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- PDB-7dw5: Crystal structure of DUX4 HD1-HD2 domain complexed with ERG sites -

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Basic information

Entry
Database: PDB / ID: 7dw5
TitleCrystal structure of DUX4 HD1-HD2 domain complexed with ERG sites
Components
  • (DNA (5'-D(P*CP*GP*AP*CP*TP*TP*GP*AP*TP*GP*AP*GP*AP*TP*TP*AP*GP*AP*CP*TP*G)-3')) x 2
  • Double homeobox protein 4-like protein 2
KeywordsDNA BINDING PROTEIN/DNA / acute lymphoblastic leukemia / DUX4/IGH / ERGalt / Clamp-like transactivation / DUX4-Responsive-Element / alternative splicing / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Helix-turn-helix motif / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
BROMIDE ION / DNA / DNA (> 10) / Double homeobox protein 4-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsZhang, H. / Cheng, N. / Li, Z. / Zhang, W. / Dong, X. / Huang, J. / Meng, G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81770142 China
National Natural Science Foundation of China (NSFC)81970132 China
CitationJournal: Cancer Commun (Lond) / Year: 2021
Title: DNA crosslinking and recombination-activating genes 1/2 (RAG1/2) are required for oncogenic splicing in acute lymphoblastic leukemia.
Authors: Zhang, H. / Cheng, N. / Li, Z. / Bai, L. / Fang, C. / Li, Y. / Zhang, W. / Dong, X. / Jiang, M. / Liang, Y. / Zhang, S. / Mi, J. / Zhu, J. / Zhang, Y. / Chen, S.J. / Zhao, Y. / Weng, X.Q. / ...Authors: Zhang, H. / Cheng, N. / Li, Z. / Bai, L. / Fang, C. / Li, Y. / Zhang, W. / Dong, X. / Jiang, M. / Liang, Y. / Zhang, S. / Mi, J. / Zhu, J. / Zhang, Y. / Chen, S.J. / Zhao, Y. / Weng, X.Q. / Hu, W. / Chen, Z. / Huang, J. / Meng, G.
History
DepositionJan 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: 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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Double homeobox protein 4-like protein 2
B: Double homeobox protein 4-like protein 2
E: DNA (5'-D(P*CP*GP*AP*CP*TP*TP*GP*AP*TP*GP*AP*GP*AP*TP*TP*AP*GP*AP*CP*TP*G)-3')
F: DNA (5'-D(P*CP*GP*AP*CP*TP*TP*GP*AP*TP*GP*AP*GP*AP*TP*TP*AP*GP*AP*CP*TP*G)-3')
C: DNA (5'-D(P*CP*GP*AP*CP*TP*TP*GP*AP*TP*GP*AP*GP*AP*TP*TP*AP*GP*AP*CP*TP*G)-3')
D: DNA (5'-D(P*CP*GP*AP*CP*TP*TP*GP*AP*TP*GP*AP*GP*AP*TP*TP*AP*GP*AP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8167
Polymers60,7376
Non-polymers801
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13850 Å2
ΔGint-55 kcal/mol
Surface area26850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.974, 64.451, 69.432
Angle α, β, γ (deg.)95.82, 92.55, 103.31
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Double homeobox protein 4-like protein 2


Mass: 17483.920 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUX4L2 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CJ85
#2: DNA chain DNA (5'-D(P*CP*GP*AP*CP*TP*TP*GP*AP*TP*GP*AP*GP*AP*TP*TP*AP*GP*AP*CP*TP*G)-3')


Mass: 6502.220 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*CP*GP*AP*CP*TP*TP*GP*AP*TP*GP*AP*GP*AP*TP*TP*AP*GP*AP*CP*TP*G)-3')


Mass: 6382.148 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.06 Å3/Da / Density % sol: 59.77 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.83→41.7 Å / Num. obs: 12265 / % possible obs: 92 % / Redundancy: 2.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.18 / Net I/σ(I): 3.9
Reflection shellResolution: 2.83→2.85 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 453 / CC1/2: 0.644 / % possible all: 85

