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- PDB-4tvr: Tandem Tudor and PHD domains of UHRF2 -

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Basic information

Entry
Database: PDB / ID: 4tvr
TitleTandem Tudor and PHD domains of UHRF2
ComponentsE3 ubiquitin-protein ligase UHRF2
KeywordsLIGASE / Structural Genomics Consortium (SGC) / Tandem Tudor / PHD
Function / homology
Function and homology information


SUMO transferase activity / protein sumoylation / protein autoubiquitination / heterochromatin / pericentric heterochromatin / SUMOylation of transcription cofactors / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / histone binding ...SUMO transferase activity / protein sumoylation / protein autoubiquitination / heterochromatin / pericentric heterochromatin / SUMOylation of transcription cofactors / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / cell differentiation / regulation of cell cycle / protein ubiquitination / cell cycle / DNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
: / : / : / : / UHRF1, tandem tudor domain / UHRF1/2-like / Tandem tudor domain within UHRF1 / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain ...: / : / : / : / 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. / SH3 type barrels. - #30 / 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 / SH3 type barrels. / 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 UHRF2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsWalker, J.R. / Dong, A. / Zhang, Q. / Ong, M. / Duan, S. / Li, Y. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Arrowsmith, C.H. ...Walker, J.R. / Dong, A. / Zhang, Q. / Ong, M. / Duan, S. / Li, Y. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Arrowsmith, C.H. / Tong, Y. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Structure of the Tandem Tudor and PHD domains of UHRF2
Authors: Walker, J.R. / Dong, A. / Zhang, Q. / Ong, M. / Duan, S. / Li, Y. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Arrowsmith, C.H. / Tong, Y. / Structural Genomics Consortium (SGC)
History
DepositionJun 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase UHRF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,55611
Polymers31,3591
Non-polymers19610
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.280, 71.280, 120.052
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Detailsbiological unit is the same as asym.

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Components

#1: Protein E3 ubiquitin-protein ligase UHRF2 / Np95/ICBP90-like RING finger protein / Np95-like RING finger protein / Nuclear protein 97 / Nuclear ...Np95/ICBP90-like RING finger protein / Np95-like RING finger protein / Nuclear protein 97 / Nuclear zinc finger protein Np97 / RING finger protein 107 / Ubiquitin-like PHD and RING finger domain-containing protein 2 / Ubiquitin-like-containing PHD and RING finger domains protein 2


Mass: 31359.346 Da / Num. of mol.: 1
Fragment: Tandem Tudor and PHD domains, UNP residues 109-395
Mutation: deletion from 169 to 176, E383A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF2, NIRF, RNF107 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2
References: UniProt: Q96PU4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG-3350, 0.2 M NaCl, 0.1 M HEPES pH 7.5, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.2822 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2822 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 14292 / % possible obs: 98.3 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.048 / Χ2: 1.318 / Net I/av σ(I): 49.59 / Net I/σ(I): 13.8 / Num. measured all: 120996
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.29-2.338.80.9676790.77598
2.33-2.378.80.8217160.78498.4
2.37-2.428.70.6236790.80298.1
2.42-2.478.80.5116910.79698.2
2.47-2.528.70.4416990.79498.2
2.52-2.588.70.3517040.78498.3
2.58-2.648.70.2737030.77498.6
2.64-2.728.70.26860.82898.1
2.72-2.798.70.1527130.8698.3
2.79-2.898.60.1177040.83799.2
2.89-2.998.60.097060.88398.7
2.99-3.118.60.077170.91998.9
3.11-3.258.50.0517180.92898.9
3.25-3.428.50.0467131.11899.4
3.42-3.638.50.047151.35698.9
3.63-3.928.40.0417341.85499.3
3.92-4.318.20.0367301.99499.6
4.31-4.9380.0317461.9799.6
4.93-6.217.80.0337652.51399.2
6.21-507.30.0397745.25191.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0071refinement
SCALEPACKdata scaling
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ASK

3ask


Resolution: 2.29→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.927 / SU B: 13.81 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25982 721 5.1 %RANDOM
Rwork0.22902 ---
obs0.23067 13552 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.091 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2---0.73 Å20 Å2
3---1.47 Å2
Refinement stepCycle: 1 / Resolution: 2.29→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1700 0 10 53 1763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191794
X-RAY DIFFRACTIONr_bond_other_d0.0010.021645
X-RAY DIFFRACTIONr_angle_refined_deg0.9731.952433
X-RAY DIFFRACTIONr_angle_other_deg0.6763.0053751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9235225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.50622.71681
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1215277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6071516
X-RAY DIFFRACTIONr_chiral_restr0.0570.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212049
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02429
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5415.545903
X-RAY DIFFRACTIONr_mcbond_other1.545.542902
X-RAY DIFFRACTIONr_mcangle_it2.5868.2961127
X-RAY DIFFRACTIONr_mcangle_other2.5858.31128
X-RAY DIFFRACTIONr_scbond_it2.2125.517891
X-RAY DIFFRACTIONr_scbond_other2.215.52892
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0918.2451306
X-RAY DIFFRACTIONr_long_range_B_refined5.20743.1311887
X-RAY DIFFRACTIONr_long_range_B_other5.21143.0641874
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.29→2.353 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 56 -
Rwork0.305 951 -
obs--97.77 %
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)
11.10380.986-0.35854.16561.39362.26890.06960.10520.26080.19590.2530.02630.02540.1898-0.32260.0117-0.00150.00950.19820.04850.1145-3.1957-19.2573-25.3267
29.2763-5.1912-1.64823.11380.38984.1178-0.44160.00160.13830.00620.2706-0.1246-0.5118-0.97550.1710.9019-0.16510.0320.3794-0.02780.5379-30.3365-23.6427-14.8936
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A113 - 329
2X-RAY DIFFRACTION2A331 - 393

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