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- PDB-5v3m: mouseZFP568-ZnF1-11 in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 5v3m
TitlemouseZFP568-ZnF1-11 in complex with DNA
Components
  • (DNA (28-MER)) x 2
  • Zinc finger protein 568
Keywordsdna binding protein/dna / C2H2 type Zinc fingers / DNA binding / transferase-dna complex / dna binding protein-dna complex
Function / homology
Function and homology information


convergent extension involved in axis elongation / convergent extension involved in neural plate elongation / embryonic placenta morphogenesis / regulation of cell communication / transcription corepressor binding / in utero embryonic development / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription ...convergent extension involved in axis elongation / convergent extension involved in neural plate elongation / embryonic placenta morphogenesis / regulation of cell communication / transcription corepressor binding / in utero embryonic development / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleus / metal ion binding
Similarity search - Function
Krueppel-associated box (KRAB) profile. / KRAB box / krueppel associated box / Krueppel-associated box / KRAB domain superfamily / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
DNA / DNA (> 10) / Zinc finger protein 568
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.091 Å
AuthorsPatel, A. / Cheng, X.
CitationJournal: Cell / Year: 2018
Title: DNA Conformation Induces Adaptable Binding by Tandem Zinc Finger Proteins.
Authors: Patel, A. / Yang, P. / Tinkham, M. / Pradhan, M. / Sun, M.A. / Wang, Y. / Hoang, D. / Wolf, G. / Horton, J.R. / Zhang, X. / Macfarlan, T. / Cheng, X.
History
DepositionMar 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (28-MER)
B: DNA (28-MER)
C: Zinc finger protein 568
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,91913
Polymers53,2643
Non-polymers65410
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8690 Å2
ΔGint-62 kcal/mol
Surface area22240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.954, 92.758, 353.667
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-131-

HOH

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Components

#1: DNA chain DNA (28-MER)


Mass: 8784.666 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#2: DNA chain DNA (28-MER)


Mass: 8428.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: Protein Zinc finger protein 568


