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- PDB-1emz: SOLUTION STRUCTURE OF FRAGMENT (350-370) OF THE TRANSMEMBRANE DOM... -

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Entry
Database: PDB / ID: 1emz
TitleSOLUTION STRUCTURE OF FRAGMENT (350-370) OF THE TRANSMEMBRANE DOMAIN OF HEPATITIS C ENVELOPE GLYCOPROTEIN E1
ComponentsENVELOPE GLYCOPROTEIN E1
KeywordsVIRAL PROTEIN / transmembrane domain / envelope protein E1 / hepatitis C virus
Function / homologyhost cell lipid droplet / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / lipid droplet / host cell endoplasmic reticulum membrane / viral envelope / virion membrane / Genome polyprotein
Function and homology information
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamic, energy minimization
AuthorsOp De Beeck, A. / Montserret, R. / Duvet, S. / Cocquerel, L. / Cacan, R. / Barberot, B. / Le Maire, M. / Penin, F. / Dubuisson, J.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: The transmembrane domains of hepatitis C virus envelope glycoproteins E1 and E2 play a major role in heterodimerization.
Authors: Op De Beeck, A. / Montserret, R. / Duvet, S. / Cocquerel, L. / Cacan, R. / Barberot, B. / Le Maire, M. / Penin, F. / Dubuisson, J.
History
DepositionMar 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 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: ENVELOPE GLYCOPROTEIN E1


Theoretical massNumber of molelcules
Total (without water)2,2381
Polymers2,2381
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)1 / 50back calculated data agree with experimental NOESY spectrum,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide ENVELOPE GLYCOPROTEIN E1


Mass: 2237.581 Da / Num. of mol.: 1 / Fragment: TRANSMEMBRANE DOMAIN (RESIDUES 350-370) / Source method: obtained synthetically
Details: This peptide was chemically synthesized. The sequence of this peptide is naturally found in hepatitis C virus.
References: UniProt: Q9Q3N3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
121TOCSY
1312D NOESY
NMR detailsText: sodium 2,2 dimethyl-2-silapentane-5-sulfonate (DSS) in the internal nmr reference

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Sample preparation

DetailsContents: 4 mM E1(350-370), 50% H2O, 50% D2 trifluoroethanol (v/v)
Solvent system: 50% H2O, 50% D2 trifluoroethanol (v/v)
Sample conditionspH: 5.7 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Varian Inc.collection
X-PLOR3.1Brunger A.T.structure solution
X-PLOR3.1Brunger A.T.refinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamic, energy minimization
Software ordinal: 1
Details: the structure is based on 337 Noe derived distance constraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 1

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