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- PDB-6m2v: Crystal structure of UHRF1 SRA complexed with fully-mCHG DNA. -

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Basic information

Entry
Database: PDB / ID: 6m2v
TitleCrystal structure of UHRF1 SRA complexed with fully-mCHG DNA.
Components
  • DNA (5'-D(*TP*CP*AP*CP*GP*(5CM)P*TP*GP*CP*GP*TP*GP*A)-3')
  • E3 ubiquitin-protein ligase UHRF1
KeywordsDNA BINDING PROTEIN/DNA / 5-methyl-cytosine / complex / epigenetics / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


histone H3 ubiquitin ligase activity / hemi-methylated DNA-binding / regulation of epithelial cell proliferation / methyl-CpG binding / negative regulation of gene expression via chromosomal CpG island methylation / mitotic spindle assembly / protein autoubiquitination / cis-regulatory region sequence-specific DNA binding / heterochromatin / heterochromatin formation ...histone H3 ubiquitin ligase activity / hemi-methylated DNA-binding / regulation of epithelial cell proliferation / methyl-CpG binding / negative regulation of gene expression via chromosomal CpG island methylation / mitotic spindle assembly / protein autoubiquitination / cis-regulatory region sequence-specific DNA binding / heterochromatin / heterochromatin formation / methylated histone binding / positive regulation of protein metabolic process / replication fork / euchromatin / RING-type E3 ubiquitin transferase / nuclear matrix / ubiquitin protein ligase activity / histone binding / ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA repair / chromatin / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
: / UHRF1, tandem tudor domain / UHRF1/2-like / Tandem tudor domain within UHRF1 / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / PUA-like superfamily ...: / UHRF1, tandem tudor domain / UHRF1/2-like / Tandem tudor domain within UHRF1 / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / PUA-like superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAbhishek, S. / Nakarakanti, N.K. / Deeksha, W. / Rajakumara, E.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
Science and Engineering Research Board (SERB) India
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: Mechanistic insights into recognition of symmetric methylated cytosines in CpG and non-CpG DNA by UHRF1 SRA.
Authors: Abhishek, S. / Nakarakanti, N.K. / Deeksha, W. / Rajakumara, E.
History
DepositionMar 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*TP*CP*AP*CP*GP*(5CM)P*TP*GP*CP*GP*TP*GP*A)-3')
D: DNA (5'-D(*TP*CP*AP*CP*GP*(5CM)P*TP*GP*CP*GP*TP*GP*A)-3')
B: E3 ubiquitin-protein ligase UHRF1
A: E3 ubiquitin-protein ligase UHRF1


Theoretical massNumber of molelcules
Total (without water)55,6814
Polymers55,6814
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-22 kcal/mol
Surface area21630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.897, 74.829, 141.505
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: DNA chain DNA (5'-D(*TP*CP*AP*CP*GP*(5CM)P*TP*GP*CP*GP*TP*GP*A)-3')


Mass: 3981.612 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: fully-mCHG DNA / Source: (synth.) synthetic construct (others)
#2: Protein E3 ubiquitin-protein ligase UHRF1 / Nuclear protein 95 / Nuclear zinc finger protein Np95 / RING-type E3 ubiquitin transferase UHRF1 / ...Nuclear protein 95 / Nuclear zinc finger protein Np95 / RING-type E3 ubiquitin transferase UHRF1 / Ubiquitin-like PHD and RING finger domain-containing protein 1 / mUhrf1 / Ubiquitin-like-containing PHD and RING finger domains protein 1


Mass: 23858.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Uhrf1, Np95 / Production host: Escherichia coli (E. coli) / Variant (production host): Rossetta2 (DE3)
References: UniProt: Q8VDF2, RING-type E3 ubiquitin transferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Bis-Tris, pH 8.0, 0.2M NaCl, 12% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 3→31.98 Å / Num. obs: 12430 / % possible obs: 99.73 % / Redundancy: 7.2 % / Biso Wilson estimate: 69.53 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1751 / Rpim(I) all: 0.06988 / Rrim(I) all: 0.1888 / Net I/σ(I): 9.24
Reflection shellResolution: 3→3.107 Å / Redundancy: 7.3 % / Num. unique obs: 1240 / CC1/2: 0.764 / % possible all: 99.92

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
MOLREP11.7.02phasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZO0

2zo0


Resolution: 3→31.98 Å / SU ML: 0.4492 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.0043
RfactorNum. reflection% reflectionSelection details
Rfree0.2761 621 5 %Random selection
Rwork0.2342 ---
obs0.2363 12426 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 59.4 Å2
Refinement stepCycle: LAST / Resolution: 3→31.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3007 528 0 10 3545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00363691
X-RAY DIFFRACTIONf_angle_d0.70775119
X-RAY DIFFRACTIONf_chiral_restr0.0462525
X-RAY DIFFRACTIONf_plane_restr0.0058588
X-RAY DIFFRACTIONf_dihedral_angle_d22.0669676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.30.36361550.31352889X-RAY DIFFRACTION99.97
3.3-3.780.28851620.26452895X-RAY DIFFRACTION99.9
3.78-4.760.27091520.2252945X-RAY DIFFRACTION99.97
4.76-31.980.24481520.20313076X-RAY DIFFRACTION99.6

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