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- PDB-4pw6: structure of UHRF2-SRA in complex with a 5hmC-containing DNA, com... -

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Basic information

Entry
Database: PDB / ID: 4pw6
Titlestructure of UHRF2-SRA in complex with a 5hmC-containing DNA, complex II
Components
  • 5hmC-containing DNA1
  • 5hmC-containing DNA2
  • E3 ubiquitin-protein ligase UHRF2
KeywordsLIGASE/DNA / SRA / 5hmC binding / 5hmC-containing DNA / hydroxymethylation / nuclear / LIGASE-DNA complex
Function / homology
Function and homology information


histone H3K9me2/3 reader activity / SUMO transferase activity / negative regulation of gene expression via chromosomal CpG island methylation / protein sumoylation / pericentric heterochromatin / heterochromatin / protein autoubiquitination / SUMOylation of transcription cofactors / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity ...histone H3K9me2/3 reader activity / SUMO transferase activity / negative regulation of gene expression via chromosomal CpG island methylation / protein sumoylation / pericentric heterochromatin / heterochromatin / protein autoubiquitination / 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 / regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / : / : / : / SRA-YDG / PUA domain-like / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / SRA-YDG ...: / : / : / : / 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 / PHD-finger / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger PHD-type signature. / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Roll / Ubiquitin-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / E3 ubiquitin-protein ligase UHRF2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.789 Å
AuthorsZhou, T. / Xiong, J. / Wang, M. / Yang, N. / Wong, J. / Zhu, B. / Xu, R.M.
CitationJournal: Mol.Cell / Year: 2014
Title: Structural Basis for Hydroxymethylcytosine Recognition by the SRA Domain of UHRF2.
Authors: Zhou, T. / Xiong, J. / Wang, M. / Yang, N. / Wong, J. / Zhu, B. / Xu, R.M.
History
DepositionMar 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Jun 25, 2014Group: Database references
Revision 1.3Sep 20, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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
B: E3 ubiquitin-protein ligase UHRF2
C: 5hmC-containing DNA1
D: 5hmC-containing DNA2


Theoretical massNumber of molelcules
Total (without water)58,5134
Polymers58,5134
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-28 kcal/mol
Surface area20280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.368, 115.368, 41.049
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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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: 25579.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF2, NIRF, RNF107 / Plasmid: pET28a-smt / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL
References: UniProt: Q96PU4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: DNA chain 5hmC-containing DNA1


Mass: 3747.465 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5hmC-containing DNA2


Mass: 3606.381 Da / Num. of mol.: 1 / Source method: obtained synthetically

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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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris pH 8.0 and 8% PEG-8000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2013 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.51
ReflectionResolution: 3.789→50 Å / Num. all: 5589 / Num. obs: 5480 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 10.8
Reflection shellResolution: 3.789→3.94 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2.8 / Num. unique all: 536 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OLN

3oln


Resolution: 3.789→38.674 Å / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.52 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2865 554 10.11 %RANDOM
Rwork0.236 ---
all0.237 5589 --
obs0.2365 5480 97.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 113.5 Å2
Refinement stepCycle: LAST / Resolution: 3.789→38.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 488 0 0 3468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023608
X-RAY DIFFRACTIONf_angle_d0.5954991
X-RAY DIFFRACTIONf_dihedral_angle_d16.931364
X-RAY DIFFRACTIONf_chiral_restr0.026513
X-RAY DIFFRACTIONf_plane_restr0.003572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7985-4.180.33531400.31931215X-RAY DIFFRACTION88
4.18-4.78310.2711330.23951212X-RAY DIFFRACTION89
4.7831-6.01960.26751390.221228X-RAY DIFFRACTION88
6.0196-31.99840.27551390.19841265X-RAY DIFFRACTION88

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