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- PDB-2rso: Solution structure of the chromodomain of Swi6 -

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Basic information

Entry
Database: PDB / ID: 2rso
TitleSolution structure of the chromodomain of Swi6
ComponentsChromatin-associated protein swi6
KeywordsTRANSCRIPTION / chromodomain / chromatin / Silencing / Chromosomal protein / Methylation
Function / homology
Function and homology information


meiotic centromeric cohesion protection in anaphase I / positive regulation of pericentric heterochromatin formation / gene conversion at mating-type locus / mating type switching / mitotic telomere tethering at nuclear periphery / mitotic sister chromatid cohesion, centromeric / mating-type region heterochromatin / heterochromatin island / heterochromatin boundary formation / mitotic sister chromatid biorientation ...meiotic centromeric cohesion protection in anaphase I / positive regulation of pericentric heterochromatin formation / gene conversion at mating-type locus / mating type switching / mitotic telomere tethering at nuclear periphery / mitotic sister chromatid cohesion, centromeric / mating-type region heterochromatin / heterochromatin island / heterochromatin boundary formation / mitotic sister chromatid biorientation / chromosome, subtelomeric region / chromatin-protein adaptor activity / condensed chromosome, centromeric region / silent mating-type cassette heterochromatin formation / heterochromatin / pericentric heterochromatin / methylated histone binding / histone reader activity / chromatin organization / histone binding / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / DNA binding / RNA binding / identical protein binding / nucleus
Similarity search - Function
Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / 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 shadow domain / Chromo shadow domain / Chromo Shadow Domain / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chromatin-associated protein swi6
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsShimojo, H. / Nishimura, Y.
CitationJournal: Mol.Cell / Year: 2012
Title: Intrinsic nucleic Acid-binding activity of chp1 chromodomain is required for heterochromatic gene silencing
Authors: Ishida, M. / Shimojo, H. / Hayashi, A. / Kawaguchi, R. / Ohtani, Y. / Uegaki, K. / Nishimura, Y. / Nakayama, J.
History
DepositionApr 18, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / 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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromatin-associated protein swi6


Theoretical massNumber of molelcules
Total (without water)10,5031
Polymers10,5031
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 600target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Chromatin-associated protein swi6


Mass: 10503.325 Da / Num. of mol.: 1 / Fragment: UNP residues 55-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / Gene: swi6 / Production host: Escherichia coli (E. coli) / References: UniProt: P40381

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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 aliphatic
1312D 1H-13C HSQC aromatic
1413D HNCO
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D C(CO)NH
1813D HBHA(CO)NH
1913D H(CCO)NH
11013D (H)CCH-TOCSY
11113D (H)CCH-COSY
11213D 1H-15N NOESY
11313D 1H-13C NOESY aliphatic
11413D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.3-0.5mM [U-99% 13C; U-99% 15N] Swi6-CD-1, 10mM potassium chloride-2, 20mM sodium phosphate-3, 5mM [U-100% 2H] DTT-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMSwi6-CD-1[U-99% 13C; U-99% 15N]0.3-0.51
10 mMpotassium chloride-21
20 mMsodium phosphate-31
5 mMDTT-4[U-100% 2H]1
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
OliviaYokochi, Sekiguchi and Inagakipeak picking
OliviaYokochi, Sekiguchi and Inagakidata analysis
OliviaYokochi, Sekiguchi and Inagakichemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANArefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 600 / Conformers submitted total number: 20 / Representative conformer: 1

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