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- PDB-2rvm: Solution structure of the chromodomain of HP1alpha with the phosp... -

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Basic information

Entry
Database: PDB / ID: 2rvm
TitleSolution structure of the chromodomain of HP1alpha with the phosphorylated N-terminal tail
ComponentsChromobox protein homolog 5
KeywordsTRANSCRIPTION / chromodomain / hp1alpha
Function / homology
Function and homology information


chromocenter / Factors involved in megakaryocyte development and platelet production / histone H3K9me2/3 reader activity / histone methyltransferase complex / site of DNA damage / histone deacetylase complex / ribonucleoprotein complex binding / heterochromatin / pericentric heterochromatin / : ...chromocenter / Factors involved in megakaryocyte development and platelet production / histone H3K9me2/3 reader activity / histone methyltransferase complex / site of DNA damage / histone deacetylase complex / ribonucleoprotein complex binding / heterochromatin / pericentric heterochromatin / : / transcription repressor complex / histone reader activity / PML body / kinetochore / histone deacetylase binding / protein-macromolecule adaptor activity / DNA-binding transcription factor binding / chromosome, telomeric region / ribonucleoprotein complex / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / : / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. ...Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / : / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily
Similarity search - Domain/homology
Chromobox protein homolog 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsKawaguchi, A. / Nishimura, Y.
CitationJournal: Sci Rep / Year: 2016
Title: Extended string-like binding of the phosphorylated HP1 alpha N-terminal tail to the lysine 9-methylated histone H3 tail
Authors: Shimojo, H. / Kawaguchi, A. / Oda, T. / Hashiguchi, N. / Omori, S. / Moritsugu, K. / Kidera, A. / Hiragami-Hamada, K. / Nakayama, J. / Sato, M. / Nishimura, Y.
History
DepositionDec 18, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_conn / struct_ref / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromobox protein homolog 5


Theoretical massNumber of molelcules
Total (without water)10,1691
Polymers10,1691
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)20 / 600structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Chromobox protein homolog 5 / Heterochromatin protein 1 homolog alpha / HP1 alpha


Mass: 10169.046 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 1-80
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Description: For phosphorylation of Ser the expression with pRSFduet (CK2)
Gene: Cbx5, Hp1a / Production host: Escherichia coli (E. coli) / References: UniProt: Q61686
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC aliphatic
1322D 1H-13C HSQC aromatic
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D HN(CO)CA
1913D HBHA(CO)NH
11013D C(CO)NH
11113D H(CCO)NH
11223D (H)CCH-TOCSY
11313D 1H-15N NOESY
11423D 1H-13C NOESY aliphatic
11523D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
110 mM [U-99% 13C; U-99% 15N] potassium phosphate-1, 20 mM [U-99% 13C; U-99% 15N] sodium chloride-2, 5 mM [U-99% 13C; U-99% 15N] DTT-3, 90% H2O/10% D2O90% H2O/10% D2O
210 mM [U-99% 13C; U-99% 15N] potassium phosphate-4, 20 mM [U-99% 13C; U-99% 15N] sodium chloride-5, 5 mM [U-99% 13C; U-99% 15N] DTT-6, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMpotassium phosphate-1[U-99% 13C; U-99% 15N]1
20 mMsodium chloride-2[U-99% 13C; U-99% 15N]1
5 mMDTT-3[U-99% 13C; U-99% 15N]1
10 mMpotassium phosphate-4[U-99% 13C; U-99% 15N]2
20 mMsodium chloride-5[U-99% 13C; U-99% 15N]2
5 mMDTT-6[U-99% 13C; U-99% 15N]2
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
OliviaYokochi, M., Sekiguchi, S. and Inagaki, F.chemical shift assignment
CYANArefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 600 / Conformers submitted total number: 20 / Representative conformer: 1

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