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- PDB-7y3k: Structure of SALL4 ZFC4 bound with 16 bp AT-rich dsDNA -

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Basic information

Entry
Database: PDB / ID: 7y3k
TitleStructure of SALL4 ZFC4 bound with 16 bp AT-rich dsDNA
Components
  • (DNA (16-mer)) x 2
  • Sal-like protein 4
KeywordsDNA BINDING PROTEIN/DNA / SALL4 / zinc finger / AT-rich DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Transcriptional regulation of pluripotent stem cells / embryonic limb morphogenesis / ventricular septum development / inner cell mass cell proliferation / somatic stem cell population maintenance / heterochromatin / Regulation of PTEN gene transcription / neural tube closure / DNA-binding transcription factor activity, RNA polymerase II-specific ...POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Transcriptional regulation of pluripotent stem cells / embryonic limb morphogenesis / ventricular septum development / inner cell mass cell proliferation / somatic stem cell population maintenance / heterochromatin / Regulation of PTEN gene transcription / neural tube closure / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular membrane-bounded organelle / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / 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) / Sal-like protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsRu, W. / Xu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
Citation
Journal: J.Biol.Chem. / Year: 2022
Title: Structural studies of SALL family protein zinc finger cluster domains in complex with DNA reveal preferential binding to an AATA tetranucleotide motif.
Authors: Ru, W. / Koga, T. / Wang, X. / Guo, Q. / Gearhart, M.D. / Zhao, S. / Murphy, M. / Kawakami, H. / Corcoran, D. / Zhang, J. / Zhu, Z. / Yao, X. / Kawakami, Y. / Xu, C.
#1: Journal: J.Biol.Chem. / Year: 2022
Title: Structural studies of SALL family protein zinc finger cluster domains in complex with DNA reveal preferential binding to an AATA tetranucleotide motif
Authors: Ru, W. / Koga, T. / Wang, X. / Guo, Q. / Gearhart, M.D. / Zhao, S. / Murphy, M. / Kawakami, H. / Corcoran, D. / Zhang, J. / Zhu, Z. / Yao, X. / Kawakami, Y. / Xu, C.
History
DepositionJun 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Nov 30, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 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

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Assembly

Deposited unit
A: Sal-like protein 4
G: DNA (16-mer)
H: DNA (16-mer)
B: Sal-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4728
Polymers27,2104
Non-polymers2624
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-41 kcal/mol
Surface area11340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.364, 49.868, 105.406
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sal-like protein 4 / Zinc finger protein 797 / Zinc finger protein SALL4


Mass: 8708.993 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SALL4, ZNF797 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJQ4
#2: DNA chain DNA (16-mer)


Mass: 4896.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (16-mer)


Mass: 4896.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M BIS-TRIS, pH 5.5, 0.2 M Sodium chloride, 25% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 8329 / % possible obs: 99.6 % / Redundancy: 10.1 % / CC1/2: 0.969 / Net I/σ(I): 19
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 8329 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Y3I

7y3i


Resolution: 2.501→28.722 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2504 831 9.98 %
Rwork0.2059 7498 -
obs0.2103 8329 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.01 Å2 / Biso mean: 59.5261 Å2 / Biso min: 26.26 Å2
Refinement stepCycle: final / Resolution: 2.501→28.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms818 656 4 16 1494
Biso mean--55.21 41.39 -
Num. residues----140
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.501-2.65730.31271340.2854120398
2.6573-2.86230.37471370.29931229100
2.8623-3.150.37321360.28911226100
3.15-3.6050.22041370.20761249100
3.605-4.53910.24571400.18371255100
4.5391-28.7220.19211470.16111336100
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)
11.52680.4275-0.58630.2354-0.53290.1478-0.0711-0.3240.31490.08380.07320.5078-0.04310.00160.00050.34050.01-0.03220.3239-0.04890.417112.72873.978823.9715
21.08120.94880.07750.7740.17750.8023-0.0936-0.07310.11880.03840.20320.10590.12820.0826-00.4011-0.00820.040.3762-0.06380.362910.00520.349515.176
30.17040.3523-0.08981.8865-0.79920.9299-0.02820.5007-0.08440.0878-0.17310.29730.0788-0.060.00060.399-0.00660.01050.4475-0.130.442210.2258-1.279912.4049
40.2734-0.3091-0.14150.77430.48450.9901-0.29820.10020.4568-0.53620.1104-0.00320.1010.2924-0.01090.6156-0.0858-0.05290.6795-0.01060.470113.076-0.49780.4626
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 868 through 921)A868 - 921
2X-RAY DIFFRACTION2(chain 'G' and resid 1 through 16)G1 - 16
3X-RAY DIFFRACTION3(chain 'H' and resid 1 through 16)H1 - 16
4X-RAY DIFFRACTION4(chain 'B' and resid 868 through 921)B868 - 921

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