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- PDB-2luy: Solution structure of the tandem zinc finger domain of fission ye... -

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Basic information

Entry
Database: PDB / ID: 2luy
TitleSolution structure of the tandem zinc finger domain of fission yeast Stc1
ComponentsMeiotic chromosome segregation protein P8B7.28c
KeywordsDNA BINDING PROTEIN / tandem zinc fingers
Function / homology
Function and homology information


CLRC complex localization to heterochromatin / pericentric heterochromatin => GO:0005721 / regulatory ncRNA-mediated heterochromatin formation / pericentric heterochromatin formation / silent mating-type cassette heterochromatin formation / subtelomeric heterochromatin formation / meiotic cell cycle / protein-macromolecule adaptor activity / nucleolus / nucleus
Similarity search - Function
Stc1 domain / Stc1 domain / Stc1 domain superfamily / Stc1 domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Meiotic chromosome segregation protein P8B7.28c
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsHe, C. / Shi, Y. / Bayne, E. / Wu, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural analysis of Stc1 provides insights into the coupling of RNAi and chromatin modification.
Authors: He, C. / Pillai, S.S. / Taglini, F. / Li, F. / Ruan, K. / Zhang, J. / Wu, J. / Shi, Y. / Bayne, E.H.
History
DepositionJun 22, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Meiotic chromosome segregation protein P8B7.28c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3553
Polymers11,2241
Non-polymers1312
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Meiotic chromosome segregation protein P8B7.28c


Mass: 11224.009 Da / Num. of mol.: 1 / Fragment: tandem zinc finger domain, UNP residues 32-126 / Mutation: C38A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: SPBP8B7.28c / Production host: Escherichia coli (E. coli) / References: UniProt: O94276
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of the tandem zinc finger domain of fission yeast Stc1
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D HBHA(CO)NH
1613D H(CCO)NH
1713D C(CO)NH
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11013D (H)CCH-TOCSY
11113D (H)CCH-COSY
11212D 1H-1H TOCSY
11312D 1H-1H NOESY

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Sample preparation

DetailsContents: 200 mM sodium chloride, 20 mM Bis-Tris, 0.8 mM [U-100% 13C; U-100% 15N] protein, 1.6 mM ZINC ION, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 mMsodium chloride-11
20 mMBis-Tris-21
0.8 mMentity_1-3[U-100% 13C; U-100% 15N]1
1.6 mMZINC ION-41
Sample conditionsIonic strength: 0.2 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SPARKYGoddardpeak picking
SPARKYGoddardchemical shift assignment
TALOSCornilescu, Delaglio and Baxchemical shift calculation
MolmolKoradi, Billeter and Wuthrichdata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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