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- PDB-7xga: NMR strucutre of chimeric protein for model of PHD-Stella complex -

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Basic information

Entry
Database: PDB / ID: 7xga
TitleNMR strucutre of chimeric protein for model of PHD-Stella complex
ComponentsChimera of E3 ubiquitin-protein ligase UHRF1 and Developmental pluripotency-associated protein 3
KeywordsTRANSCRIPTION / zinc-finger / complex / chimeric model / DNA methylation
Function / homology
Function and homology information


: / : / epigenetic programing of female pronucleus / histone H3 ubiquitin ligase activity / hemi-methylated DNA-binding / embryonic cleavage / regulation of epithelial cell proliferation / methyl-CpG binding / male pronucleus / female pronucleus ...: / : / epigenetic programing of female pronucleus / histone H3 ubiquitin ligase activity / hemi-methylated DNA-binding / embryonic cleavage / regulation of epithelial cell proliferation / methyl-CpG binding / male pronucleus / female pronucleus / negative regulation of gene expression via chromosomal CpG island methylation / mitotic spindle assembly / protein autoubiquitination / cis-regulatory region sequence-specific DNA binding / heterochromatin / heterochromatin formation / methylated histone binding / positive regulation of protein metabolic process / replication fork / RING-type E3 ubiquitin transferase / euchromatin / nuclear matrix / ubiquitin protein ligase activity / chromatin organization / histone binding / ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA repair / chromatin / negative 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 / UHRF1/2-like / Tandem tudor domain within UHRF1 / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. ...Developmental pluripotency-associated protein 3 / PGC7/Stella/Dppa3 domain / : / UHRF1, tandem tudor domain / UHRF1/2-like / Tandem tudor domain within UHRF1 / 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 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-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 speciesMus musculus (house mouse)
MethodSOLUTION NMR / molecular dynamics
AuthorsKobayashi, N. / Konuma, T. / Arita, K.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP18H02392 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05294 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05741 Japan
Japan Science and Technology14530337 Japan
Japan Society for the Promotion of Science (JSPS)19J22030 Japan
Japan Society for the Promotion of Science (JSPS)JP18K06152 Japan
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Structural basis for the unique multifaceted interaction of DPPA3 with the UHRF1 PHD finger.
Authors: Hata, K. / Kobayashi, N. / Sugimura, K. / Qin, W. / Haxholli, D. / Chiba, Y. / Yoshimi, S. / Hayashi, G. / Onoda, H. / Ikegami, T. / Mulholland, C.B. / Nishiyama, A. / Nakanishi, M. / ...Authors: Hata, K. / Kobayashi, N. / Sugimura, K. / Qin, W. / Haxholli, D. / Chiba, Y. / Yoshimi, S. / Hayashi, G. / Onoda, H. / Ikegami, T. / Mulholland, C.B. / Nishiyama, A. / Nakanishi, M. / Leonhardt, H. / Konuma, T. / Arita, K.
History
DepositionApr 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 22, 2023Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)14,7784
Polymers14,5821
Non-polymers1963
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein Chimera of E3 ubiquitin-protein ligase UHRF1 and Developmental pluripotency-associated protein 3 / RING-type E3 ubiquitin transferase UHRF1 / Ubiquitin-like PHD and RING finger domain-containing ...RING-type E3 ubiquitin transferase UHRF1 / Ubiquitin-like PHD and RING finger domain-containing protein 1 / mUhrf1 / Ubiquitin-like-containing PHD and RING finger domains protein 1


Mass: 14581.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Uhrf1, Dppa3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8VDF2, UniProt: Q8QZY3, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
232isotropic12D 1H-13C HSQC aliphatic
141isotropic13D HNCO
151isotropic13D HN(CO)CA
161isotropic13D HN(CA)CB
171isotropic13D CBCA(CO)NH
181isotropic12D 1H-13C HSQC aromatic
292isotropic12D 1H-13C HSQC aromatic
1101isotropic13D (H)CCH-TOCSY
1111isotropic13D H(CCO)NH
1121isotropic13D C(CO)NH
1131isotropic13D 1H-15N NOESY
1141isotropic13D 1H-13C NOESY aliphatic
2152isotropic23D 1H-13C NOESY aliphatic
1161isotropic23D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.66 mM [U-100% 13C; U-100% 15N] PHD_Stella, 10 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2OPHD_Stella90% H2O/10% D2O
solution20.66 mM [U-100% 13C; U-100% 15N] PHD_Stella, 10 mM sodium phosphate, 50 mM sodium chloride, 100% D2OPHD_Stella_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.66 mMPHD_Stella[U-100% 13C; U-100% 15N]1
10 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
0.66 mMPHD_Stella[U-100% 13C; U-100% 15N]2
10 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
150 mMPHD_Stella7.0 1 atm293 K
250 mMPHD_Stella_D2O7.0 pD1 atm293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III5001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospincollection
NMRPipe2017Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA3.98Guntert, Mumenthaler and Wuthrichchemical shift assignment
MAGRO2.01.41Kobayashi, N.peak picking
NMRViewJ9Johnson, B. J.data analysis
CYANA3.98Guntert, Mumenthaler and Wuthrichstructure calculation
Amber12Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 7
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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