
13X-RAY DIFFRACTION13(chain D and resid 14:17)
14X-RAY DIFFRACTION14(chain D and resid 18:21)
15X-RAY DIFFRACTION15(chain D and resid 22:25)
16X-RAY DIFFRACTION16(chain D and resid 26:29)
17X-RAY DIFFRACTION17(chain D and resid 30:34)
18X-RAY DIFFRACTION18(chain D and resid 35:38)
19X-RAY DIFFRACTION19(chain D and resid 39:42)
20X-RAY DIFFRACTION20(chain D and resid 43:46)
21X-RAY DIFFRACTION21(chain D and resid 47:50)
22X-RAY DIFFRACTION22(chain D and resid 51:54)
23X-RAY DIFFRACTION23(chain D and resid 55:58)
24X-RAY DIFFRACTION24(chain D and resid 59:61)
25X-RAY DIFFRACTION25(chain E and resid 2:5)
26X-RAY DIFFRACTION26(chain E and resid 6:9)
27X-RAY DIFFRACTION27(chain E and resid 10:15)
28X-RAY DIFFRACTION28(chain F and resid 12:15)
29X-RAY DIFFRACTION29(chain F and resid 16:19)
30X-RAY DIFFRACTION30(chain F and resid 20:24)

+
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