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- PDB-7y3l: Structure of SALL3 ZFC4 bound with 12 bp AT-rich dsDNA -

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Basic information

Entry
Database: PDB / ID: 7y3l
TitleStructure of SALL3 ZFC4 bound with 12 bp AT-rich dsDNA
Components
  • (DNA (12-mer)) x 2
  • Sal-like protein 3
KeywordsDNA BINDING PROTEIN/DNA / SALL3 / zinc finger / DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / metal ion binding / nucleus
Similarity search - Function
: / Zinc-finger of C2H2 type / 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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 3
G: DNA (12-mer)
H: DNA (12-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0995
Polymers14,9693
Non-polymers1312
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-23 kcal/mol
Surface area7730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.549, 39.422, 37.986
Angle α, β, γ (deg.)90.000, 103.200, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Sal-like protein 3 / Zinc finger protein 796 / Zinc finger protein SALL3 / hSALL3


Mass: 7645.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SALL3, ZNF796 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BXA9
#2: DNA chain DNA (12-mer)


Mass: 3670.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (12-mer)


Mass: 3652.402 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.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES monohydrate, pH 6.5, 0.2 M Ammonium sulfate, 30% w/v polyethylene glycol monomethyl ether 5000

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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: Oct 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→37.06 Å / Num. obs: 5606 / % possible obs: 98.4 % / Redundancy: 6.1 % / CC1/2: 0.997 / Net I/σ(I): 13
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 644 / CC1/2: 0.979

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Processing

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

7y3i


Resolution: 2.5→37.056 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2604 262 4.7 %
Rwork0.2174 5317 -
obs0.2197 5579 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.94 Å2 / Biso mean: 39.3404 Å2 / Biso min: 18.32 Å2
Refinement stepCycle: final / Resolution: 2.5→37.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms439 492 2 36 969
Biso mean--34.76 38.88 -
Num. residues----81
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5001-3.14960.35481300.2693264698
3.1496-37.0560.2271320.1985267197

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