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- PDB-8xv7: Crystal structure of TTD-PHD domain of UHRF1 in complex with hSte... -

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Basic information

Entry
Database: PDB / ID: 8xv7
TitleCrystal structure of TTD-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


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 / 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 / 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
ACETIC ACID / Developmental pluripotency-associated protein 3 / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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

Downloads & links

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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)129,72225
Polymers128,5628
Non-polymers1,16017
Water6,666370
1
A: E3 ubiquitin-protein ligase UHRF1
B: Developmental pluripotency-associated protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5818
Polymers32,1402
Non-polymers4406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-12 kcal/mol
Surface area15480 Å2
MethodPISA
2
C: E3 ubiquitin-protein ligase UHRF1
D: Developmental pluripotency-associated protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3375
Polymers32,1402
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-11 kcal/mol
Surface area14670 Å2
MethodPISA
3
E: E3 ubiquitin-protein ligase UHRF1
F: Developmental pluripotency-associated protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4026
Polymers32,1402
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-55 kcal/mol
Surface area15960 Å2
MethodPISA
4
G: E3 ubiquitin-protein ligase UHRF1
H: Developmental pluripotency-associated protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4026
Polymers32,1402
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-56 kcal/mol
Surface area13850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.548, 153.548, 61.311
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ACEGBDFH

#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.: 4 / 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 / Stella-related protein


Mass: 5683.603 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6W0C5

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Non-polymers , 4 types, 387 molecules

#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.25 Å3/Da / Density % sol: 62.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 4% v/v Tacsimate pH 7.0, 12% PEG 3350

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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: 2.25→76.77 Å / Num. obs: 76760 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.045 / Rrim(I) all: 0.124 / Χ2: 1 / Net I/σ(I): 11.7 / Num. measured all: 574184
Reflection shellResolution: 2.25→2.3 Å / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.869 / Num. measured all: 31753 / Num. unique obs: 4582 / CC1/2: 0.7 / Rpim(I) all: 0.358 / Rrim(I) all: 0.942 / Χ2: 0.96 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
MOLREPphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.55 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22581 3682 4.8 %RANDOM
Rwork0.19305 ---
obs0.1946 73018 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.801 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0.25 Å20 Å2
2---0.49 Å2-0 Å2
3---1.59 Å2
Refinement stepCycle: 1 / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8194 0 30 370 8594
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0128418
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167881
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.67511344
X-RAY DIFFRACTIONr_angle_other_deg0.4031.59218062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35851000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.0065106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83101483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0580.21181
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210193
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022043
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_it3.5874.6134034
X-RAY DIFFRACTIONr_mcbond_other3.5874.6134034
X-RAY DIFFRACTIONr_mcangle_it5.6178.2665022
X-RAY DIFFRACTIONr_mcangle_other5.6168.2675023
X-RAY DIFFRACTIONr_scbond_it4.0445.1184384
X-RAY DIFFRACTIONr_scbond_other4.0445.1194385
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6199.1856323
X-RAY DIFFRACTIONr_long_range_B_refined9.14643.138728
X-RAY DIFFRACTIONr_long_range_B_other9.16743.038657
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 270 -
Rwork0.265 5374 -
obs--100 %

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