[English] 日本語
Yorodumi
- PDB-8xv6: Crystal structure of PHD domain of UHRF1 in complex with mStella ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xv6
TitleCrystal structure of 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 / 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
THIOCYANATE ION / 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: 1.6 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,35821
Polymers25,2634
Non-polymers1,09517
Water2,198122
1
A: E3 ubiquitin-protein ligase UHRF1
B: Developmental pluripotency-associated protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,22511
Polymers12,6322
Non-polymers5939
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-88 kcal/mol
Surface area6190 Å2
MethodPISA
2
C: E3 ubiquitin-protein ligase UHRF1
D: Developmental pluripotency-associated protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,13310
Polymers12,6322
Non-polymers5018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-84 kcal/mol
Surface area5980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.940, 75.720, 96.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein / Protein/peptide , 2 types, 4 molecules ACBD

#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.: 2 / 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 / 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

-
Non-polymers , 4 types, 139 molecules

#3: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: CNS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M Potassium thiocyanate, 30% PEG MME2000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→19.95 Å / Num. obs: 34602 / % possible obs: 99.8 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.017 / Rrim(I) all: 0.042 / Χ2: 0.65 / Net I/σ(I): 21 / Num. measured all: 213799
Reflection shellResolution: 1.6→1.63 Å / % possible obs: 98.3 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.321 / Num. measured all: 8346 / Num. unique obs: 1748 / CC1/2: 0.913 / Rpim(I) all: 0.162 / Rrim(I) all: 0.361 / Χ2: 0.69 / Net I/σ(I) obs: 3.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→19.95 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.693 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16803 1794 5.2 %RANDOM
Rwork0.15228 ---
obs0.15307 32780 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.975 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0.21 Å20 Å2
3---0.2 Å2
Refinement stepCycle: 1 / Resolution: 1.6→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 0 34 122 1678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121585
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161512
X-RAY DIFFRACTIONr_angle_refined_deg1.811.8752104
X-RAY DIFFRACTIONr_angle_other_deg0.8311.8473475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2815188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.729521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.54310297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021854
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02354
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_it1.6381.77764
X-RAY DIFFRACTIONr_mcbond_other1.5131.761758
X-RAY DIFFRACTIONr_mcangle_it2.1983.159941
X-RAY DIFFRACTIONr_mcangle_other2.1973.16942
X-RAY DIFFRACTIONr_scbond_it2.6872.099821
X-RAY DIFFRACTIONr_scbond_other2.6882.102822
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8853.6941163
X-RAY DIFFRACTIONr_long_range_B_refined6.32118.991770
X-RAY DIFFRACTIONr_long_range_B_other6.3218.991771
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 126 -
Rwork0.196 2377 -
obs--98.78 %
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)
11.4609-1.5044-0.51344.06551.14573.39-0.07-0.07310.05760.11970.2032-0.0527-0.0498-0.1055-0.13320.02660.03890.01380.05940.02340.029913.0392.031210.4449
24.12461.68482.52814.20073.20578.19660.0164-0.22430.01240.1482-0.20530.48510.2429-0.76390.18890.10550.04260.06030.16150.03820.1564.7003-3.788214.5301
33.6474-1.63251.32842.2827-0.72512.88960.09530.0405-0.0377-0.0685-0.09550.03630.1170.0360.00020.05970.04720.01590.04090.01190.016232.7565-14.590113.3681
44.63291.93072.4754.49622.54096.8182-0.14610.20510.5164-0.1853-0.0472-0.1553-0.53510.30080.19330.13090.0540.02140.10450.08210.149139.4797-6.57979.1058
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A299 - 366
2X-RAY DIFFRACTION2B87 - 113
3X-RAY DIFFRACTION3C299 - 366
4X-RAY DIFFRACTION4D87 - 113

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more