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- PDB-6w92: Human UHRF1 TTD domain -

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Basic information

Entry
Database: PDB / ID: 6w92
TitleHuman UHRF1 TTD domain
ComponentsE3 ubiquitin-protein ligase UHRF1
KeywordsLIGASE
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 / heterochromatin / cis-regulatory region sequence-specific DNA binding / 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 / RING-type E3 ubiquitin transferase / euchromatin / 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. / PUA-like superfamily ...: / 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
Similarity search - Domain/homology
E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsCampbell, J.C. / Chang, L. / Sankaran, B. / Young, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)5P20CA221731-02 United States
CitationJournal: Sci Rep / Year: 2021
Title: Discovery of small molecules targeting the tandem tudor domain of the epigenetic factor UHRF1 using fragment-based ligand discovery.
Authors: Chang, L. / Campbell, J. / Raji, I.O. / Guduru, S.K.R. / Kandel, P. / Nguyen, M. / Liu, S. / Tran, K. / Venugopal, N.K. / Taylor, B.C. / Holt, M.V. / Young, N.L. / Samuel, E.L.G. / Jain, P. ...Authors: Chang, L. / Campbell, J. / Raji, I.O. / Guduru, S.K.R. / Kandel, P. / Nguyen, M. / Liu, S. / Tran, K. / Venugopal, N.K. / Taylor, B.C. / Holt, M.V. / Young, N.L. / Samuel, E.L.G. / Jain, P. / Santini, C. / Sankaran, B. / MacKenzie, K.R. / Young, D.W.
History
DepositionMar 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 UHRF1


Theoretical massNumber of molelcules
Total (without water)19,2121
Polymers19,2121
Non-polymers00
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.380, 54.870, 66.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 19212.295 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 1.93 Å3/Da / Density % sol: 36.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.75 / Details: 0.1 M Bis-Tris, pH = 5.5, 25 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.3→66.55 Å / Num. obs: 37049 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 10.44 Å2 / CC1/2: 0.999 / Net I/σ(I): 20.9
Reflection shellResolution: 1.3→1.32 Å / Num. unique obs: 1746 / CC1/2: 0.967

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QQD

4qqd


Resolution: 1.3→42.34 Å / SU ML: 0.1069 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.695
RfactorNum. reflection% reflection
Rfree0.1849 2000 5.41 %
Rwork0.1737 --
obs0.1743 36990 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.07 Å2
Refinement stepCycle: LAST / Resolution: 1.3→42.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1261 0 0 224 1485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841296
X-RAY DIFFRACTIONf_angle_d0.8981766
X-RAY DIFFRACTIONf_chiral_restr0.0816191
X-RAY DIFFRACTIONf_plane_restr0.0067236
X-RAY DIFFRACTIONf_dihedral_angle_d20.3101472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.23191370.23042391X-RAY DIFFRACTION97.38
1.33-1.370.23831400.20662454X-RAY DIFFRACTION99.39
1.37-1.410.19731400.19552453X-RAY DIFFRACTION99.62
1.41-1.450.22441420.18262479X-RAY DIFFRACTION99.89
1.45-1.510.21171410.18512469X-RAY DIFFRACTION99.96
1.51-1.570.1721420.17552483X-RAY DIFFRACTION100
1.57-1.640.22781420.17332479X-RAY DIFFRACTION100
1.64-1.720.2031410.17212488X-RAY DIFFRACTION99.92
1.72-1.830.17231440.1722513X-RAY DIFFRACTION99.96
1.83-1.970.16811420.16492481X-RAY DIFFRACTION99.92
1.97-2.170.18391440.15422519X-RAY DIFFRACTION100
2.17-2.490.15531450.16322532X-RAY DIFFRACTION99.93
2.49-3.130.17531460.17352565X-RAY DIFFRACTION100
3.13-42.340.18431540.17532684X-RAY DIFFRACTION99.96
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)
10.6360080985020.305824008274-0.4655862566180.26581968922-0.551385707594.54279520110.01394759170450.2114885903360.1970377361270.01438759254690.05959127081090.0686045876473-0.351492689274-0.143798889317-0.0634128705040.08673771657680.01261091786720.004493439090720.08976386775870.01846822955740.11368999678325.643487849-1.23157210616-28.3699557114
21.44802789239-0.817132934898-1.455557127411.03590907441.206700002442.31668128083-0.0428703522084-0.0122242673153-0.05726117983770.0506877437266-0.01273325973320.09253821213060.0823704388636-0.05151731512570.04392944671110.0461941793553-0.000885432133544-0.00968654554940.044583416710.01371816731590.064808034609317.0599258367-0.567110049071-6.77677758054
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 127 through 184 )
2X-RAY DIFFRACTION2chain 'A' and (resid 185 through 285 )

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