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- PDB-8wms: Crystal structure of human DPPA3 in complex with human UHRF1 PHD ... -

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Basic information

Entry
Database: PDB / ID: 8wms
TitleCrystal structure of human DPPA3 in complex with human UHRF1 PHD domain
Components
  • Developmental pluripotency-associated protein 3
  • E3 ubiquitin-protein ligase UHRF1
KeywordsGENE REGULATION / DNA methylation
Function / homology
Function and homology information


positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / epigenetic programing of female pronucleus / histone H3 ubiquitin ligase activity / DNA damage sensor activity / hemi-methylated DNA-binding / histone H3K9me2/3 reader activity / homologous recombination / regulation of epithelial cell proliferation / female pronucleus / methyl-CpG binding ...positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / epigenetic programing of female pronucleus / histone H3 ubiquitin ligase activity / DNA damage sensor activity / hemi-methylated DNA-binding / histone H3K9me2/3 reader activity / homologous recombination / regulation of epithelial cell proliferation / female pronucleus / methyl-CpG binding / negative regulation of gene expression via chromosomal CpG island methylation / positive regulation of protein metabolic process / mitotic spindle assembly / heterochromatin / cis-regulatory region sequence-specific DNA binding / protein autoubiquitination / : / DNA methylation / Chromatin modifications during the maternal to zygotic transition (MZT) / epigenetic regulation of gene expression / replication fork / euchromatin / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / spindle / nuclear matrix / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / heterochromatin formation / ubiquitin-dependent protein catabolic process / histone binding / 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 / cytoplasm
Similarity search - Function
Developmental pluripotency-associated protein 3 / PGC7/Stella/Dppa3 domain / : / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. ...Developmental pluripotency-associated protein 3 / PGC7/Stella/Dppa3 domain / : / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / 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 / PHD-finger / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger PHD-type signature. / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger RING-type profile. / Zinc finger, RING-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
Developmental pluripotency-associated protein 3 / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsShiraishi, N. / Arita, K.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP18H02392, Japan
Japan Society for the Promotion of Science (JSPS)JP19H05741 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05294 Japan
Japan Science and Technology14530337 Japan
CitationJournal: Commun Biol / Year: 2024
Title: Structure of human DPPA3 bound to the UHRF1 PHD finger reveals its functional and structural differences from mouse DPPA3.
Authors: Shiraishi, N. / Konuma, T. / Chiba, Y. / Hokazono, S. / Nakamura, N. / Islam, M.H. / Nakanishi, M. / Nishiyama, A. / Arita, K.
History
DepositionOct 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase UHRF1
B: Developmental pluripotency-associated protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5896
Polymers12,3272
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-11 kcal/mol
Surface area6550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.802, 77.802, 140.674
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-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: 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: unidentified plasmid (others)
References: UniProt: Q96T88, RING-type E3 ubiquitin transferase
#2: Protein/peptide Developmental pluripotency-associated protein 3 / Stella-related protein


Mass: 4564.400 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPPA3, STELLAR / Production host: unidentified plasmid (others) / References: UniProt: Q6W0C5
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 4.32 Å3/Da / Density % sol: 71.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris-HCl (pH 7.0), 200 mM tri-potassium phosphate and 20% (w/v) PEG3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→43.33 Å / Num. obs: 8775 / % possible obs: 99.7 % / Redundancy: 5.4 % / Biso Wilson estimate: 64.6 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.5
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 903 / CC1/2: 0.896

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→43.33 Å / SU ML: 0.2939 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.7463
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2664 424 4.88 %
Rwork0.2329 8269 -
obs0.2346 8693 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.77 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms704 0 4 0 708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042717
X-RAY DIFFRACTIONf_angle_d0.803964
X-RAY DIFFRACTIONf_chiral_restr0.0479102
X-RAY DIFFRACTIONf_plane_restr0.0082127
X-RAY DIFFRACTIONf_dihedral_angle_d4.756199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.750.34051280.3482679X-RAY DIFFRACTION98.39
2.75-3.460.34951330.29932736X-RAY DIFFRACTION98.73
3.46-43.330.23491630.22854X-RAY DIFFRACTION99.08

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