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- PDB-2jrd: Influenza Hemagglutinin Fusion Domain Mutant F9A -

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Basic information

Entry
Database: PDB / ID: 2jrd
TitleInfluenza Hemagglutinin Fusion Domain Mutant F9A
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / influenza / hemagglutinin / fusion domain / F9A
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / host cell surface receptor binding / apical plasma membrane / 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 ...viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / host cell surface receptor binding / apical plasma membrane / 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 / virion membrane / 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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodSOLUTION NMR / simulated annealing
Model detailsInfluenza Hemagglutinin Fusion Domain Mutant F9A in DPC micelles, pH 5
AuthorsLai, A.L. / Tamm, L.K.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Locking the kink in the influenza hemagglutinin fusion domain structure.
Authors: Lai, A.L. / Tamm, L.K.
History
DepositionJun 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)2,7121
Polymers2,7121
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 35structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Hemagglutinin /


Mass: 2712.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Genus: Influenzavirus A / Gene: HA / References: UniProt: P11134, UniProt: A0A2Y1*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Influenza Hemagglutinin Fusion Domain Mutant F9A in DPC micelles, pH 5
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY

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Sample preparation

DetailsContents: 2 mM HA_FP_F9A peptide, 200 mM [U-2H] d38-DPC, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMHA_FP_F9A peptide1
200 mMd38-DPC[U-2H]1
Sample conditionspH: 5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
DYANAGuntert, Braun and Wuthrichstructure solution
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
SparkyGoddardchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 35 / Conformers submitted total number: 30

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