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- PDB-2ly8: The budding yeast chaperone Scm3 recognizes the partially unfolde... -

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Basic information

Entry
Database: PDB / ID: 2ly8
TitleThe budding yeast chaperone Scm3 recognizes the partially unfolded dimer of the centromere-specific Cse4/H4 histone variant
ComponentsBudding yeast chaperone Scm3
KeywordsCHAPERONE / centromere protein / CenH3 variants / Partially unfolded
Function / homology
Function and homology information


2-micrometer circle DNA / 2-micrometer plasmid partitioning / centromeric DNA binding / kinetochore assembly / condensed chromosome, centromeric region / mitotic sister chromatid segregation / rRNA transcription / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / structural constituent of chromatin ...2-micrometer circle DNA / 2-micrometer plasmid partitioning / centromeric DNA binding / kinetochore assembly / condensed chromosome, centromeric region / mitotic sister chromatid segregation / rRNA transcription / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / structural constituent of chromatin / sequence-specific DNA binding / protein heterodimerization activity / nucleus
Similarity search - Function
Histone, subunit A / Histone, subunit A / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H3-like centromeric protein CSE4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model 1
AuthorsHong, J. / Feng, H. / Zhou, Z. / Ghirlando, R. / Bai, Y.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Identification of Functionally Conserved Regions in the Structure of the Chaperone/CenH3/H4 Complex.
Authors: Hong, J. / Feng, H. / Zhou, Z. / Ghirlando, R. / Bai, Y.
History
DepositionSep 13, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Feb 20, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Budding yeast chaperone Scm3


Theoretical massNumber of molelcules
Total (without water)13,7181
Polymers13,7181
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)10 / 30structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Budding yeast chaperone Scm3


Mass: 13717.882 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: Cse4p / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus-RIPL / References: UniProt: P36012*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: This is a structure of re-engineering single chain of Cse4-LVPRGS-H4
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-1H NOESY
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1613D HNCA
1713D HN(CO)CA
1823D HBHA(CO)NH
1923D (H)CCH-TOCSY
11023D 1H-15N NOESY
11123D 1H-13C NOESY
11232D 1H-1H NOESY
11323D H(CCO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 15N] sC4, 0.8 mM [U-100% 13C; U-100% 15N] sC4, 0.8 mM [U-13C; U-15N; U-2H] sC4, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-100% 13C; U-100% 15N] sC4, 100% D2O100% D2O
30.8 mM sC4, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMsC4-1[U-100% 15N]1
0.8 mMsC4-2[U-100% 13C; U-100% 15N]1
0.8 mMsC4-3[U-13C; U-15N; U-2H]1
0.8 mMsC4-4[U-100% 13C; U-100% 15N]2
0.8 mMsC4-53
Sample conditionspH: 5.4 / Pressure: ambient / Temperature: 308.1 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeupdatedDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewupdatedJohnson, One Moon Scientificchemical shift assignment
X-PLOR NIHupdatedSchwieters, Kuszewski, Tjandra and Clorestructure solution
NMRDrawCornilescu, Delaglio and Baxdata analysis
ProcheckNMRupdatedLaskowski and MacArthurstructure solution
MOLMOLKoradi, Billeter and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 3382 / NOE intraresidue total count: 912 / NOE long range total count: 466 / NOE medium range total count: 1151 / NOE sequential total count: 853 / Protein phi angle constraints total count: 85 / Protein psi angle constraints total count: 85
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 30 / Conformers submitted total number: 10

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