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- PDB-4pw5: structure of UHRF2-SRA in complex with a 5hmC-containing DNA, com... -

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Basic information

Entry
Database: PDB / ID: 4pw5
Titlestructure of UHRF2-SRA in complex with a 5hmC-containing DNA, complex I
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: 2.204 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
E: E3 ubiquitin-protein ligase UHRF2
F: E3 ubiquitin-protein ligase UHRF2
G: 5hmC-containing DNA1
H: 5hmC-containing DNA2


Theoretical massNumber of molelcules
Total (without water)116,9538
Polymers116,9538
Non-polymers00
Water10,971609
1
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)58,4764
Polymers58,4764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-23 kcal/mol
Surface area20500 Å2
MethodPISA
2
E: E3 ubiquitin-protein ligase UHRF2
F: E3 ubiquitin-protein ligase UHRF2
G: 5hmC-containing DNA1
H: 5hmC-containing DNA2


Theoretical massNumber of molelcules
Total (without water)58,4764
Polymers58,4764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-25 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.273, 82.807, 82.864
Angle α, β, γ (deg.)90.05, 90.00, 89.98
Int Tables number1
Space group name H-MP1

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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.: 4
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: 3724.428 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain 5hmC-containing DNA2


Mass: 3592.358 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 2.48 Å3/Da / Density % sol: 50.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% ethanol and 0.1 M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 25, 2013 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 56609 / Num. obs: 54600 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 8.6
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.483 / % possible all: 95.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1491)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OLN

3oln


Resolution: 2.204→41.432 Å / SU ML: 0.23 / Isotropic thermal model: 31.2 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 21.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 2739 5.02 %RANDOM
Rwork0.1608 ---
obs0.1631 54592 96.2 %-
all-56609 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.204→41.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5940 944 0 609 7493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067308
X-RAY DIFFRACTIONf_angle_d0.95210132
X-RAY DIFFRACTIONf_dihedral_angle_d17.4252797
X-RAY DIFFRACTIONf_chiral_restr0.0391050
X-RAY DIFFRACTIONf_plane_restr0.0041172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2041-2.24210.26281340.20962427X-RAY DIFFRACTION90
2.2421-2.28290.23711270.21362553X-RAY DIFFRACTION96
2.2829-2.32680.28931400.20412595X-RAY DIFFRACTION96
2.3268-2.37430.3111520.21242577X-RAY DIFFRACTION96
2.3743-2.42590.2571250.19932569X-RAY DIFFRACTION97
2.4259-2.48240.25951400.1942628X-RAY DIFFRACTION96
2.4824-2.54440.24911290.18722581X-RAY DIFFRACTION97
2.5444-2.61320.21851360.17982608X-RAY DIFFRACTION96
2.6132-2.69010.27281410.17972591X-RAY DIFFRACTION97
2.6901-2.77690.2541150.17442652X-RAY DIFFRACTION97
2.7769-2.87610.23091250.17852665X-RAY DIFFRACTION98
2.8761-2.99130.19171480.16692633X-RAY DIFFRACTION97
2.9913-3.12730.20471470.15772581X-RAY DIFFRACTION98
3.1273-3.29220.22511560.15322630X-RAY DIFFRACTION96
3.2922-3.49830.17531330.13742628X-RAY DIFFRACTION97
3.4983-3.76830.18951520.13292591X-RAY DIFFRACTION97
3.7683-4.14720.15571340.12972606X-RAY DIFFRACTION97
4.1472-4.74650.1711380.12622556X-RAY DIFFRACTION95
4.7465-5.97730.18461250.16082531X-RAY DIFFRACTION94
5.9773-41.43930.17951420.16892651X-RAY DIFFRACTION99

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