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- PDB-8yzs: Structure of the NACC1 BEN domain in complex with its target DNA -

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Basic information

Entry
Database: PDB / ID: 8yzs
TitleStructure of the NACC1 BEN domain in complex with its target DNA
Components
  • CATG-containing DNA
  • Nucleus accumbens-associated protein 1
KeywordsDNA BINDING PROTEIN / NACC1 / BEN domain
Function / homology
Function and homology information


DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / cell junction / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / nucleoplasm ...DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / cell junction / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
BEN domain / BEN domain / BEN domain profile. / BEN / : / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Nucleus accumbens-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 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 ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleus accumbens-associated protein 1
B: Nucleus accumbens-associated protein 1
C: Nucleus accumbens-associated protein 1
D: Nucleus accumbens-associated protein 1
E: CATG-containing DNA
F: CATG-containing DNA
G: CATG-containing DNA
H: CATG-containing DNA


Theoretical massNumber of molelcules
Total (without water)76,6198
Polymers76,6198
Non-polymers00
Water2,378132
1
A: Nucleus accumbens-associated protein 1
E: CATG-containing DNA
F: CATG-containing DNA


Theoretical massNumber of molelcules
Total (without water)22,5023
Polymers22,5023
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-13 kcal/mol
Surface area11130 Å2
MethodPISA
2
B: Nucleus accumbens-associated protein 1
G: CATG-containing DNA
H: CATG-containing DNA


Theoretical massNumber of molelcules
Total (without water)22,5023
Polymers22,5023
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-12 kcal/mol
Surface area10580 Å2
MethodPISA
3
C: Nucleus accumbens-associated protein 1


Theoretical massNumber of molelcules
Total (without water)15,8071
Polymers15,8071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6840 Å2
MethodPISA
4
D: Nucleus accumbens-associated protein 1


Theoretical massNumber of molelcules
Total (without water)15,8071
Polymers15,8071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.126, 83.883, 133.845
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
Nucleus accumbens-associated protein 1 / NAC-1 / BTB/POZ domain-containing protein 14B


Mass: 15807.461 Da / Num. of mol.: 4 / Fragment: BEN domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NACC1, BTBD14B, NAC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96RE7
#2: DNA chain
CATG-containing DNA


Mass: 3347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.85 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M imidazole at pH of 7.0 and 12% (w/v) polyethylene glycol 20,000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 38861 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 44.16 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 21.4
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 1.096 / Num. unique obs: 1926

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.31→28.83 Å / SU ML: 0.3201 / Cross valid method: FREE R-VALUE / σ(F): 1.2 / Phase error: 26.9913 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2423 1938 5 %
Rwork0.206 36803 -
obs0.2079 38741 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.86 Å2
Refinement stepCycle: LAST / Resolution: 2.31→28.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3834 888 0 132 4854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00944892
X-RAY DIFFRACTIONf_angle_d1.09286782
X-RAY DIFFRACTIONf_chiral_restr0.0602756
X-RAY DIFFRACTIONf_plane_restr0.007732
X-RAY DIFFRACTIONf_dihedral_angle_d23.90761907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.360.36931220.27992418X-RAY DIFFRACTION93.55
2.36-2.430.32111690.26322594X-RAY DIFFRACTION100
2.43-2.50.32411400.25132594X-RAY DIFFRACTION100
2.5-2.580.32651340.24492622X-RAY DIFFRACTION100
2.58-2.670.3011200.24582623X-RAY DIFFRACTION100
2.67-2.780.27881360.24012629X-RAY DIFFRACTION100
2.78-2.910.35131210.25532625X-RAY DIFFRACTION100
2.91-3.060.32231230.24682631X-RAY DIFFRACTION100
3.06-3.250.24641360.23662648X-RAY DIFFRACTION99.75
3.25-3.50.24841230.21622633X-RAY DIFFRACTION99.28
3.5-3.850.24221430.19692645X-RAY DIFFRACTION99.86
3.85-4.410.20091550.17582658X-RAY DIFFRACTION100
4.41-5.550.2081540.16892673X-RAY DIFFRACTION99.96
5.55-28.830.19641620.17472810X-RAY DIFFRACTION99.77

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