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A8R
Resolution: 2.83→41.7 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.83 / Phase error: 28.63
RfactorNum. reflection% reflection
Rfree0.2416 559 4.56 %
Rwork0.2228 --
obs0.2237 12254 71.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.83→41.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2184 1722 1 8 3915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054176
X-RAY DIFFRACTIONf_angle_d0.8786001
X-RAY DIFFRACTIONf_dihedral_angle_d27.3052231
X-RAY DIFFRACTIONf_chiral_restr0.045633
X-RAY DIFFRACTIONf_plane_restr0.005501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.83-3.11180.4974500.35831453X-RAY DIFFRACTION35
3.1118-3.56180.29421620.26152792X-RAY DIFFRACTION69
3.5618-4.48670.24621680.22953550X-RAY DIFFRACTION86
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.99690.5927-0.07171.7685-0.04851.95280.0553-0.24470.30990.22770.08170.38140.0521-0.26570.09240.3407-0.12790.17480.62290.07350.40922.956612.934350.6061
20.18110.18570.13470.35080.40220.54050.1583-0.2513-0.2105-0.1849-0.29660.4794-0.1075-0.729-0.41970.11050.2023-0.16370.5829-0.06140.3567-2.474621.09736.1173
31.56481.2074-0.57020.996-0.33640.3567-0.0345-0.24530.55960.00240.20090.6617-0.1564-0.2286-0.09410.1580.3134-0.05620.6381-0.01880.4539-2.241727.270145.0794
41.0501-0.0840.44380.44940.20171.4956-0.2068-0.18690.19480.0251-0.1533-0.0525-0.03160.28-0.8656-0.35960.1889-0.33520.32360.0390.08196.346317.771537.9358
54.24471.60891.95752.96920.84440.90870.0325-0.4702-0.11050.5967-0.1794-0.10810.5333-0.0051-0.14760.4712-0.05690.01150.5419-0.030.088610.500310.451424.3317
65.543-2.0202-1.92378.2192-2.83126.02940.24080.1934-0.6448-0.30670.22720.68210.0136-0.5371-0.18930.14710.2359-0.06840.7086-0.05190.37719.63911.08213.0365
78.8137-7.132-6.88086.09255.6725.42650.04220.34650.2342-0.4007-0.18990.779-0.4198-0.54910.12551.56-0.03040.62931.3504-0.21971.45734.84972.62146.8111
80.763-1.27260.37942.1456-0.62020.18120.11610.0209-0.07490.2393-0.06890.0687-0.3273-0.2838-0.21980.6132-0.0699-0.04750.5827-0.17150.795519.5035-10.19641.2857
91.47850.1282-0.6721.62570.32033.545-0.1104-0.25010.24530.52260.0006-0.4781-0.15880.2793-0.32360.48090.0287-0.38610.5081-0.23430.388138.2361-16.02043.6703
101.7948-0.20150.05922.16651.48551.49530.163-0.390.2173-0.14760.1304-0.944-0.40650.55-0.12460.3035-0.0114-0.07060.4289-0.08450.464634.677-7.70254.3896
116.8614-2.96492.06422.0206-0.58211.1436-0.1147-0.1897-0.01190.31460.0489-0.53120.05470.6038-0.04920.747-0.04390.15080.63640.05730.463333.292212.2903-0.161
121.54121.2529-1.64071.4946-2.19873.331-0.03670.42190.3571-0.6689-0.10890.1545-0.7075-0.0842-0.03080.88830.19490.03330.47850.05030.562118.243216.2519-1.6528
131.0250.9841-0.65521.0523-0.79011.2488-0.01020.6108-0.0746-1.12730.08130.0998-0.0636-0.01050.15340.59970.1357-0.02190.7046-0.15410.540916.87076.1835-2.6597
141.9956-0.0357-0.72361.6935-0.16541.6447-0.1201-0.1478-0.3193-0.2528-0.2562-0.4172-0.0570.52350.03930.43240.0415-0.00560.42340.07740.225321.61959.83127.593
151.05810.3553-0.6390.62250.60592.7931-0.09990.41610.1075-0.4572-0.01670.0122-0.34660.2218-0.1150.65310.0965-0.05950.5290.03240.148911.332319.411822.6241
161.11770.63940.8310.49190.59771.02350.18590.1569-0.1857-0.35440.08360.28810.3075-0.137-0.15541.08820.3087-0.28520.67880.1820.68034.260732.657927.4406
171.0315-0.05170.30560.0585-0.11330.25060.0302-0.1699-0.0165-0.0431-0.2039-0.42240.00430.18660.44280.62850.088-0.14170.32420.12690.379611.800835.56846.5376
180.84410.0621-0.37511.0650.27471.2239-0.2559-0.3544-0.12430.20720.1648-0.09580.0491-0.01650.03550.16150.01660.01370.24940.01360.162218.580825.680757.4405
190.72220.39671.01830.7751-0.40163.3625-0.46050.08430.2451-0.6037-0.2423-0.1886-1.30890.413-0.84080.4712-0.15-0.00010.1878-0.00890.566623.629436.440242.5535
