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- PDB-3f8i: Mouse UHRF1 SRA domain bound with hemi-methylated CpG, crystal st... -

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Basic information

Entry
Database: PDB / ID: 3f8i
TitleMouse UHRF1 SRA domain bound with hemi-methylated CpG, crystal structure in space group P21
Components
  • 5'-D(*DCP*DCP*DAP*DTP*DGP*(5CM)P*DGP*DCP*DTP*DGP*DAP*DC)-3'
  • 5'-D(*DGP*DTP*DCP*DAP*DGP*DCP*DGP*DCP*DAP*DTP*DGP*DG)-3'
  • E3 ubiquitin-protein ligase UHRF1
KeywordsLIGASE/DNA / UHRF1 / base flipping / 5-methylcytosine / CpG methylation / Cell cycle / Developmental protein / DNA damage / DNA repair / DNA-binding / Ligase / Metal-binding / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Ubl conjugation / Ubl conjugation pathway / Zinc / Zinc-finger / LIGASE-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 / histone H3K9me2/3 reader activity / negative regulation of gene expression via chromosomal CpG island methylation / : / positive regulation of protein metabolic process / mitotic spindle assembly / heterochromatin ...histone H3 ubiquitin ligase activity / hemi-methylated DNA-binding / regulation of epithelial cell proliferation / methyl-CpG binding / histone H3K9me2/3 reader activity / negative regulation of gene expression via chromosomal CpG island methylation / : / positive regulation of protein metabolic process / mitotic spindle assembly / heterochromatin / protein autoubiquitination / cis-regulatory region sequence-specific DNA binding / replication fork / euchromatin / RING-type E3 ubiquitin transferase / nuclear matrix / ubiquitin protein ligase activity / heterochromatin formation / ubiquitin-dependent protein catabolic process / histone binding / DNA repair / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
SRA-YDG / PUA domain-like / : / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. ...SRA-YDG / PUA domain-like / : / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / 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 / PHD-finger / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger PHD-type signature. / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsHashimoto, H. / Horton, J.R. / Zhang, X. / Cheng, X.
Citation
Journal: Epigenetics / Year: 2009
Title: UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications.
Authors: Hashimoto, H. / Horton, J.R. / Zhang, X. / Cheng, X.
#1: Journal: Nature / Year: 2008
Title: The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix.
Authors: Hashimoto, H. / Horton, J.R. / Zhang, X. / Bostick, M. / Jacobsen, S.E. / Cheng, X.
History
DepositionNov 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_initial_refinement_model / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_ec / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase UHRF1
B: E3 ubiquitin-protein ligase UHRF1
D: 5'-D(*DCP*DCP*DAP*DTP*DGP*(5CM)P*DGP*DCP*DTP*DGP*DAP*DC)-3'
E: 5'-D(*DGP*DTP*DCP*DAP*DGP*DCP*DGP*DCP*DAP*DTP*DGP*DG)-3'
F: 5'-D(*DCP*DCP*DAP*DTP*DGP*(5CM)P*DGP*DCP*DTP*DGP*DAP*DC)-3'
G: 5'-D(*DGP*DTP*DCP*DAP*DGP*DCP*DGP*DCP*DAP*DTP*DGP*DG)-3'


Theoretical massNumber of molelcules
Total (without water)62,5136
Polymers62,5136
Non-polymers00
Water2,432135
1
A: E3 ubiquitin-protein ligase UHRF1
D: 5'-D(*DCP*DCP*DAP*DTP*DGP*(5CM)P*DGP*DCP*DTP*DGP*DAP*DC)-3'
E: 5'-D(*DGP*DTP*DCP*DAP*DGP*DCP*DGP*DCP*DAP*DTP*DGP*DG)-3'


Theoretical massNumber of molelcules
Total (without water)31,2573
Polymers31,2573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-14.3 kcal/mol
Surface area13310 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase UHRF1
F: 5'-D(*DCP*DCP*DAP*DTP*DGP*(5CM)P*DGP*DCP*DTP*DGP*DAP*DC)-3'
G: 5'-D(*DGP*DTP*DCP*DAP*DGP*DCP*DGP*DCP*DAP*DTP*DGP*DG)-3'


Theoretical massNumber of molelcules
Total (without water)31,2573
Polymers31,2573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-14.9 kcal/mol
Surface area13270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.084, 62.416, 113.447
Angle α, β, γ (deg.)90.00, 98.92, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAsymmetric unit contains two SRA-DNA complexes.

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Components

#1: Protein E3 ubiquitin-protein ligase UHRF1


Mass: 23915.711 Da / Num. of mol.: 2 / Fragment: YDG domain: UNP residues 419-628
Source method: isolated from a genetically manipulated source
Details: hexahistidine-SUMO-tagged construct / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Uhrf1 / Plasmid: pXC666 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VDF2
#2: DNA chain 5'-D(*DCP*DCP*DAP*DTP*DGP*(5CM)P*DGP*DCP*DTP*DGP*DAP*DC)-3'


Mass: 3637.395 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic DNA oligo
#3: DNA chain 5'-D(*DGP*DTP*DCP*DAP*DGP*DCP*DGP*DCP*DAP*DTP*DGP*DG)-3'


Mass: 3703.416 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic DNA oligo
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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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: 2.81 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 277 K / pH: 7
Details: 20% PEG 3350, 0.4M NaCl, pH 7.0, VAPOR DIFFUSION, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2NaCl11
3PEG 335012
4NaCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→34.53 Å / Num. obs: 30041 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.5
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 2.3 / % possible all: 90.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZO0

2zo0


Resolution: 2.29→34.53 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 622448.07 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1351 4.9 %RANDOM
Rwork0.223 ---
obs0.223 27777 88.5 %-
all-30041 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.0138 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 35.1 Å2
Baniso -1Baniso -2Baniso -3
1-19.56 Å20 Å27.74 Å2
2---17.03 Å20 Å2
3----2.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-35 Å
Luzzati sigma a0.45 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.29→34.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3204 974 0 135 4313
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.952.5
LS refinement shellResolution: 2.29→2.37 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.422 101 5.1 %
Rwork0.359 1869 -
obs--63.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION4DNA-RNA_REP.PARAM

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