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- PDB-2mb1: NMR Structure of the Complete Internal Fusion Loop mutant I544A f... -

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Basic information

Entry
Database: PDB / ID: 2mb1
TitleNMR Structure of the Complete Internal Fusion Loop mutant I544A from Ebolavirus GP2 at pH 5.5
ComponentsVirion spike glycoprotein
KeywordsVIRAL PROTEIN / Fusion Loop
Function / homologyFiloviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / membrane => GO:0016020 / viral envelope / extracellular region / Envelope glycoprotein
Function and homology information
Biological speciesZaire ebolavirus
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 8
AuthorsTamm, L.K. / Gregory, S.M.
CitationJournal: J.Virol. / Year: 2014
Title: Ebolavirus Entry Requires a Compact Hydrophobic Fist at the Tip of the Fusion Loop.
Authors: Gregory, S.M. / Larsson, P. / Nelson, E.A. / Kasson, P.M. / White, J.M. / Tamm, L.K.
History
DepositionJul 22, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Jun 4, 2014Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
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_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Virion spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)5,9061
Polymers5,9061
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Virion spike glycoprotein


Mass: 5905.612 Da / Num. of mol.: 1 / Fragment: UNP residues 507-560 / Mutation: I544A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus / Gene: GP / Production host: Escherichia coli (E. coli) / References: UniProt: L7QI57

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D 1H-15N NOESY
1613D 1H-13C NOESY
1713D C(CO)NH
1813D H(CCO)NH

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Sample preparation

DetailsContents: 30 mM potassium phosphate, 50 mM sodium chloride, 600 uM [U-99% 13C; U-99% 15N] I544A Ebov FL, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
30 mMpotassium phosphate-11
50 mMsodium chloride-21
600 uMI544A Ebov FL-3[U-99% 13C; U-99% 15N]1
Sample conditionspH: 5.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 306 / NOE intraresidue total count: 93 / NOE long range total count: 19 / NOE medium range total count: 60 / NOE sequential total count: 134 / Protein phi angle constraints total count: 32 / Protein psi angle constraints total count: 33
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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