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- PDB-2rlj: NMR Structure of Ebola fusion peptide in SDS micelles at pH 7 -

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Basic information

Entry
Database: PDB / ID: 2rlj
TitleNMR Structure of Ebola fusion peptide in SDS micelles at pH 7
ComponentsEnvelope glycoprotein
KeywordsVIRAL PROTEIN / Fusion Peptide / SDS micelles / Ebola virus / Filovirus
Function / homology
Function and homology information


host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / suppression by virus of host tetherin activity / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane ...host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / suppression by virus of host tetherin activity / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / host cell plasma membrane / virion membrane / extracellular region / identical protein binding
Similarity search - Function
Envelope glycoprotein GP2-like, HR1-HR2 / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesZaire ebolavirus
MethodSOLUTION NMR / simulated annealing
AuthorsFreitas, M.S. / Gaspar, L.P. / Lorenzoni, M. / Almeida, F.C. / Tinoco, L.W. / Almeida, M.S. / Maia, L.F. / Degreve, L. / Valente, A.P. / Silva, J.L.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structure of the Ebola fusion peptide in a membrane-mimetic environment and the interaction with lipid rafts.
Authors: Freitas, M.S. / Gaspar, L.P. / Lorenzoni, M. / Almeida, F.C. / Tinoco, L.W. / Almeida, M.S. / Maia, L.F. / Degreve, L. / Valente, A.P. / Silva, J.L.
History
DepositionJul 5, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 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 1.3May 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: Envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)1,5751
Polymers1,5751
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 Envelope glycoprotein


Mass: 1574.820 Da / Num. of mol.: 1 / Fragment: Ebola fusion peptide
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus / Genus: Ebola-like viruses / Production host: Escherichia coli (E. coli) / References: UniProt: Q05320

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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: 400mM SDS, 10% D2O, 15mM potassium phosphate, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
400 mMSDS1
10 %D2O1
15 mMpotassium phosphate1
Sample conditionsIonic strength: 0.015 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
ProcheckNMRLaskowski and MacArthurdata analysis
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readrefinement
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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