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- PDB-2zkf: Crystal structure of the SRA domain of mouse Np95 in complex with... -

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Basic information

Entry
Database: PDB / ID: 2zkf
TitleCrystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA
Components
  • DNA (5'-D(*DCP*DTP*DAP*DTP*DCP*(5CM)P*DGP*DGP*DTP*DGP*DA)-3')
  • DNA (5'-D(P*DCP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DAP*DGP*DA)-3')
  • E3 ubiquitin-protein ligase UHRF1
KeywordsLIGASE / Protein-DNA interaction / Cell cycle / Developmental protein / DNA damage / DNA repair / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Ubl conjugation pathway / Zinc-finger
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
SRA-YDG / PUA domain-like / : / UHRF1, tandem tudor domain / UHRF1/2-like / Tandem tudor domain within UHRF1 / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. ...SRA-YDG / PUA domain-like / : / 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 / 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: 2.55 Å
AuthorsArita, K. / Ariyoshi, M. / Tochio, H. / Nakamura, Y. / Shirakawa, M.
CitationJournal: Nature / Year: 2008
Title: Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism
Authors: Arita, K. / Ariyoshi, M. / Tochio, H. / Nakamura, Y. / Shirakawa, M.
History
DepositionMar 19, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 11, 2017Group: Other
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: DNA (5'-D(P*DCP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DAP*DGP*DA)-3')
D: DNA (5'-D(*DCP*DTP*DAP*DTP*DCP*(5CM)P*DGP*DGP*DTP*DGP*DA)-3')


Theoretical massNumber of molelcules
Total (without water)30,1383
Polymers30,1383
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-13.4 kcal/mol
Surface area12080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.878, 58.878, 182.309
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-43-

HOH

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Components

#1: 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: 23407.109 Da / Num. of mol.: 1 / Fragment: UNP residues 404-613
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Uhrf1, Np95 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q8VDF2, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: DNA chain DNA (5'-D(P*DCP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DAP*DGP*DA)-3') / oligonucleotides containing hemi-methylated CpG site


Mass: 3367.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Nucleotide Synthesis
#3: DNA chain DNA (5'-D(*DCP*DTP*DAP*DTP*DCP*(5CM)P*DGP*DGP*DTP*DGP*DA)-3') / oligonucleotides containing hemi-methylated CpG site


Mass: 3363.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Nucleotide Synthesis
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Bis-Tris-propane (pH7.5), 0.2M sodium fluoride, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Bis-Tris-propane11
2sodium fluoride11
3PEG335011
4HOH11
5Bis-Tris-propane12
6sodium fluoride12
7PEG335012
8HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 25, 2008 / Details: undulator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 11160 / % possible obs: 99.6 % / Biso Wilson estimate: 51.232 Å2 / Rmerge(I) obs: 0.079
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.171 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZKD

2zkd


Resolution: 2.55→49.46 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.885 / SU B: 22.21 / SU ML: 0.235 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.568 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2745 532 4.8 %RANDOM
Rwork0.2143 ---
obs0.21716 10594 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.456 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.55→49.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1641 451 0 45 2137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212187
X-RAY DIFFRACTIONr_bond_other_d0.0020.021392
X-RAY DIFFRACTIONr_angle_refined_deg2.0122.213052
X-RAY DIFFRACTIONr_angle_other_deg1.0173.0013352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1275208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00922.58885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.83215271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1281519
X-RAY DIFFRACTIONr_chiral_restr0.0890.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022158
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02412
X-RAY DIFFRACTIONr_nbd_refined0.2110.2462
X-RAY DIFFRACTIONr_nbd_other0.2280.21559
X-RAY DIFFRACTIONr_nbtor_refined0.2040.2991
X-RAY DIFFRACTIONr_nbtor_other0.0960.21070
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.288
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.120.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3010.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2540.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7881.51290
X-RAY DIFFRACTIONr_mcbond_other0.1331.5432
X-RAY DIFFRACTIONr_mcangle_it1.05721647
X-RAY DIFFRACTIONr_scbond_it1.58431523
X-RAY DIFFRACTIONr_scangle_it2.4824.51405
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.551→2.617 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 36 -
Rwork0.252 751 -
obs--99.37 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1093-0.21860.67510.6688-0.35381.5104-0.06950.0123-0.00250.02940.05770.0101-0.0639-0.09380.01180.0235-0.0165-0.00240.06960.02950.046217.9604-11.9558-15.5114
28.44472.18123.39482.88051.63457.03880.4351-0.4207-0.32830.3449-0.5185-0.27320.3286-0.63260.0834-0.00220.1038-0.01930.05340.0721-0.014915.8382-12.45193.1956
34.64363.19491.53552.32661.81345.60480.0143-0.46140.1231-0.082-0.4539-0.2371-0.2356-0.52520.4396-0.05050.0545-0.05510.11430.0260.038418.9351-9.2742.5323
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA406 - 6133 - 210
2X-RAY DIFFRACTION2CB2 - 121 - 11
3X-RAY DIFFRACTION3DC2 - 121 - 11

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