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- PDB-5iay: NMR structure of UHRF1 Tandem Tudor Domains in a complex with Spa... -

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Basic information

Entry
Database: PDB / ID: 5iay
TitleNMR structure of UHRF1 Tandem Tudor Domains in a complex with Spacer peptide
Components
  • E3 ubiquitin-protein ligase UHRF1
  • Spacer
KeywordsLIGASE / UHRF1 / TTD / Spacer
Function / homology
Function and homology information


histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / methyl-CpG binding / negative regulation of gene expression via chromosomal CpG island methylation / mitotic spindle assembly ...histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / methyl-CpG binding / negative regulation of gene expression via chromosomal CpG island methylation / mitotic spindle assembly / protein autoubiquitination / heterochromatin / cis-regulatory region sequence-specific DNA binding / heterochromatin formation / epigenetic regulation of gene expression / methylated histone binding / positive regulation of protein metabolic process / DNA methylation / Chromatin modifications during the maternal to zygotic transition (MZT) / replication fork / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / euchromatin / nuclear matrix / spindle / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / histone binding / ubiquitin-dependent protein catabolic process / 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
Similarity search - Function
: / 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. / SH3 type barrels. - #30 ...: / 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. / SH3 type barrels. - #30 / SH3 type barrels. - #140 / 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 / SH3 type barrels. / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsFang, J. / Cheng, J. / Wang, J. / Zhang, Q. / Liu, M. / Gong, R. / Wang, P. / Zhang, X. / Feng, Y. / Lan, W. ...Fang, J. / Cheng, J. / Wang, J. / Zhang, Q. / Liu, M. / Gong, R. / Wang, P. / Zhang, X. / Feng, Y. / Lan, W. / Gong, Z. / Tang, C. / Wong, J. / Yang, H. / Cao, C. / Xu, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Basic Research Program of China2011CB965300 China
National Basic Research Program of China2011CB966300 China
CitationJournal: Nat Commun / Year: 2016
Title: Hemi-methylated DNA opens a closed conformation of UHRF1 to facilitate its histone recognition
Authors: Fang, J. / Cheng, J. / Wang, J. / Zhang, Q. / Liu, M. / Gong, R. / Wang, P. / Zhang, X. / Feng, Y. / Lan, W. / Gong, Z. / Tang, C. / Wong, J. / Yang, H. / Cao, C. / Xu, Y.
History
DepositionFeb 22, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase UHRF1
B: Spacer


Theoretical massNumber of molelcules
Total (without water)19,4122
Polymers19,4122
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1090 Å2
ΔGint1 kcal/mol
Surface area12000 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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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 / hNp95 / RING finger protein 106 / 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: 17804.875 Da / Num. of mol.: 1 / Fragment: UNP residues 134-285
Source method: isolated from a genetically manipulated source
Details: UHRF1 Tandem Tudor Domains / Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF1, ICBP90, NP95, RNF106 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96T88, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Spacer


Mass: 1606.849 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: UHRF1(642-658) / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q96T88*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC
121isotropic12D 1H-15N HSQC
131isotropic13D HNCA
141isotropic13D HNCO
151isotropic13D HN(CA)CB
1151isotropic13D CBCA(CO)NH
1141isotropic13D HN(CO)CA
1131isotropic13D (H)CCH-TOCSY
1121isotropic1MQ-CCH-TOCSY
1111isotropic13D 1H-13C NOESY aliphatic
1101isotropic13D 1H-13C NOESY aromatic
191isotropic13D 1H-15N NOESY
181isotropic1(HB)CB(CGCD)HD
171isotropic1(HB)CB(CGCDCE)HE
161isotropic1w2 x-filter TOCSY
1201isotropic1w1,w2 x-filter NOESY
1191isotropic113C-filer HSQC-NOESY
1182isotropic12D 1H-15N HSQC
1172isotropic13D 1H-15N NOESY
1162isotropic13D 1H-15N TOCSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11.0 mM [U-13C; U-15N] TTD, 1.2 mM Spacer, 90% H2O/10% D2O1.0mM [U-13C; U-15N] protein_TTD, 1.2mM protein_Spacer, 90% H2O/10% D2O,15N,13C_TTD/Spacer90% H2O/10% D2O
solution21.0 mM [U-15N] Spacer, TTD, 90% H2O/10% D2O1.0mM [ U-15N] protein_Spacer, 1.2mM protein_TTD, 90% H2O/10% D2O,15N_Spacer/TTD90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMTTD[U-13C; U-15N]1
1.2 mMSpacernatural abundance1
1.0 mMSpacer[U-15N]2
TTDnatural abundance2
Sample conditionsDetails: PBS Buffer:pH 7.4, 10% D2O, 0.01% NaN3 / Ionic strength units: Not defined / Label: NMR condition / pH: 7.4 / Temperature: 297.15 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMRVariancollection
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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