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- PDB-6vyj: Human UHRF1 TTD domain in complex with a fragment -

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Basic information

Entry
Database: PDB / ID: 6vyj
TitleHuman UHRF1 TTD domain in complex with a fragment
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 / 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. / 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
beta-D-glucopyranose / 2,4-dimethylpyridine / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsCampbell, J.C. / Chang, L. / 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
DepositionFeb 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6074
Polymers19,2121
Non-polymers3943
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.280, 55.350, 66.260
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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q96T88, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-RVV / 2,4-dimethylpyridine


Mass: 107.153 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9N / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.92 Å3/Da / Density % sol: 36.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 50 mM Bis-Tris, pH 5.75, 35 % w/v PEG 3350. The crystals were cryo-preserved by 25% glucose

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Data collection

DiffractionMean temperature: 83 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: Feb 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.39→66.26 Å / Num. obs: 30553 / % possible obs: 100 % / Redundancy: 6 % / Biso Wilson estimate: 14.13 Å2 / CC1/2: 0.993 / Net I/σ(I): 7
Reflection shellResolution: 1.39→1.41 Å / Num. unique obs: 1464 / CC1/2: 0.364

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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: 1.39→42.48 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.586 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.226 1510 4.95 %
Rwork0.1976 28973 -
obs0.199 30483 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.88 Å2
Refinement stepCycle: LAST / Resolution: 1.39→42.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1200 0 28 154 1382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081271
X-RAY DIFFRACTIONf_angle_d0.9841726
X-RAY DIFFRACTIONf_chiral_restr0.0777185
X-RAY DIFFRACTIONf_plane_restr0.0066225
X-RAY DIFFRACTIONf_dihedral_angle_d20.0855458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.430.37211400.35382573X-RAY DIFFRACTION99.82
1.43-1.490.31141360.31842602X-RAY DIFFRACTION99.85
1.49-1.550.34671490.28932561X-RAY DIFFRACTION99.89
1.55-1.620.2991330.26332621X-RAY DIFFRACTION99.96
1.62-1.70.28081280.24222589X-RAY DIFFRACTION99.85
1.7-1.810.25781480.21252609X-RAY DIFFRACTION100
1.81-1.950.21131280.19422631X-RAY DIFFRACTION100
1.95-2.140.18251390.16512636X-RAY DIFFRACTION100
2.14-2.450.23061420.1632647X-RAY DIFFRACTION99.96
2.45-3.090.19021380.17342688X-RAY DIFFRACTION99.89
3.09-42.480.20011290.18152816X-RAY DIFFRACTION99.93
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)
13.63249462844-0.4259496209361.036233308514.12474643896-0.1749880537533.88935130384-0.0779282538201-0.1699284524720.09570070436850.1326703060530.00565634973904-0.202211849991-0.1684020802090.1952903238480.06964761458650.0741513666932-0.00222052707657-0.004178449106210.1059299461-0.01262914323280.08746931494946.94398877047-1.841740697730.9535847071
23.02630796208-1.017622565163.207155619570.965856041605-0.2081286860644.654291966540.05161524155050.19208821572-0.190816479365-0.08945848800750.05667053168880.05934813881930.06883376105040.0906784901661-0.0886234697150.103557449581-0.04128301364090.003214234003550.106982830730.0004065746722280.112809933053-6.694200736333.989841120389.24535200928
32.29873441382-0.96740306427-0.3582307828565.262642061424.445217771724.98707088281-0.03774213492310.137774116953-0.1319249706960.08435927633110.142239996091-0.1209997933460.002024689503350.136514269846-0.09614750087890.0938129716071-0.0177944263927-0.004208440329280.1114053768060.01004555558980.11600531816-5.969791107956.831274049336.67986929846
41.4668934371-0.6574689976370.6086326963572.73764633064-3.20346910265.57297833925-0.06378740939570.005519235006890.0040697718751-0.1180637399670.1135204422680.02170429859190.153742984549-0.279251827913-0.02341261583460.0773833940422-0.00732806590354-0.01415524612330.0664816659983-0.02412883991670.0845047315036-3.16414394736-0.082562254340717.4393947243
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 214 through 283 )
2X-RAY DIFFRACTION2chain 'A' and (resid 125 through 162 )
3X-RAY DIFFRACTION3chain 'A' and (resid 163 through 196 )
4X-RAY DIFFRACTION4chain 'A' and (resid 197 through 213 )

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