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- PDB-5xpi: Structure of UHRF1 TTD in complex with NV01 -

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Basic information

Entry
Database: PDB / ID: 5xpi
TitleStructure of UHRF1 TTD in complex with NV01
ComponentsE3 ubiquitin-protein ligase UHRF1
KeywordsLIGASE / TTD domain / small molecule
Function / homology
Function and homology information


histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / methyl-CpG binding / negative regulation of gene expression via chromosomal CpG island methylation / mitotic spindle assembly ...histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / 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 / epigenetic regulation of gene expression / methylated histone binding / positive regulation of protein metabolic process / DNA methylation / Chromatin modifications during the maternal to zygotic transition (MZT) / replication fork / double-strand break repair via homologous recombination / euchromatin / RING-type E3 ubiquitin transferase / nuclear matrix / spindle / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / histone binding / ubiquitin-dependent protein catabolic process / nucleic acid binding / protein ubiquitination / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / 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 ...: / 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
Chem-8C3 / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLuo, X. / Zhao, K.
CitationJournal: SLAS Discov / Year: 2018
Title: Discovery of Small-Molecule Antagonists of the H3K9me3 Binding to UHRF1 Tandem Tudor Domain
Authors: Senisterra, G. / Zhu, H.Y. / Luo, X. / Zhang, H. / Xun, G. / Lu, C. / Xiao, W. / Hajian, T. / Loppnau, P. / Chau, I. / Li, F. / Allali-Hassani, A. / Atadja, P. / Oyang, C. / Li, E. / Brown, ...Authors: Senisterra, G. / Zhu, H.Y. / Luo, X. / Zhang, H. / Xun, G. / Lu, C. / Xiao, W. / Hajian, T. / Loppnau, P. / Chau, I. / Li, F. / Allali-Hassani, A. / Atadja, P. / Oyang, C. / Li, E. / Brown, P.J. / Arrowsmith, C.H. / Zhao, K. / Yu, Z. / Vedadi, M.
History
DepositionJun 2, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,8252
Polymers18,4501
Non-polymers3751
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8660 Å2
Unit cell
Length a, b, c (Å)99.001, 99.001, 41.315
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

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Components

#1: Protein E3 ubiquitin-protein ligase UHRF1 / Inverted CCAAT box-binding protein of 90 kDa / Nuclear protein 95 / Nuclear zinc finger protein ...Inverted CCAAT box-binding protein of 90 kDa / Nuclear protein 95 / Nuclear zinc finger protein Np95 / hNp95 / RING finger protein 106 / RING-type E3 ubiquitin transferase UHRF1 / Transcription factor ICBP90 / Ubiquitin-like PHD and RING finger domain-containing protein 1 / hUHRF1 / Ubiquitin-like-containing PHD and RING finger domains protein 1


Mass: 18449.549 Da / Num. of mol.: 1 / Fragment: UNP residues 127-283
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF1, ICBP90, NP95, RNF106 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96T88, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-8C3 / N-[3-(diethylamino)propyl]-2-(12-methyl-9-oxidanylidene-5-thia-1,10,11-triazatricyclo[6.4.0.0^2,6]dodeca-2(6),3,7,11-tetraen-10-yl)ethanamide


Mass: 375.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H25N5O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 3.17 Å3/Da / Density % sol: 64.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2 / Details: 2.7 M Na formate and 0.1 M Na acetate pH 5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 11915 / % possible obs: 99.9 % / Redundancy: 11.1 % / Biso Wilson estimate: 42.75 Å2 / Rmerge(I) obs: 0.079 / Χ2: 1.335 / Net I/σ(I): 16.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
2.2-2.2811.30.2141.3041100
2.28-2.3711.20.1891.2431100
2.37-2.4811.20.1511.2781100
2.48-2.6111.20.1321.3151100
2.61-2.7711.20.1081.3111100
2.77-2.9911.20.0891.3921100
2.99-3.2911.20.0741.4631100
3.29-3.7611.10.0711.111100
3.76-4.7410.90.0821.6091100
4.74-5010.30.0561.334198.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
BUSTER2.9.6refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DB3

3db3


Resolution: 2.2→42.87 Å / Cor.coef. Fo:Fc: 0.9196 / Cor.coef. Fo:Fc free: 0.9094 / SU R Cruickshank DPI: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.205 / SU Rfree Blow DPI: 0.163 / SU Rfree Cruickshank DPI: 0.16
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 566 4.76 %RANDOM
Rwork0.2 ---
obs0.2009 11900 99.63 %-
Displacement parametersBiso max: 127.85 Å2 / Biso mean: 44.83 Å2 / Biso min: 19.37 Å2
Baniso -1Baniso -2Baniso -3
1-9.2579 Å20 Å20 Å2
2--9.2579 Å20 Å2
3----18.5159 Å2
Refine analyzeLuzzati coordinate error obs: 0.276 Å
Refinement stepCycle: final / Resolution: 2.2→42.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1173 0 26 116 1315
Biso mean--89.17 47.73 -
Num. residues----140
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d431SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes48HARMONIC2
X-RAY DIFFRACTIONt_gen_planes174HARMONIC5
X-RAY DIFFRACTIONt_it1224HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion147SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1322SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1224HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1658HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.63
X-RAY DIFFRACTIONt_other_torsion19.05
LS refinement shellResolution: 2.2→2.41 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2654 129 4.62 %
Rwork0.2307 2664 -
all0.2324 2793 -
obs--99.63 %

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