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

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Basic information

Entry
Database: PDB / ID: 2zkd
TitleCrystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA
Components
  • DNA (5'-D(*DCP*DTP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DGP*DC)-3')
  • DNA (5'-D(*DGP*DCP*DAP*DAP*DTP*DCP*(5CM)P*DGP*DGP*DTP*DAP*DG)-3')
  • E3 ubiquitin-protein ligase UHRF1
KeywordsLIGASE / Protein-DNA complex / 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
ACETATE ION / DNA / DNA (> 10) / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,6158
Polymers61,4946
Non-polymers1212
Water11,944663
1
C: DNA (5'-D(*DCP*DTP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DGP*DC)-3')
D: DNA (5'-D(*DGP*DCP*DAP*DAP*DTP*DCP*(5CM)P*DGP*DGP*DTP*DAP*DG)-3')
A: E3 ubiquitin-protein ligase UHRF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8685
Polymers30,7473
Non-polymers1212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-15.2 kcal/mol
Surface area12710 Å2
MethodPISA
2
E: DNA (5'-D(*DCP*DTP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DGP*DC)-3')
F: DNA (5'-D(*DGP*DCP*DAP*DAP*DTP*DCP*(5CM)P*DGP*DGP*DTP*DAP*DG)-3')
B: E3 ubiquitin-protein ligase UHRF1


Theoretical massNumber of molelcules
Total (without water)30,7473
Polymers30,7473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-14.8 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.587, 104.036, 65.586
Angle α, β, γ (deg.)90.00, 99.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-57-

HOH

21E-491-

HOH

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Components

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DNA chain , 2 types, 4 molecules CEDF

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


Mass: 3638.379 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Nucleotide Synthesis
#2: DNA chain DNA (5'-D(*DGP*DCP*DAP*DAP*DTP*DCP*(5CM)P*DGP*DGP*DTP*DAP*DG)-3') / hemi-methylated CpG DNA


Mass: 3701.444 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Nucleotide Synthesis

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Protein , 1 types, 2 molecules AB

#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: 23407.109 Da / Num. of mol.: 2 / 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)

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Non-polymers , 3 types, 665 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 663 / 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: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium citrate (pH5.6), 0.2M sodium acetate, 30% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium citrate11
2sodium acetate11
3PEG400011
4HOH11
5sodium citrate12
6sodium acetate12
7PEG400012
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: 1.6→50 Å / Num. obs: 77879 / % possible obs: 99.1 % / Biso Wilson estimate: 20.136 Å2 / Rmerge(I) obs: 0.062
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.329 / Num. unique all: 7102 / % possible all: 91.9

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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 2ZKG

2zkg


Resolution: 1.6→28.24 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.637 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18452 3872 5 %RANDOM
Rwork0.15483 ---
obs0.15636 73317 99.12 %-
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: 17.825 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å2-0.11 Å2
2--0.94 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3283 974 8 663 4928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214626
X-RAY DIFFRACTIONr_bond_other_d0.0020.022930
X-RAY DIFFRACTIONr_angle_refined_deg1.5152.2226489
X-RAY DIFFRACTIONr_angle_other_deg0.9683.0017065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5825451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51222.674172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4915560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0961538
X-RAY DIFFRACTIONr_chiral_restr0.0830.2665
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024627
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02872
X-RAY DIFFRACTIONr_nbd_refined0.20.2830
X-RAY DIFFRACTIONr_nbd_other0.2260.23328
X-RAY DIFFRACTIONr_nbtor_refined0.190.22074
X-RAY DIFFRACTIONr_nbtor_other0.0840.22168
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2531
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1940.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7761.52804
X-RAY DIFFRACTIONr_mcbond_other0.1511.5904
X-RAY DIFFRACTIONr_mcangle_it0.88923490
X-RAY DIFFRACTIONr_scbond_it1.44433246
X-RAY DIFFRACTIONr_scangle_it1.9854.52999
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.601→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 234 -
Rwork0.182 4868 -
obs--89.57 %
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)
11.23960.1838-0.03150.6520.00930.93430.02730.0512-0.07330.02360.0099-0.0274-0.03170.0199-0.0372-0.0749-0.0073-0.0009-0.067-0.0108-0.066721.2178-1.662926.2995
20.874-0.25620.25231.3072-0.12671.19390.0434-0.06490.05320.0439-0.0114-0.0690.07230.0342-0.0321-0.0761-0.0056-0.0033-0.0684-0.0119-0.076426.2869-37.85177.2175
31.2142-0.24010.09742.44270.89651.76860.08490.0208-0.1587-0.0291-0.098-0.06350.1033-0.2270.0131-0.0621-0.02080.0257-0.04670.0024-0.06886.788-11.398432.9557
40.9067-0.1286-0.3070.89360.30621.96180.06710.0954-0.11070.0615-0.0778-0.06990.1245-0.28130.0106-0.0513-0.0356-0.0047-0.0393-0.021-0.04347.0311-11.886232.5138
51.3801-0.3983-0.3271.15850.16520.08230.0584-0.00650.1823-0.0344-0.0358-0.07970.0073-0.044-0.0226-0.02370.023-0.0138-0.0399-0.0108-0.075914.2409-28.5595-3.5878
60.507-0.0713-0.18151.09220.39991.3850.09380.0240.1125-0.1233-0.16790.017-0.0833-0.18330.0741-0.03710.0458-0.0009-0.0454-0.0258-0.036714.389-28-3.0089
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AE404 - 6131 - 210
2X-RAY DIFFRACTION2BF404 - 6121 - 209
3X-RAY DIFFRACTION3CA1 - 121 - 12
4X-RAY DIFFRACTION4DB1 - 121 - 12
5X-RAY DIFFRACTION5EC1 - 121 - 12
6X-RAY DIFFRACTION6FD1 - 121 - 12

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