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- PDB-2jyn: A novel solution NMR structure of protein yst0336 from Saccharomy... -

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Basic information

Entry
Database: PDB / ID: 2jyn
TitleA novel solution NMR structure of protein yst0336 from Saccharomyces cerevisiae. Northeast Structural Genomics Consortium target YT51/Ontario Centre for Structural Proteomics target yst0336
ComponentsUPF0368 protein YPL225W
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / novel fold / yst0336 / YT51 / Ontario Centre for Structural Proteomics / OCSP / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Cytoplasm
Function / homology
Function and homology information


nascent polypeptide-associated complex binding / 'de novo' cotranslational protein folding / translation elongation factor binding / misfolded protein binding / protein folding chaperone / ribosome binding / cytoplasm
Similarity search - Function
yst0336 like fold / yst0336 like domain / Protein PBDC1, metazoa/fungi / PBDC1-like domain superfamily / PBDC1 protein / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein PBDC1 homolog
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsWu, B. / Yee, A. / Fares, C. / Lemak, A. / Gutmanas, A. / Semest, A. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG) / Ontario Centre for Structural Proteomics (OCSP)
CitationJournal: To be Published
Title: A novel solution NMR structure of protein yst0336 from Saccharomyces cerevisiae.
Authors: Wu, B. / Yee, A. / Fares, C. / Lemak, A. / Gutmanas, A. / Semest, A. / Arrowsmith, C.H.
History
DepositionDec 14, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0368 protein YPL225W


Theoretical massNumber of molelcules
Total (without water)17,4691
Polymers17,4691
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein UPF0368 protein YPL225W


Mass: 17468.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: YPL225W / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q08971

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HN(CO)CA
1513D HNCA
1613D C(CO)NH
1713D H(CCO)NH
1813D (H)CCH-TOCSY
1913D CCH-TOCSY
11013D HBHA(CO)NH
11113D 1H-15N NOESY
11213D 1H-13C NOESY
11323D 1H-13C NOESY
11413D 1H-13C NOESY aromatic
11532D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] protein yst0336, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 0.01 % sodium azide, 10 mM benzamidine, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C; U-100% 15N] protein yst0336, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 0.01 % sodium azide, 10 mM benzamidine, 99.9% D2O99.9% D2O
30.5 mM [U-100% 13C; U-100% 15N] protein yst0336, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 0.01 % sodium azide, 10 mM benzamidine, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMprotein yst0336[U-100% 13C; U-100% 15N]1
10 mMTRIS[U-100% 2H]1
300 mMsodium chloride1
0.01 %sodium azide1
10 mMbenzamidine1
0.5 mMprotein yst0336[U-100% 13C; U-100% 15N]2
10 mMTRIS[U-100% 2H]2
300 mMsodium chloride2
0.01 %sodium azide2
10 mMbenzamidine2
0.5 mMprotein yst0336[U-100% 13C; U-100% 15N]3
10 mMTRIS[U-100% 2H]3
300 mMsodium chloride3
0.01 %sodium azide3
10 mMbenzamidine3
Sample conditionsIonic strength: 300 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.95Goddarddata analysis
Sparky3.95Goddardpeak picking
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructureHuang, Tejero, Powers and Montelionenmr structure quality assessment
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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