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- PDB-1xoo: NMR structure of G1S mutant of influenza hemagglutinin fusion pep... -

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Basic information

Entry
Database: PDB / ID: 1xoo
TitleNMR structure of G1S mutant of influenza hemagglutinin fusion peptide in DPC micelles at pH 5
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / helix-kink-helix
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / plasma membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLi, Y. / Han, X. / Lai, A.L. / Bushweller, J.H. / Cafiso, D.S. / Tamm, L.K.
CitationJournal: J.Virol. / Year: 2005
Title: Membrane structures of the hemifusion-inducing fusion peptide mutant G1S and the fusion-blocking mutant G1V of influenza virus hemagglutinin suggest a mechanism for pore opening in membrane fusion.
Authors: Li, Y. / Han, X. / Lai, A.L. / Bushweller, J.H. / Cafiso, D.S. / Tamm, L.K.
History
DepositionOct 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999sequence No suitable sequence database reference was available for this protein.

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)2,0841
Polymers2,0841
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 / 20structures with the lowest energy
RepresentativeModel #6closest to the average

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Components

#1: Protein/peptide Hemagglutinin /


Mass: 2084.310 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence is derived from influenza hemagglutinin HA2 subunit residues 1 to 20, except that the first residue G was replaced with S.
References: UniProt: Q6VMJ9*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D NOESY
1312D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 2 mM peptide in the presence of 200 mM d38-DPC in 0.05% NaN3, 5 mM DTT, 20 mM d4-acetic acid, pH 5
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 0.02 / pH: 5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Varian UNITYPLUSVarianUNITYPLUS6002

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntert, P.structure solution
OPAL2.6Luginbulh, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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