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- PDB-2l3r: NMR structure of UHRF1 Tandem Tudor Domains in a complex with His... -

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Basic information

Entry
Database: PDB / ID: 2l3r
TitleNMR structure of UHRF1 Tandem Tudor Domains in a complex with Histone H3 peptide
Components
  • E3 ubiquitin-protein ligase UHRF1
  • Histone H3
KeywordsDNA BINDING PROTEIN/GENE REGULATION / tudor domain / heterochromatin / transcriptional repression / Structural Genomics / Structural Genomics Consortium / SGC / DNA BINDING PROTEIN / DNA BINDING PROTEIN-GENE REGULATION complex
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 / cis-regulatory region sequence-specific DNA binding / heterochromatin / 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 / euchromatin / RING-type E3 ubiquitin transferase / nuclear matrix / spindle / structural constituent of chromatin / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / nucleosome / histone binding / ubiquitin-dependent protein catabolic process / nucleic acid binding / protein ubiquitination / protein heterodimerization activity / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / 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 / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Zinc finger RING-type profile. / Zinc finger, RING-type / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / SH3 type barrels. / Histone-fold / 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
Histone H3 / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsNady, N. / Lemak, A. / Fares, C. / Gutmanas, A. / Avvakumov, G. / Xue, S. / Arrowsmith, C. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Recognition of Multivalent Histone States Associated with Heterochromatin by UHRF1 Protein.
Authors: Nady, N. / Lemak, A. / Walker, J.R. / Avvakumov, G.V. / Kareta, M.S. / Achour, M. / Xue, S. / Duan, S. / Allali-Hassani, A. / Zuo, X. / Wang, Y.X. / Bronner, C. / Chedin, F. / Arrowsmith, C.H. / Dhe-Paganon, S.
History
DepositionSep 21, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase UHRF1
B: Histone H3


Theoretical massNumber of molelcules
Total (without water)20,1752
Polymers20,1752
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein E3 ubiquitin-protein ligase UHRF1


Mass: 18881.014 Da / Num. of mol.: 1 / Fragment: unp residues 126-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF1, ICBP90, NP95, RNF106 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q96T88
#2: Protein/peptide Histone H3


Mass: 1293.516 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: Q3BDD9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HNCA
1613D HBHA(CO)NH
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY
1101Aro-NOESY
1111Aro-2D-1H-13C HSQC
1121Aro-3D-TOCSY
11312D-TOCSY
11413D-Edited-15N/13C NOESY
1151IPAP-15N-1H HSQC
1161J-evolution-13CO-13CA
1171J-evolution-15N-13CO
2181IPAP-15N-1H HSQC
3191IPAP-15N-1H HSQC
4201IPAP-15N-1H HSQC
4211J-evolution-13CO-13CA
4221J-evolution-15N-13CO

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Sample preparation

DetailsContents: 0.6 mM [U-100% 15N] protein, 0.6 mM [U-100% 13C] protein, 3 mM protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMentity_1-1[U-100% 15N]1
0.6 mMentity_1-2[U-100% 13C]1
3 mMentity_2-31
Sample conditionsIonic strength: 250 / pH: 7 / Pressure: 1 ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
ABACUSLemakchemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
SparkyGoddardpeak picking
FuDAFlemming Hansenprocessing
TALOSCornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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