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- PDB-2zkg: Crystal structure of unliganded SRA domain of mouse Np95 -

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Basic information

Entry
Database: PDB / ID: 2zkg
TitleCrystal structure of unliganded SRA domain of mouse Np95
ComponentsE3 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
E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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_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_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

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase UHRF1
B: E3 ubiquitin-protein ligase UHRF1
C: E3 ubiquitin-protein ligase UHRF1
D: E3 ubiquitin-protein ligase UHRF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8778
Polymers93,6284
Non-polymers2484
Water9,260514
1
A: E3 ubiquitin-protein ligase UHRF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5313
Polymers23,4071
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E3 ubiquitin-protein ligase UHRF1


Theoretical massNumber of molelcules
Total (without water)23,4071
Polymers23,4071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: E3 ubiquitin-protein ligase UHRF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4692
Polymers23,4071
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: E3 ubiquitin-protein ligase UHRF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4692
Polymers23,4071
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.334, 67.013, 69.572
Angle α, β, γ (deg.)91.11, 65.01, 84.48
Int Tables number1
Space group name H-MP1

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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.: 4 / 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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 2.88 Å3/Da / Density % sol: 57.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl (pH8.0), 0.1M Sodium acetate, 12% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 96644 / % possible obs: 95.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 23.02 Å2 / Rmerge(I) obs: 0.071
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.372 / % possible all: 77.3

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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 3BI7

3bi7


Resolution: 1.77→29.31 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.181 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21678 4845 5 %RANDOM
Rwork0.18648 ---
obs0.18797 91798 95.24 %-
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: 25.491 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20.45 Å20.83 Å2
2---0.27 Å20.46 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.77→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5917 0 16 514 6447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0216115
X-RAY DIFFRACTIONr_bond_other_d0.0020.024333
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9358269
X-RAY DIFFRACTIONr_angle_other_deg0.995310387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9715745
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5522.652313
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70415972
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1231566
X-RAY DIFFRACTIONr_chiral_restr0.1050.2815
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026955
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021343
X-RAY DIFFRACTIONr_nbd_refined0.1960.21201
X-RAY DIFFRACTIONr_nbd_other0.2160.24627
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22913
X-RAY DIFFRACTIONr_nbtor_other0.0860.23282
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2394
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2331.54741
X-RAY DIFFRACTIONr_mcbond_other0.2271.51541
X-RAY DIFFRACTIONr_mcangle_it1.38925925
X-RAY DIFFRACTIONr_scbond_it2.29632897
X-RAY DIFFRACTIONr_scangle_it3.2934.52344
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.773→1.819 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 293 -
Rwork0.214 5024 -
obs--71.74 %
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)
10.8670.2297-0.26481.174-0.4040.6937-0.05730.0189-0.00640.14250.0445-0.0270.0222-0.09370.0128-0.0031-0.0097-0.0003-0.049-0.0237-0.0417-0.14830.3657-0.2313
20.746-0.3181-0.00540.9717-0.5441.8611-0.00160.0230.0088-0.0282-0.0067-0.0766-0.0432-0.08230.0083-0.0790.0045-0.0081-0.0181-0.0009-0.0352-18.099232.8581-20.9841
31.51580.13610.2460.79770.18591.22590.00050.0130.04260.07950.0347-0.0051-0.06970.1525-0.0352-0.038-0.016-0.0032-0.0397-0.0106-0.032421.735231.2426-0.2213
41.69760.3249-0.40971.5160.47241.10540.0410.08650.0101-0.0695-0.025-0.00580.001-0.0203-0.016-0.050.00550.004-0.03150.0104-0.066817.609158.1886-28.5529
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA413 - 48810 - 85
2X-RAY DIFFRACTION1AA500 - 61397 - 210
3X-RAY DIFFRACTION2BB413 - 48810 - 85
4X-RAY DIFFRACTION2BB500 - 61297 - 209
5X-RAY DIFFRACTION3CC415 - 48812 - 85
6X-RAY DIFFRACTION3CC502 - 61099 - 207
7X-RAY DIFFRACTION4DD415 - 48812 - 85
8X-RAY DIFFRACTION4DD500 - 60997 - 206

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