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- PDB-2l5a: Structural basis for recognition of centromere specific histone H... -

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Basic information

Entry
Database: PDB / ID: 2l5a
TitleStructural basis for recognition of centromere specific histone H3 variant by nonhistone Scm3
ComponentsHistone H3-like centromeric protein CSE4, Protein SCM3, Histone H4
KeywordsNUCLEAR PROTEIN / a single chain of Cse4+Scm3+H4 / fusion protein / chimera protein
Function / homology
Function and homology information


CENP-A containing nucleosome binding / condensed chromosome, centromeric region => GO:0000779 / 2-micrometer circle DNA / 2-micrometer plasmid partitioning / HDMs demethylate histones / HATs acetylate histones / Condensation of Prophase Chromosomes / RNA polymerase I upstream activating factor complex / centromeric DNA binding / SUMOylation of chromatin organization proteins ...CENP-A containing nucleosome binding / condensed chromosome, centromeric region => GO:0000779 / 2-micrometer circle DNA / 2-micrometer plasmid partitioning / HDMs demethylate histones / HATs acetylate histones / Condensation of Prophase Chromosomes / RNA polymerase I upstream activating factor complex / centromeric DNA binding / SUMOylation of chromatin organization proteins / protein localization to chromosome, centromeric region / kinetochore assembly / condensed chromosome, centromeric region / replication fork protection complex / RMTs methylate histone arginines / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / mitotic sister chromatid segregation / rRNA transcription / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / negative regulation of ubiquitin-dependent protein catabolic process / chromosome segregation / nucleosome assembly / structural constituent of chromatin / G2/M transition of mitotic cell cycle / nucleosome / chromatin organization / histone binding / sequence-specific DNA binding / protein heterodimerization activity / regulation of DNA-templated transcription / DNA binding / nucleus / cytoplasm
Similarity search - Function
Centromere protein Scm3/HJURP / Centromere protein Scm3 / Histone, subunit A / Histone, subunit A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold ...Centromere protein Scm3/HJURP / Centromere protein Scm3 / Histone, subunit A / Histone, subunit A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / 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 H4 / Histone H3-like centromeric protein CSE4 / Protein SCM3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsZhou, Z. / Feng, H. / Zhou, B. / Ghirlando, R. / Hu, K. / Zwolak, A. / Jenkins, L. / Xiao, H. / Tjandra, N. / Wu, C. / Bai, Y.
CitationJournal: Nature / Year: 2011
Title: Structural basis for recognition of centromere histone variant CenH3 by the chaperone Scm3.
Authors: Zhou, Z. / Feng, H. / Zhou, B.R. / Ghirlando, R. / Hu, K. / Zwolak, A. / Miller Jenkins, L.M. / Xiao, H. / Tjandra, N. / Wu, C. / Bai, Y.
History
DepositionOct 28, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Remark 999Author states the protein is one chimera protein composed of folded cores of Cse4(PDB residues 0-87 ...Author states the protein is one chimera protein composed of folded cores of Cse4(PDB residues 0-87 coresponds to UNP residues 151-228), Scm3(PDB residues 88-173 corresponds to UNP residues 93-172) and H4(PDB residues 174-235 corresponds to UNP residues 42-103).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H3-like centromeric protein CSE4, Protein SCM3, Histone H4


Theoretical massNumber of molelcules
Total (without water)27,0341
Polymers27,0341
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 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Histone H3-like centromeric protein CSE4, Protein SCM3, Histone H4 / CENP-A homolog / Chromosome segregation protein 4 / Suppressor of chromosome missegregation protein 3 /


Mass: 27034.113 Da / Num. of mol.: 1 / Fragment: Cse4(151-228), Scm3(93-172), H4(42-103)
Source method: isolated from a genetically manipulated source
Details: Fusion protein of Cse4, Scm3 and H4
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CSE4, CSL2, YKL049C, YKL262, SCM3, YDL139C, D2155, HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752
Plasmid: pET42b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) condon plus RPL
References: UniProt: P36012, UniProt: Q12334, UniProt: P02309

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: A structure of single chain protein complex containing Cse4, Scm3 and H4 folded core.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N TROSY
1262D 1H-1H NOESY
1332D 1H-13C HMQC
1423D trHNCACB
1523D trHNCOCACB
1623D trHNCA
1723D trHNCOCA
1823D trHNCO
1923D trHNCACO
11053D (H)CCH-TOCSY
11153D CCCH-TOCSY
11253D HBHA(CO)NH
11353D H(CCO)NH
11413D 1H-15N NOESY
11533D 1H-15N NOESY
11653D 1H-13C NOESY
11733D 1H-13C NOESY
11843D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8-1.0 mM [U-100% 15N] scCSH-1, 90% H2O/10% D2O90% H2O/10% D2O
20.8-0.85 mM [U-100% 15N] scCSH-2, 90% H2O/10% D2O90% H2O/10% D2O
30.8-0.85 mM [U-13C methyl; U-15N; U-2H] scCSH-3, 90% H2O/10% D2O90% H2O/10% D2O
40.8-0.85 mM [U-13C ; U-15N; 35%-2H] scCSH-4, 90% H2O/10% D2O90% H2O/10% D2O
50.8-0.85 mM [U-13C ; U-15N] scCSH-5, 100% D2O100% D2O
60.8-0.85 mM scCSH-6, 100% D2O100% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMscCSH-1[U-100% 15N]0.8-1.01
mMscCSH-2[U-100% 15N]0.8-0.852
mMscCSH-3[U-13C methyl; U-15N; U-2H]0.8-0.853
mMscCSH-4[U-13C ; U-15N; 35%-2H]0.8-0.854
mMscCSH-5[U-13C; U-15N]0.8-0.855
mMscCSH-60.8-0.856
Sample conditionsIonic strength: 0.00 / pH: 5.4 / Pressure: ambient atm / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX8003
Bruker DRXBrukerDRX9004
Varian INOVAVarianINOVA8005

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeupdated versionDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRView7.9.1Johnson, One Moon Scientificdata analysis
TALOSupdated versionCornilescu, Delaglio and Baxdata analysis
X-PLOR_NIH2.25Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR_NIH2.25Schwieters, Kuszewski, Tjandra and Clorerefinement
ProcheckNMRLaskowski and MacArthurstructure evaluation
MolmolpyMolKoradi, Billeter and Wuthrichpdb display
MolProbity3.17Richardsonstructure evaluation
RefinementMethod: DGSA-distance geometry simulated annealing, molecular dynamics
Software ordinal: 1
NMR constraintsNOE constraints total: 3871 / NOE intraresidue total count: 1198 / NOE long range total count: 686 / NOE medium range total count: 909 / NOE sequential total count: 1067 / Hydrogen bond constraints total count: 168 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 142 / Protein psi angle constraints total count: 142
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.1 Å / Maximum torsion angle constraint violation: 3 ° / Maximum upper distance constraint violation: 0.3 Å
NMR ensemble rmsDistance rms dev: 0.029 Å / Distance rms dev error: 0.002 Å

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