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- PDB-5t42: Structure of the Ebola virus envelope protein MPER/TM domain and ... -

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Basic information

Entry
Database: PDB / ID: 5t42
TitleStructure of the Ebola virus envelope protein MPER/TM domain and its interaction with the fusion loop explains their fusion activity
ComponentsEnvelope glycoprotein
KeywordsVIRAL PROTEIN / Ebola virus / membrane protein / protein-protein interaction / membrane fusion
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell plasma membrane / virion membrane ...clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell plasma membrane / virion membrane / extracellular region / membrane
Similarity search - Function
Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesZaire ebolavirus
MethodSOLUTION NMR / simulated annealing
AuthorsLee, J. / Nyenhuis, D.A. / Nelson, E.A. / Cafiso, D.S. / White, J.M. / Tamm, L.K.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI030557 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI114776 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01 GM072693 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structure of the Ebola virus envelope protein MPER/TM domain and its interaction with the fusion loop explains their fusion activity.
Authors: Lee, J. / Nyenhuis, D.A. / Nelson, E.A. / Cafiso, D.S. / White, J.M. / Tamm, L.K.
History
DepositionAug 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 18, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 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
Revision 1.5May 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

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)5,1351
Polymers5,1351
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Envelope glycoprotein / GP1 / 2 / GP


Mass: 5134.819 Da / Num. of mol.: 1 / Fragment: UNP residues 632-676
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus (strain Kikwit-95) / Strain: Kikwit-95 / Gene: GP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P87666

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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
122isotropic13D HNCA
132isotropic13D HNCO
142isotropic13D HN(CO)CA
152isotropic13D HN(CA)CO
192isotropic13D CBCANH
182isotropic13D 1H-15N NOESY
172isotropic23D 1H-13C NOESY
162isotropic13D 1H-13C NOESY aromatic
1122isotropic13D (H)CCH-TOCSY
1112isotropic1(H)CC(CO)NH

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
micelle1500 uM [U-99% 15N] EBOV_MPER/TM, 90% H2O/10% D2OEBOV_DPC90% H2O/10% D2O
micelle2500 uM [U-99% 13C; U-99% 15N] EBOV_MPER/TM, 90% H2O/10% D2O13C_15N_EBOV_DPC90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMEBOV_MPER/TM[U-99% 15N]1
500 uMEBOV_MPER/TM[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 125 mM / Label: CONDITION 1 / pH: 5.5 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
TALOSCornilescu, Delaglio and Baxchemical shift calculation
ProcheckNMRLaskowski and MacArthurdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxgeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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