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- PDB-8xv8: Crystal structure of PHD domain of UHRF1 in complex with hStella ... -

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Basic information

Entry
Database: PDB / ID: 8xv8
TitleCrystal structure of PHD domain of UHRF1 in complex with hStella peptide (residues 75-121)
Components
  • Developmental pluripotency-associated protein 3
  • E3 ubiquitin-protein ligase UHRF1
KeywordsGENE REGULATION / Inhibitor / complex
Function / homology
Function and homology information


histone H3 ubiquitin ligase activity / epigenetic programing of female pronucleus / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / methyl-CpG binding / female pronucleus / histone H3K9me2/3 reader activity / negative regulation of gene expression via chromosomal CpG island methylation ...histone H3 ubiquitin ligase activity / epigenetic programing of female pronucleus / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / methyl-CpG binding / female pronucleus / histone H3K9me2/3 reader activity / negative regulation of gene expression via chromosomal CpG island methylation / : / positive regulation of protein metabolic process / mitotic spindle assembly / heterochromatin / protein autoubiquitination / cis-regulatory region sequence-specific DNA binding / DNA methylation / epigenetic regulation of gene expression / Chromatin modifications during the maternal to zygotic transition (MZT) / 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: 2.05 Å
AuthorsDu, X. / Gan, Q. / Xu, J. / Liu, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
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

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase UHRF1
B: Developmental pluripotency-associated protein 3
C: E3 ubiquitin-protein ligase UHRF1
D: Developmental pluripotency-associated protein 3
E: E3 ubiquitin-protein ligase UHRF1
F: Developmental pluripotency-associated protein 3
G: E3 ubiquitin-protein ligase UHRF1
H: Developmental pluripotency-associated protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,98022
Polymers56,0648
Non-polymers91614
Water1,08160
1
A: E3 ubiquitin-protein ligase UHRF1
B: Developmental pluripotency-associated protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2786
Polymers14,0162
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: E3 ubiquitin-protein ligase UHRF1
D: Developmental pluripotency-associated protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2786
Polymers14,0162
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: E3 ubiquitin-protein ligase UHRF1
F: Developmental pluripotency-associated protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2125
Polymers14,0162
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: E3 ubiquitin-protein ligase UHRF1
H: Developmental pluripotency-associated protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2125
Polymers14,0162
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.029, 46.020, 82.910
Angle α, β, γ (deg.)90.00, 112.76, 90.00
Int Tables number4
Space group name H-MP1211

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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: 8332.430 Da / Num. of mol.: 4 / Fragment: 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 / Stella-related protein


Mass: 5683.603 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6W0C5
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.07 Å3/Da / Density % sol: 40.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 25% PEG 3350
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.05→38.23 Å / Num. obs: 28518 / % possible obs: 97.9 % / Redundancy: 5.8 % / CC1/2: 0.991 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.044 / Rrim(I) all: 0.108 / Χ2: 1.07 / Net I/σ(I): 10.4 / Num. measured all: 164753
Reflection shellResolution: 2.05→2.11 Å / % possible obs: 85.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.656 / Num. measured all: 8590 / Num. unique obs: 1941 / CC1/2: 0.8 / Rpim(I) all: 0.348 / Rrim(I) all: 0.749 / Χ2: 0.93 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SHB

3shb


Resolution: 2.05→38.23 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.958 / SU B: 5.407 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 1369 4.8 %RANDOM
Rwork0.18623 ---
obs0.18728 27124 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.977 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å2-0 Å2-1.38 Å2
2--7.3 Å20 Å2
3----2.95 Å2
Refinement stepCycle: 1 / Resolution: 2.05→38.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2993 0 14 60 3067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123108
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162890
X-RAY DIFFRACTIONr_angle_refined_deg1.741.8854154
X-RAY DIFFRACTIONr_angle_other_deg0.551.8086635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.785371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.5538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99410556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0760.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023621
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02701
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_it3.7334.0651508
X-RAY DIFFRACTIONr_mcbond_other3.7254.0651508
X-RAY DIFFRACTIONr_mcangle_it5.3177.2731871
X-RAY DIFFRACTIONr_mcangle_other5.3167.2751872
X-RAY DIFFRACTIONr_scbond_it5.1624.7561600
X-RAY DIFFRACTIONr_scbond_other5.1614.7581601
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1338.4982284
X-RAY DIFFRACTIONr_long_range_B_refined10.25251.373279
X-RAY DIFFRACTIONr_long_range_B_other10.25851.053272
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 80 -
Rwork0.31 1745 -
obs--84.14 %

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