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- PDB-2lat: Solution structure of a Human minimembrane protein OST4 -

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Basic information

Entry
Database: PDB / ID: 2lat
TitleSolution structure of a Human minimembrane protein OST4
ComponentsDolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4
KeywordsMEMBRANE PROTEIN / oligosaccharyltransferase / integral membrane protein
Function / homologyOligosaccaryltransferase / Oligosaccharyltransferase subunit ost4p superfamily / Oligosaccaryltransferase / oligosaccharyltransferase complex / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / endoplasmic reticulum membrane / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsGayen, S. / Kang, C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: Solution structure of a human minimembrane protein Ost4, a subunit of the oligosaccharyltransferase complex.
Authors: Gayen, S. / Kang, C.
History
DepositionMar 21, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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 / _pdbx_nmr_spectrometer.model
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: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4


Theoretical massNumber of molelcules
Total (without water)4,1961
Polymers4,1961
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/peptide Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4


Mass: 4196.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P0C6T2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 2-3 mM protein, 44%CDCl3/44%Cd3OH/12%H2O / Solvent system: 44%CDCl3/44%Cd3OH/12%H2O
SampleUnits: mM / Component: protein-1 / Conc. range: 2-3
Sample conditionspH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: A total 100 structures were calculated, from which 20 of lowest CYANA target function were selected
NMR constraintsNOE constraints total: 338 / NOE intraresidue total count: 125 / NOE long range total count: 0 / NOE medium range total count: 102 / NOE sequential total count: 111 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 26 / Protein psi angle constraints total count: 0
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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