Mass: 36051.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Znf568, chato, Zfp568
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: E9PYI1
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10% Isopropanol, 0.1M Bicine(pH 8.5) and 30% (W/V) PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→32.245 Å / Num. obs: 53292 / % possible obs: 81.7 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.067 / Χ2: 0.996 / Net I/σ(I): 26
Reflection shellResolution: 2.09→2.16 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1160 / CC1/2: 0.91 / Rsym value: 0.159 / Χ2: 1.002 / % possible all: 32.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.091→32.245 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2532 2661 5 %
Rwork0.2128 --
obs0.2148 53174 78.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.091→32.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 1142 10 139 3352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0253441
X-RAY DIFFRACTIONf_angle_d1.0954827
X-RAY DIFFRACTIONf_dihedral_angle_d23.9391825
X-RAY DIFFRACTIONf_chiral_restr0.055516
X-RAY DIFFRACTIONf_plane_restr0.008435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0914-2.12950.5048370.3364774X-RAY DIFFRACTION23
2.1295-2.17040.4071600.31351087X-RAY DIFFRACTION33
2.1704-2.21470.2773680.29591259X-RAY DIFFRACTION38
2.2147-2.26290.3871880.28041727X-RAY DIFFRACTION50
2.2629-2.31550.36741010.28651907X-RAY DIFFRACTION58
2.3155-2.37340.3181190.26212437X-RAY DIFFRACTION69
2.3734-2.43750.34361420.27672639X-RAY DIFFRACTION80
2.4375-2.50920.33931600.27323000X-RAY DIFFRACTION89
2.5092-2.59020.3151640.27073117X-RAY DIFFRACTION91
2.5902-2.68270.30471680.27123138X-RAY DIFFRACTION95
2.6827-2.79010.3111680.27833249X-RAY DIFFRACTION95
2.7901-2.9170.34481760.26633303X-RAY DIFFRACTION98
2.917-3.07060.32541720.26983244X-RAY DIFFRACTION96
3.0706-3.26280.26241730.22953174X-RAY DIFFRACTION93
3.2628-3.51450.24111710.20213176X-RAY DIFFRACTION96
3.5145-3.86760.25721700.18453258X-RAY DIFFRACTION96
3.8676-4.42610.1841770.17083326X-RAY DIFFRACTION98
4.4261-5.57170.20161760.17723357X-RAY DIFFRACTION100
5.5717-32.24920.18831710.1673341X-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)
15.19653.9071-5.29674.1859-2.81776.8996-0.1421-0.01790.38180.0820.16522.30211.0151-1.249-0.03790.8108-0.16840.10840.7576-0.02061.0667-26.7694-14.8552-38.0945
23.4726-0.6510.58037.2646-2.76252.0399-0.16660.411-0.7119-0.2390.361-0.25341.21240.2905-0.18930.50530.04810.02880.2584-0.12580.4638-8.9466-12.3972-25.7044
31.98670.0495-2.13822.18582.21014.65480.09030.1379-0.71020.27490.1105-0.18381.39140.1467-0.2050.5815-0.03120.03490.1984-0.0250.3862-12.2499-10.2295-14.2596
43.1752-0.04820.37951.9745-1.20951.2044-0.0568-0.24470.24410.33690.14860.5048-0.4607-0.5-0.04490.28840.07760.04240.2256-0.05380.2821-22.89823.5603-14.4485
51.8852-1.7762-1.42462.25131.58621.1824-0.1276-0.02150.4545-0.07820.07040.6254-0.7949-0.44590.00630.63480.1542-0.12910.2763-0.02570.4269-21.900513.5254-17.0157
61.48760.18260.61642.04330.76471.1751-0.43420.63710.1286-0.39030.4739-0.1269-0.64340.5456-0.04140.7977-0.39140.08580.53450.00570.3059-8.60288.0248-33.9261
75.09380.9367-2.01587.0174-6.2886.1485-0.14620.5610.342-0.0428-0.0193-0.1428-0.8817-0.20150.08551.0004-0.3270.02780.81730.15840.1823-20.511211.6556-49.1375
82.8244-0.5845-1.29190.45530.04690.7340.65750.671.12220.194-0.3997-0.3431-0.99660.081-0.40211.793-0.45020.0151.24460.5720.8649-11.280424.6159-55.4182
92.1346-0.0725-1.77811.4791-0.08372.97460.08740.72130.0318-0.8177-0.201-0.605-0.66720.72710.09911.2322-0.52770.10712.21420.10260.5369-2.683611.4458-68.3257
101.23660.86770.68891.97811.45942.13840.08040.5138-0.1314-0.9698-0.18760.26260.2875-0.16080.02711.9685-0.0355-0.15412.127-0.08920.3362-14.97679.1036-80.6795
112.012-1.8588-0.99751.83730.75392.71610.07510.95320.3576-0.6136-0.1722-0.0833-0.6608-0.1473-0.11390.8963-0.520.11551.31560.05770.2902-12.26889.1992-56.4762
122.04120.911-2.14281.5624-1.93573.1275-0.40710.42720.0521-0.43920.35690.0915-0.93440.46420.0680.5196-0.1559-0.01940.20170.01370.273-8.73057.7963-19.9468
130.50011.01750.26092.1525-0.08746.1654-0.00840.08820.0332-0.0330.2178-0.1491-0.9310.5262-0.21450.3321-0.09030.00830.2253-0.00270.2565-9.63916.0896-13.9297
140.44230.20171.06260.99110.72082.6287-0.0261.18750.1032-0.27050.4486-0.1209-0.72620.5001-0.22670.9848-0.4508-0.04720.98970.11130.3716-10.33279.314-47.208
152.3734-0.2293-0.43950.4726-0.20628.930.04480.8268-0.11640.25460.56080.1427-0.7655-1.2086-0.52251.5326-0.4068-0.33132.20280.13760.6653-18.953811.8059-70.0867
160.612-0.64691.05981.9632-0.51542.12110.171-0.61180.2136-1.09230.4733-0.5276-1.41521.8579-0.59112.0454-0.37880.08873.11140.13150.7788-12.60516.6048-83.8078
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 362 through 388 )
2X-RAY DIFFRACTION2chain 'C' and (resid 389 through 413 )
3X-RAY DIFFRACTION3chain 'C' and (resid 414 through 430 )
4X-RAY DIFFRACTION4chain 'C' and (resid 431 through 452 )
5X-RAY DIFFRACTION5chain 'C' and (resid 453 through 468 )
6X-RAY DIFFRACTION6chain 'C' and (resid 469 through 564 )
7X-RAY DIFFRACTION7chain 'C' and (resid 565 through 580 )
8X-RAY DIFFRACTION8chain 'C' and (resid 581 through 598 )
9X-RAY DIFFRACTION9chain 'C' and (resid 599 through 638 )
10X-RAY DIFFRACTION10chain 'A' and (resid 1 through 5 )
11X-RAY DIFFRACTION11chain 'A' and (resid 6 through 15 )
12X-RAY DIFFRACTION12chain 'A' and (resid 16 through 28 )
13X-RAY DIFFRACTION13chain 'B' and (resid 1 through 10 )
14X-RAY DIFFRACTION14chain 'B' and (resid 11 through 20 )
15X-RAY DIFFRACTION15chain 'B' and (resid 21 through 25 )
16X-RAY DIFFRACTION16chain 'B' and (resid 26 through 28 )

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