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- PDB-2zo1: Mouse NP95 SRA domain DNA specific complex 2 -

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Basic information

Entry
Database: PDB / ID: 2zo1
TitleMouse NP95 SRA domain DNA specific complex 2
Components
  • DNA (5'-D(*DGP*DTP*DCP*DAP*DGP*(5CM)P*DGP*DCP*DAP*DAP*DTP*DGP*DG)-3')
  • DNA (5'-D(*DTP*DCP*DCP*DAP*DTP*DGP*DCP*DGP*DCP*DTP*DGP*DAP*DC)-3')
  • E3 ubiquitin-protein ligase UHRF1
KeywordsLIGASE/DNA / Base flipping / 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 / Oxidoreductase / Pyruvate / 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 / negative regulation of gene expression via chromosomal CpG island methylation / mitotic spindle assembly / cis-regulatory region sequence-specific DNA binding / protein autoubiquitination / heterochromatin / positive regulation of protein metabolic process ...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 / cis-regulatory region sequence-specific DNA binding / protein autoubiquitination / heterochromatin / positive regulation of protein metabolic process / methylated histone binding / replication fork / RING-type E3 ubiquitin transferase / euchromatin / heterochromatin formation / 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
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 / 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 / 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: 1.96 Å
AuthorsHashimoto, H. / Horton, J.R. / Cheng, X.
CitationJournal: 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
DepositionMay 5, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,9985
Polymers31,8743
Non-polymers1242
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-6 kcal/mol
Surface area12340 Å2
MethodPISA
2
D: DNA (5'-D(*DTP*DCP*DCP*DAP*DTP*DGP*DCP*DGP*DCP*DTP*DGP*DAP*DC)-3')
E: DNA (5'-D(*DGP*DTP*DCP*DAP*DGP*(5CM)P*DGP*DCP*DAP*DAP*DTP*DGP*DG)-3')


Theoretical massNumber of molelcules
Total (without water)7,9582
Polymers7,9582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-5 kcal/mol
Surface area4770 Å2
MethodPISA
3
B: E3 ubiquitin-protein ligase UHRF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0403
Polymers23,9161
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.026, 62.026, 164.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: DNA chain DNA (5'-D(*DTP*DCP*DCP*DAP*DTP*DGP*DCP*DGP*DCP*DTP*DGP*DAP*DC)-3')


Mass: 3927.561 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 12 base pair DNA duplex
#2: DNA chain DNA (5'-D(*DGP*DTP*DCP*DAP*DGP*(5CM)P*DGP*DCP*DAP*DAP*DTP*DGP*DG)-3')


Mass: 4030.650 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 12 base pair DNA duplex
#3: Protein E3 ubiquitin-protein ligase UHRF1 / Ubiquitin-like PHD and RING finger domain-containing protein 1 / Ubiquitin-like-containing PHD and ...Ubiquitin-like PHD and RING finger domain-containing protein 1 / Ubiquitin-like-containing PHD and RING finger domains protein 1 / Nuclear zinc finger protein Np95 / Nuclear protein 95


Mass: 23915.711 Da / Num. of mol.: 1 / Fragment: SRA domain, residues 419-628
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Np95 / Plasmid: pXC666 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Gold cells
References: UniProt: Q8VDF2, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% (v/v) polyethylene glycol 3350, 0.4M NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2NaCL11
3H2O11
4PEG 335012
5NaCL12
6H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→34.23 Å / Num. obs: 23766 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 14.2 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 17.4
Reflection shellResolution: 1.96→2.03 Å / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2276 / % possible all: 98.1

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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: 1.96→34.23 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 898993.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: The density for the nucleotide at position 9 in chain E indicated an extrahelical conformation (E429) as well as an intrahelical conformation (E430). The depositors made a model as if an ...Details: The density for the nucleotide at position 9 in chain E indicated an extrahelical conformation (E429) as well as an intrahelical conformation (E430). The depositors made a model as if an additional nucleotide A10 was inserted.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1069 4.7 %RANDOM
Rwork0.221 ---
obs0.221 22899 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.1026 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 44.8 Å2
Baniso -1Baniso -2Baniso -3
1--6.18 Å20 Å20 Å2
2---6.18 Å20 Å2
3---12.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.26 Å
Luzzati d res low-35 Å
Luzzati sigma a0.19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.96→34.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1608 430 8 97 2143
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it3.442
X-RAY DIFFRACTIONc_scangle_it5.52.5
LS refinement shellResolution: 1.96→2.03 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.299 57 2.9 %
Rwork0.282 1901 -
obs-1901 84.3 %

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