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- PDB-4pw7: structure of UHRF2-SRA in complex with a 5mC-containing DNA -

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Basic information

Entry
Database: PDB / ID: 4pw7
Titlestructure of UHRF2-SRA in complex with a 5mC-containing DNA
Components
  • 5mC-containing DNA1
  • 5mC-containing DNA2
  • E3 ubiquitin-protein ligase UHRF2
KeywordsLIGASE/DNA / SRA / 5hmC binding / 5hmC-containing DNA / methylation / nuclear / LIGASE-DNA complex
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 / metal ion binding / nucleus
Similarity search - Function
: / : / : / : / SRA-YDG / PUA domain-like / UHRF1, tandem tudor domain / UHRF1/2-like / Tandem tudor domain within UHRF1 / SRA-YDG ...: / : / : / : / 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
DNA / DNA (> 10) / E3 ubiquitin-protein ligase UHRF2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 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 19, 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: 5mC-containing DNA1
D: 5mC-containing DNA2
E: E3 ubiquitin-protein ligase UHRF2
F: E3 ubiquitin-protein ligase UHRF2
G: 5mC-containing DNA1
H: 5mC-containing DNA2


Theoretical massNumber of molelcules
Total (without water)116,9218
Polymers116,9218
Non-polymers00
Water16,790932
1
A: E3 ubiquitin-protein ligase UHRF2
B: E3 ubiquitin-protein ligase UHRF2
C: 5mC-containing DNA1
D: 5mC-containing DNA2


Theoretical massNumber of molelcules
Total (without water)58,4604
Polymers58,4604
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-19 kcal/mol
Surface area20980 Å2
MethodPISA
2
E: E3 ubiquitin-protein ligase UHRF2
F: E3 ubiquitin-protein ligase UHRF2
G: 5mC-containing DNA1
H: 5mC-containing DNA2


Theoretical massNumber of molelcules
Total (without water)58,4604
Polymers58,4604
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-21 kcal/mol
Surface area21000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.331, 83.694, 83.686
Angle α, β, γ (deg.)89.97, 89.94, 90.02
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 5mC-containing DNA1


Mass: 3708.429 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain 5mC-containing DNA2


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


Mass: 18.015 Da / Num. of mol.: 932 / 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: 2.54 Å3/Da / Density % sol: 51.49 %
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: BSRF / Beamline: 1W2B / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 11, 2013 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 77335 / Num. obs: 75805 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2 / Num. unique all: 7677 / % possible all: 97

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Processing

Software
NameVersionClassification
MAR345dtbdata 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: 2.001→28.05 Å / SU ML: 0.22 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 20.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 3802 5.02 %RANDOM
Rwork0.1634 ---
all0.166 77335 --
obs0.1657 75755 97.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.5 Å2
Refinement stepCycle: LAST / Resolution: 2.001→28.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6107 974 0 932 8013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067554
X-RAY DIFFRACTIONf_angle_d0.96310480
X-RAY DIFFRACTIONf_dihedral_angle_d17.6532925
X-RAY DIFFRACTIONf_chiral_restr0.0421087
X-RAY DIFFRACTIONf_plane_restr0.0041214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0012-2.02650.29881280.24642512X-RAY DIFFRACTION94
2.0265-2.05320.27611370.23112663X-RAY DIFFRACTION97
2.0532-2.08130.26641330.21732643X-RAY DIFFRACTION97
2.0813-2.1110.27551500.21242657X-RAY DIFFRACTION97
2.111-2.14250.29621340.21482641X-RAY DIFFRACTION97
2.1425-2.1760.22031510.18932644X-RAY DIFFRACTION97
2.176-2.21160.26461440.19222641X-RAY DIFFRACTION97
2.2116-2.24980.22591420.19412627X-RAY DIFFRACTION97
2.2498-2.29060.25421440.18922658X-RAY DIFFRACTION97
2.2906-2.33470.25041460.18652734X-RAY DIFFRACTION98
2.3347-2.38230.20941450.18732575X-RAY DIFFRACTION98
2.3823-2.43410.23731240.18272622X-RAY DIFFRACTION98
2.4341-2.49070.24911180.18052720X-RAY DIFFRACTION98
2.4907-2.55290.24411420.16722663X-RAY DIFFRACTION98
2.5529-2.62190.21221680.16512696X-RAY DIFFRACTION98
2.6219-2.6990.21281490.16642671X-RAY DIFFRACTION98
2.699-2.7860.20081460.15872636X-RAY DIFFRACTION98
2.786-2.88550.21351380.1662665X-RAY DIFFRACTION98
2.8855-3.00090.20621490.15732697X-RAY DIFFRACTION99
3.0009-3.13730.2131360.16182700X-RAY DIFFRACTION99
3.1373-3.30250.19381350.14352699X-RAY DIFFRACTION99
3.3025-3.5090.15861300.14242690X-RAY DIFFRACTION99
3.509-3.77940.18171280.12842701X-RAY DIFFRACTION99
3.7794-4.15860.17951480.12982686X-RAY DIFFRACTION99
4.1586-4.75780.16811540.11912720X-RAY DIFFRACTION99
4.7578-5.98480.18941490.15492729X-RAY DIFFRACTION100
5.9848-28.05240.1971340.16472663X-RAY DIFFRACTION98

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