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- PDB-6xcr: NMR structure of Ost4 in DPC micelles -

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Basic information

Entry
Database: PDB / ID: 6xcr
TitleNMR structure of Ost4 in DPC micelles
ComponentsOligosaccharyltransferase
KeywordsMEMBRANE PROTEIN / TRANSFERASE
Function / homology
Function and homology information


oligosaccharyltransferase complex / protein N-linked glycosylation / transferase activity / protein-macromolecule adaptor activity / endoplasmic reticulum membrane / mitochondrion
Similarity search - Function
Oligosaccaryltransferase / Oligosaccharyltransferase subunit ost4p superfamily / Oligosaccaryltransferase
Similarity search - Domain/homology
Oligosaccharyltransferase / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsChaudhary, B.P.
CitationJournal: Glycobiology / Year: 2021
Title: NMR and MD simulations reveal the impact of the V23D mutation on the function of yeast oligosaccharyltransferase subunit Ost4.
Authors: Chaudhary, B.P. / Zoetewey, D.L. / McCullagh, M.J. / Mohanty, S.
History
DepositionJun 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 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: Oligosaccharyltransferase


Theoretical massNumber of molelcules
Total (without water)5,2151
Polymers5,2151
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Oligosaccharyltransferase / Ost4


Mass: 5215.042 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain YJM789) (yeast)
Strain: YJM789 / Gene: OST4, SCY_0690 / Production host: Escherichia coli (E. coli)
References: UniProt: A6ZXA2, UniProt: Q99380*PLUS, EC: 2.4.1.119

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic13D 1H-15N TOCSY
151isotropic33D 1H-15N NOESY
161isotropic13D 1H-15N NOESY
171isotropic43D (H)CCH-TOCSY

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Sample preparation

DetailsType: micelle
Contents: 400 uM [U-13C; U-15N] Yeast Oligosaccharyltransferase subunit Ost4, 100 mM DPC micelle, 90% H2O/10% D2O
Details: Added 100 mM DPC micelle to solubilize the protein / Label: 13C, 15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMYeast Oligosaccharyltransferase subunit Ost4[U-13C; U-15N]1
100 mMDPC micellenatural abundance1
Sample conditionsIonic strength: 400 mM / Label: Condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Varian INOVAVarianINOVA9002
Bruker AVANCEBrukerAVANCE7003
Bruker AVANCEBrukerAVANCE6004

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRFAM-SPARKYLee, W., Tonelli, M., and Markley, J. Lchemical shift assignment
NMRFAM-SPARKYLee, W., Tonelli, M., and Markley, J. Lpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / 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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