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- PDB-2m9v: Structure of Saccharomyces cerevisiae Est3 protein -

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Basic information

Entry
Database: PDB / ID: 2m9v
TitleStructure of Saccharomyces cerevisiae Est3 protein
ComponentsTelomere replication protein EST3
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


DNA/RNA helicase activity / telomerase holoenzyme complex / telomeric DNA binding / telomere maintenance via telomerase / chromosome, telomeric region / viral translational frameshifting / GTPase activity / nucleus / cytosol
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #960 / Shelterin complex subunit TPP1/Est3 / Shelterin complex subunit, TPP1/ACD / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Telomere replication protein EST3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / Molecular fragment replacement
AuthorsRao, T. / Armstrong, G.S. / Wuttke, D.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure of Est3 reveals a bimodal surface with differential roles in telomere replication.
Authors: Rao, T. / Lubin, J.W. / Armstrong, G.S. / Tucey, T.M. / Lundblad, V. / Wuttke, D.S.
History
DepositionJun 21, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Jan 22, 2014Group: 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 / 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_software.name / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Telomere replication protein EST3


Theoretical massNumber of molelcules
Total (without water)19,2981
Polymers19,2981
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 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Telomere replication protein EST3 / Ever shorter telomeres protein 3


Mass: 19297.859 Da / Num. of mol.: 1 / Fragment: UNP residues 13-181 / Mutation: C142S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: EST3, YIL009C-A / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q03096

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC TROSY
1213D HNCA TROSY
1313D HN(CA)CB TROSY
1413D HN(CO)CA TROSY
1513D HN(COCA)CB TROSY
1613D HNCO TROSY
1713D 1H-15N NOESY
1842D 1H-13C HMQC
1943D HMCMCBCA
11043D HMCMCGCBCA
11143D methyl 1H-1H 13C HMQC NOESY
11222D 1H-15N HSQC
11322D 1H-15N HSQC TROSY
11432D 1H-15N HSQC
11532D 1H-15N HSQC TROSY
NMR detailsText: The structure was calculated by a combination of NOE and Residual dipolar coupling

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM Bis tris propane, 150 mM MOPS, 50 mM sodium sulfate, 100 mM arginine, 100 mM glutamate, 100 mM NDSB, 2 mM DTT, 7 % D2O, 0.15 mM TSP, 93% H2O/7% D2O93% H2O/7% D2O
250 mM Bis tris propane, 150 mM MOPS, 50 mM sodium sulfate, 100 mM arginine, 100 mM glutamate, 100 mM NDSB, 2 mM DTT, 10 % D2O, 9.6 mg/mL Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
350 mM Bis tris propane, 150 mM MOPS, 50 mM sodium sulfate, 100 mM arginine, 100 mM glutamate, 100 mM NDSB, 2 mM DTT, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
450 mM Bis tris propane, 150 mM MOPS, 50 mM sodium sulfate, 100 mM arginine, 100 mM glutamate, 100 mM NDSB, 2 mM DTT, 7 % D2O, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
50 mMBis tris propane-11
150 mMMOPS-21
50 mMsodium sulfate-31
100 mMarginine-41
100 mMglutamate-51
100 mMNDSB-195-61
2 mMDTT-71
7 %D2O-81
0.15 mMTSP-91
50 mMBis tris propane-102
150 mMMOPS-112
50 mMsodium sulfate-122
100 mMarginine-132
100 mMglutamate-142
100 mMNDSB-195-152
2 mMDTT-162
10 %D2O-172
9.6 mg/mLPf1 phage-182
50 mMBis tris propane-193
150 mMMOPS-203
50 mMsodium sulfate-213
100 mMarginine-223
100 mMglutamate-233
100 mMNDSB-195-243
2 mMDTT-253
10 %D2O-263
50 mMBis tris propane-274
150 mMMOPS-284
50 mMsodium sulfate-294
100 mMarginine-304
100 mMglutamate-314
100 mMNDSB-195-324
2 mMDTT-334
7 %D2O-344
Sample conditionspH: 7.1 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNMRSVarianVNMRS8001
Agilent DD2AgilentDD29002

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ3.1Variancollection
CcpNmr Analysis2.1.5CCPNdata analysis
CcpNmr Analysis2.1.5CCPNpeak picking
CcpNmr Analysis2.1.5CCPNchemical shift assignment
NMRPipe2011Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichconstraints list generation for structure solution
Rosetta3.4David Bakerstructure solution
CS-Rosetta_toolbox1.3David Bakerstructure solution
X-PLOR NIH2.29Schwieters, Kuszewski, Tjandra and Clorestructure and constraints validation
Rosetta3.4David Bakerrefinement
RefinementMethod: Molecular fragment replacement / Software ordinal: 1
NMR constraintsNOE constraints total: 292 / NOE intraresidue total count: 0 / NOE long range total count: 124 / NOE medium range total count: 57 / NOE sequential total count: 111
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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