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- PDB-6iiw: Crystal structure of human UHRF1 PHD finger in complex with PAF15 -

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Basic information

Entry
Database: PDB / ID: 6iiw
TitleCrystal structure of human UHRF1 PHD finger in complex with PAF15
Components
  • E3 ubiquitin-protein ligase UHRF1
  • PCNA-associated factor
KeywordsLIGASE / DNA methylation / histone modification / replication
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 / negative regulation of gene expression via chromosomal CpG island methylation / regulation of epithelial cell proliferation / methyl-CpG binding / centrosome cycle ...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 / negative regulation of gene expression via chromosomal CpG island methylation / regulation of epithelial cell proliferation / methyl-CpG binding / centrosome cycle / mitotic spindle assembly / translesion synthesis / protein autoubiquitination / heterochromatin / cis-regulatory region sequence-specific DNA binding / heterochromatin formation / epigenetic regulation of gene expression / response to UV / methylated histone binding / positive regulation of protein metabolic process / DNA methylation / Chromatin modifications during the maternal to zygotic transition (MZT) / replication fork / Termination of translesion DNA synthesis / double-strand break repair via homologous recombination / euchromatin / RING-type E3 ubiquitin transferase / spindle / nuclear matrix / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / histone binding / ubiquitin-dependent protein catabolic process / DNA replication / nucleic acid binding / molecular adaptor activity / regulation of cell cycle / centrosome / DNA damage response / chromatin binding / chromatin / perinuclear region of cytoplasm / 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
PCNA-associated factor, histone-like domain / PCNA-associated factor / PCNA-associated factor histone like domain / : / UHRF1, tandem tudor domain / UHRF1/2-like / Tandem tudor domain within UHRF1 / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain ...PCNA-associated factor, histone-like domain / PCNA-associated factor / PCNA-associated factor histone like domain / : / 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/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PCNA-associated factor / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.699 Å
AuthorsArita, K. / Kori, S.
CitationJournal: Nat Commun / Year: 2020
Title: Two distinct modes of DNMT1 recruitment ensure stable maintenance DNA methylation.
Authors: Nishiyama, A. / Mulholland, C.B. / Bultmann, S. / Kori, S. / Endo, A. / Saeki, Y. / Qin, W. / Trummer, C. / Chiba, Y. / Yokoyama, H. / Kumamoto, S. / Kawakami, T. / Hojo, H. / Nagae, G. / ...Authors: Nishiyama, A. / Mulholland, C.B. / Bultmann, S. / Kori, S. / Endo, A. / Saeki, Y. / Qin, W. / Trummer, C. / Chiba, Y. / Yokoyama, H. / Kumamoto, S. / Kawakami, T. / Hojo, H. / Nagae, G. / Aburatani, H. / Tanaka, K. / Arita, K. / Leonhardt, H. / Nakanishi, M.
History
DepositionOct 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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 ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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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
B: PCNA-associated factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5328
Polymers8,7942
Non-polymers7386
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-6 kcal/mol
Surface area5500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.716, 36.716, 220.147
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-404-

ZN

21A-508-

HOH

31A-582-

HOH

41B-102-

HOH

51B-105-

HOH

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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: 7762.821 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) / Strain (production host): Rsetta2 (DE3)
References: UniProt: Q96T88, RING-type E3 ubiquitin transferase
#2: Protein/peptide PCNA-associated factor / PAF15


Mass: 1031.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15004
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES (pH 7.5), 70% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.699→44.03 Å / Num. obs: 10762 / % possible obs: 100 % / Redundancy: 17.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Net I/σ(I): 27.5
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 538 / CC1/2: 0.976 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ASL

3asl


Resolution: 1.699→36.691 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.52
RfactorNum. reflection% reflection
Rfree0.1888 542 5.09 %
Rwork0.1763 --
obs0.1771 10653 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.699→36.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms561 0 30 96 687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005613
X-RAY DIFFRACTIONf_angle_d0.928827
X-RAY DIFFRACTIONf_dihedral_angle_d9.146530
X-RAY DIFFRACTIONf_chiral_restr0.05583
X-RAY DIFFRACTIONf_plane_restr0.005107
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6987-1.86960.21441190.19012442X-RAY DIFFRACTION100
1.8696-2.14020.20361310.17992447X-RAY DIFFRACTION100
2.1402-2.69620.18731390.18322505X-RAY DIFFRACTION100
2.6962-36.69970.18251530.17022717X-RAY DIFFRACTION100
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)
17.9915-4.02882.47232.4829-3.14479.3454-0.2906-0.7532-0.54120.63370.19320.9753-0.3286-0.23480.28410.33530.04760.03860.26820.06530.4028-21.39574.629-4.0456
22.8776-0.82484.75892.0441-2.45678.7266-0.11470.02630.1826-0.0932-0.17770.3685-0.7763-0.69260.32170.32350.09580.00240.23110.01640.2689-16.60498.2304-10.7213
32.2628-0.58460.89132.80330.08443.72620.03510.06-0.0207-0.1983-0.1059-0.0032-0.13920.08930.11970.21770.0180.01970.14920.02550.1679-9.98082.2148-9.7083
46.8367-1.57231.53378.6159-2.81424.22980.09760.4197-0.0901-0.8659-0.1395-0.0652-0.0357-0.13260.01010.31320.06560.02490.1498-0.00620.1893-9.3039-6.298-13.6563
55.5125-1.809-3.75717.24121.13145.5225-0.2014-0.0486-0.3140.81480.07330.35580.713-0.0175-0.10040.26910.04070.02430.15410.02950.1973-9.0105-9.0134-2.6222
65.6805-1.6015-1.7467.4591-2.07282.6453-0.1531-0.17680.1817-0.3156-0.2605-0.8243-0.1420.68610.44960.20490.04940.05190.20440.06960.2121-2.4505-1.6073-11.903
73.1654-0.55760.34395.3527-4.21523.31890.07140.1141-0.1466-0.7906-0.5324-0.88240.7860.88780.19040.31090.15020.13940.36210.12010.4292.9032-5.7766-15.4554
86.37044.3738-4.29326.4754-3.80858.0730.24070.2349-0.7318-0.5499-0.5129-1.23790.82450.20880.32840.41240.15190.03980.25060.00640.3392-3.2539-15.9715-13.9525
93.3748-0.0329-0.32494.01475.32527.3120.0089-0.5165-0.2210.48440.2698-0.29650.64630.3022-0.15260.2870.11640.00490.21710.03480.2015-2.2851-9.8512-3.6747
103.3294-3.6194.54844.0953-5.20097.10290.50110.2394-0.3663-0.2104-0.27170.50090.27130.0307-0.14580.3230.0215-0.02220.1792-0.01470.2717-11.8228-10.5752-12.6941
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 299 through 308 )
2X-RAY DIFFRACTION2chain 'A' and (resid 309 through 313 )
3X-RAY DIFFRACTION3chain 'A' and (resid 314 through 326 )
4X-RAY DIFFRACTION4chain 'A' and (resid 327 through 332 )
5X-RAY DIFFRACTION5chain 'A' and (resid 333 through 338 )
6X-RAY DIFFRACTION6chain 'A' and (resid 339 through 346 )
7X-RAY DIFFRACTION7chain 'A' and (resid 347 through 351 )
8X-RAY DIFFRACTION8chain 'A' and (resid 352 through 356 )
9X-RAY DIFFRACTION9chain 'A' and (resid 357 through 364 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 6 )

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