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- PDB-8yzt: Crystal structure of the BANP BEN domain in complex with its targ... -

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Basic information

Entry
Database: PDB / ID: 8yzt
TitleCrystal structure of the BANP BEN domain in complex with its target DNA
Components
  • CGCG-containing DNA
  • Protein BANP
KeywordsDNA BINDING PROTEIN / BANP / CpG island / BEN domain / DNA binding domain
Function / homology
Function and homology information


Regulation of TP53 Activity through Association with Co-factors / protein localization to nucleus / negative regulation of protein catabolic process / chromatin organization / nuclear body / DNA binding / nucleoplasm / identical protein binding
Similarity search - Function
Protein BANP / BEN domain / BEN domain / BEN domain profile. / BEN
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein BANP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsRen, J. / Wang, Z.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071204 China
National Natural Science Foundation of China (NSFC)32125008 China
National Natural Science Foundation of China (NSFC)32100977 China
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structural basis of DNA recognition by BEN domain proteins reveals a role for oligomerization in unmethylated DNA selection by BANP.
Authors: Ren, J. / Wang, J. / Ren, Y. / Zhang, Y. / Wei, P. / Wang, M. / Zhang, Y. / Li, M. / Yuan, C. / Gong, H. / Jiang, J. / Wang, Z.
History
DepositionApr 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein BANP
B: Protein BANP
C: Protein BANP
D: Protein BANP
E: CGCG-containing DNA
F: CGCG-containing DNA


Theoretical massNumber of molelcules
Total (without water)64,6486
Polymers64,6486
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.995, 58.060, 214.381
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Protein BANP / BEN domain-containing protein 1 / Btg3-associated nuclear protein / Scaffold/matrix-associated ...BEN domain-containing protein 1 / Btg3-associated nuclear protein / Scaffold/matrix-associated region-1-binding protein


Mass: 14186.171 Da / Num. of mol.: 4 / Fragment: BEN domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BANP, BEND1, SMAR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N9N5
#2: DNA chain CGCG-containing DNA


Mass: 3951.586 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: containing 0.02 M citric acid, 0.08 M BIS-Tris propane (pH: 8.8) and 16% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.58→39.36 Å / Num. obs: 23248 / % possible obs: 99.1 % / Redundancy: 8 % / Biso Wilson estimate: 49.36 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 16.6
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.591 / Num. unique obs: 1109

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.58→39.36 Å / SU ML: 0.3355 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 36.6143 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.3046 1078 4.69 %
Rwork0.2253 21905 -
obs0.2289 22983 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.97 Å2
Refinement stepCycle: LAST / Resolution: 2.58→39.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3921 524 0 15 4460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00934591
X-RAY DIFFRACTIONf_angle_d0.98376296
X-RAY DIFFRACTIONf_chiral_restr0.0561674
X-RAY DIFFRACTIONf_plane_restr0.0069717
X-RAY DIFFRACTIONf_dihedral_angle_d24.73421776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.70.38441260.3042436X-RAY DIFFRACTION89.08
2.7-2.840.37911150.27382695X-RAY DIFFRACTION97.27
2.84-3.020.32861270.27822753X-RAY DIFFRACTION98.83
3.02-3.250.35731190.25512740X-RAY DIFFRACTION97.91
3.25-3.580.30911540.2142705X-RAY DIFFRACTION98.05
3.58-4.10.26391380.19482783X-RAY DIFFRACTION99.39
4.1-5.160.25421320.18832842X-RAY DIFFRACTION99.83
5.16-39.360.31391670.23382951X-RAY DIFFRACTION99.33

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