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- PDB-2lcy: NMR Structure of the Complete Internal Fusion Loop from Ebolaviru... -

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Basic information

Entry
Database: PDB / ID: 2lcy
TitleNMR Structure of the Complete Internal Fusion Loop from Ebolavirus GP2 at pH 5.5
ComponentsVirion spike glycoprotein
KeywordsVIRAL PROTEIN
Function / homologyFiloviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / extracellular region / membrane / GP1,2
Function and homology information
Biological speciesZaire ebolavirus
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsGregory, S.M. / Harada, E. / Liang, B. / Tamm, L.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structure and function of the complete internal fusion loop from Ebolavirus glycoprotein 2.
Authors: Gregory, S.M. / Harada, E. / Liang, B. / Delos, S.E. / White, J.M. / Tamm, L.K.
History
DepositionMay 12, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Virion spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)5,9481
Polymers5,9481
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20020 structures for lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Virion spike glycoprotein


Mass: 5947.692 Da / Num. of mol.: 1 / Fragment: sequence database residues 507-560
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus / Gene: GP / Production host: Escherichia coli (E. coli) / References: UniProt: A9QPL9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D HNCA
1513D HN(CO)CA
1613D HN(CA)CB
1713D HNCO
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11013D 1H-13C NOESY aliphatic
11113D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1 mM [U-13C; U-15N] Ebolavirus Fusion Loop pH 5.5, 90% H2O/10% D2O90% H2O/10% D2O
20.5-1 mM [U-15N] Ebolavirus Fusion Loop pH 5.5, 90% H2O/10% D2O90% H2O/10% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMEbolavirus Fusion Loop pH 5.5-1[U-13C; U-15N]0.5-11
mMEbolavirus Fusion Loop pH 5.5-2[U-15N]0.5-12
Sample conditionsIonic strength: 50 / pH: 5.5 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002
Varian NMRSVarianNMRS6003

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 structures for lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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