201.11650.3424-0.23412.36181.04533.2989-0.0905-0.4798-0.3938-0.2319-0.60.37241.1923-0.2377-1.49850.5358-0.0641-0.01380.27520.18010.56669.77965.405142.6589
211.96790.1921-0.30251.7330.37932.07530.0354-0.2002-0.7991-0.0092-0.2681-0.3570.73040.1989-0.17790.8251-0.18010.20080.19860.0980.84277.4827-4.435740.2618
221.32210.4325-0.020.70370.00850.80970.1215-0.1689-0.1278-0.2145-0.2678-0.1447-0.06120.1035-0.06590.2086-0.07770.070.25510.0020.201616.714718.807142.5153
230.7864-0.6884-0.56431.69171.45971.26190.4027-0.35620.67590.1038-0.49340.107-0.71150.0440.14521.025-0.38010.05310.5288-0.06580.653221.688941.902744.5062
240.0225-0.00190.04160.1613-0.27010.5077-0.0167-0.0993-0.07680.0292-0.0601-0.1263-0.04560.12850.02951.0735-0.5848-0.29680.75670.44761.111132.62848.755248.5101
252.5034-0.0235-1.3353.4044-0.95444.0199-0.0952-0.1683-0.3277-0.10140.0480.8775-0.0827-0.6422-0.03760.9971-0.25590.03440.48260.06810.817617.0277-23.981116.2873
260.8725-0.10580.05531.0533-0.38531.05890.21460.17740.14390.2347-0.3219-0.04710.2588-0.2443-0.07340.33430.0868-0.08870.3184-0.13620.346622.0632-8.04558.9017
272.21461.2413-0.97991.003-0.68121.306-0.1659-0.5212-0.0079-0.708-0.4146-0.7993-0.56730.74360.31250.622-0.19240.11420.6025-0.01070.757932.860513.65112.3559
280.3850.79390.50462.17241.35840.85-0.0889-0.1640.34930.37050.0637-0.6714-0.31420.494-0.01391.3027-0.4703-0.40361.0295-0.34711.227434.833832.695310.2486
297.67561.25593.57732.39162.08373.8647-0.4252-0.11470.50470.224-0.098-0.7769-0.83280.81740.23741.0315-0.41220.00730.74510.01391.035436.200824.956615.0484
300.13570.1274-0.14371.22370.00810.24230.68240.20110.6425-0.5831-0.6595-0.23890.25070.55-0.23910.54750.07290.1460.46790.03480.379331.32758.90488.3692
310.851-0.5833-0.26252.72261.0451.6967-0.2794-0.163-0.63540.1013-0.22440.17690.6918-0.10190.29890.6818-0.03490.12280.4088-0.03560.601920.3833-12.456612.9636
326.37-5.7106-3.12925.32043.00461.73520.00820.0931-0.0241-0.1242-0.0254-0.17860.23170.2553-0.06090.7423-0.21020.22690.60070.08631.196319.7495-32.308112.0379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 45 )
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 59 )
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 77 )
5X-RAY DIFFRACTION5chain 'A' and (resid 78 through 82 )
6X-RAY DIFFRACTION6chain 'A' and (resid 83 through 87 )
7X-RAY DIFFRACTION7chain 'A' and (resid 88 through 92 )
8X-RAY DIFFRACTION8chain 'A' and (resid 93 through 102 )
9X-RAY DIFFRACTION9chain 'A' and (resid 103 through 115 )
10X-RAY DIFFRACTION10chain 'A' and (resid 116 through 150 )
11X-RAY DIFFRACTION11chain 'B' and (resid 20 through 27 )
12X-RAY DIFFRACTION12chain 'B' and (resid 28 through 38 )
13X-RAY DIFFRACTION13chain 'B' and (resid 39 through 59 )
14X-RAY DIFFRACTION14chain 'B' and (resid 60 through 77 )
15X-RAY DIFFRACTION15chain 'B' and (resid 78 through 87 )
16X-RAY DIFFRACTION16chain 'B' and (resid 88 through 92 )
17X-RAY DIFFRACTION17chain 'B' and (resid 93 through 102 )
18X-RAY DIFFRACTION18chain 'B' and (resid 103 through 150 )
19X-RAY DIFFRACTION19chain 'E' and (resid 1 through 10 )
20X-RAY DIFFRACTION20chain 'E' and (resid 11 through 21 )
21X-RAY DIFFRACTION21chain 'F' and (resid 1 through 5 )
22X-RAY DIFFRACTION22chain 'F' and (resid 6 through 15 )
23X-RAY DIFFRACTION23chain 'F' and (resid 16 through 20 )
24X-RAY DIFFRACTION24chain 'F' and (resid 21 through 21 )
25X-RAY DIFFRACTION25chain 'C' and (resid 1 through 5 )
26X-RAY DIFFRACTION26chain 'C' and (resid 6 through 10 )
27X-RAY DIFFRACTION27chain 'C' and (resid 11 through 20 )
28X-RAY DIFFRACTION28chain 'C' and (resid 21 through 21 )
29X-RAY DIFFRACTION29chain 'D' and (resid 1 through 5 )
30X-RAY DIFFRACTION30chain 'D' and (resid 6 through 10 )
31X-RAY DIFFRACTION31chain 'D' and (resid 11 through 20 )
32X-RAY DIFFRACTION32chain 'D' and (resid 21 through 21 )

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