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- PDB-8xv4: Crystal structure of TTD-PHD domain of UHRF1 in complex with mSte... -

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Basic information

Entry
Database: PDB / ID: 8xv4
TitleCrystal structure of TTD-PHD domain of UHRF1 in complex with mStella peptide (residues 85-119)
Components
  • Developmental pluripotency-associated protein 3
  • E3 ubiquitin-protein ligase UHRF1
KeywordsGENE REGULATION/INHIBITOR / UHFR1 / STELLA / Complex / Inhibitor / GENE REGULATION / GENE REGULATION-INHIBITOR complex
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 / embryonic cleavage / regulation of epithelial cell proliferation / male pronucleus ...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 / embryonic cleavage / regulation of epithelial cell proliferation / male pronucleus / 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 / double-strand break repair via homologous recombination / euchromatin / 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 / cytosol / 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)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsDu, X. / Gan, Q. / Xu, J. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2022YFA1303101 China
CitationJournal: Nat Commun / Year: 2025
Title: Defining ortholog-specific UHRF1 inhibition by STELLA for cancer therapy.
Authors: Bai, W. / Xu, J. / Gu, W. / Wang, D. / Cui, Y. / Rong, W. / Du, X. / Li, X. / Xia, C. / Gan, Q. / He, G. / Guo, H. / Deng, J. / Wu, Y. / Yen, R.C. / Yegnasubramanian, S. / Rothbart, S.B. / ...Authors: Bai, W. / Xu, J. / Gu, W. / Wang, D. / Cui, Y. / Rong, W. / Du, X. / Li, X. / Xia, C. / Gan, Q. / He, G. / Guo, H. / Deng, J. / Wu, Y. / Yen, R.C. / Yegnasubramanian, S. / Rothbart, S.B. / Luo, C. / Wu, L. / Liu, J. / Baylin, S.B. / Kong, X.
History
DepositionJan 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: 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

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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: E3 ubiquitin-protein ligase UHRF1
C: Developmental pluripotency-associated protein 3
D: Developmental pluripotency-associated protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,97011
Polymers61,5124
Non-polymers4587
Water18010
1
A: E3 ubiquitin-protein ligase UHRF1
C: Developmental pluripotency-associated protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0186
Polymers30,7562
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-21 kcal/mol
Surface area14370 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase UHRF1
D: Developmental pluripotency-associated protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9525
Polymers30,7562
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-16 kcal/mol
Surface area14530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.713, 72.365, 63.065
Angle α, β, γ (deg.)90.00, 108.05, 90.00
Int Tables number5
Space group name H-MC121

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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 / HuNp95 / 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: 26456.887 Da / Num. of mol.: 2 / Fragment: TTD-PHD domain
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: Protein/peptide Developmental pluripotency-associated protein 3 / Compaction-associated protein 1 / Primordial germ cell protein 7 / Stella


Mass: 4299.193 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8QZY3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.6 M NaCl, 0.1 M MES pH6.5, 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.2→19.99 Å / Num. obs: 9681 / % possible obs: 95.8 % / Redundancy: 2.5 % / CC1/2: 0.968 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.126 / Rrim(I) all: 0.209 / Χ2: 0.99 / Net I/σ(I): 5.7 / Num. measured all: 23901
Reflection shellResolution: 3.2→3.46 Å / % possible obs: 95.7 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.447 / Num. measured all: 4512 / Num. unique obs: 1984 / CC1/2: 0.784 / Rpim(I) all: 0.358 / Rrim(I) all: 0.576 / Χ2: 0.89 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→19.99 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.871 / SU B: 27.876 / SU ML: 0.455 / Cross valid method: THROUGHOUT / ESU R Free: 0.579 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26563 439 4.5 %RANDOM
Rwork0.22654 ---
obs0.22833 9234 95.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.736 Å2
Baniso -1Baniso -2Baniso -3
1--4.36 Å20 Å20.94 Å2
2---5.09 Å2-0 Å2
3---7.29 Å2
Refinement stepCycle: 1 / Resolution: 3.2→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4012 0 7 10 4029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0124118
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163892
X-RAY DIFFRACTIONr_angle_refined_deg1.0551.8645553
X-RAY DIFFRACTIONr_angle_other_deg0.4041.8118920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6795487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.835552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51310735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.050.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024967
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02993
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9526.4881966
X-RAY DIFFRACTIONr_mcbond_other2.9496.4881966
X-RAY DIFFRACTIONr_mcangle_it5.04111.6562447
X-RAY DIFFRACTIONr_mcangle_other5.04111.6582448
X-RAY DIFFRACTIONr_scbond_it2.6536.7722152
X-RAY DIFFRACTIONr_scbond_other2.6526.7752153
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.58512.3763107
X-RAY DIFFRACTIONr_long_range_B_refined7.45461.724308
X-RAY DIFFRACTIONr_long_range_B_other7.45461.734309
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 32 -
Rwork0.319 634 -
obs--94.2 %

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