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- PDB-2lwa: Conformational ensemble for the G8A mutant of the influenza hemag... -

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Basic information

Entry
Database: PDB / ID: 2lwa
TitleConformational ensemble for the G8A mutant of the influenza hemagglutinin fusion peptide
ComponentsHEMAGGLUTININ FUSION PEPTIDE G8A MUTANT
KeywordsMEMBRANE PROTEIN / influenza virus / hemagglutinin / fusion peptide / G8A mutant
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 / virion 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
Biological speciesInfluenza A virus
MethodSOLUTION NMR / simulated annealing
AuthorsLorieau, J.L. / Louis, J.M. / Schwieters, C.D. / Bax, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: pH-triggered, activated-state conformations of the influenza hemagglutinin fusion peptide revealed by NMR.
Authors: Lorieau, J.L. / Louis, J.M. / Schwieters, C.D. / Bax, A.
History
DepositionJul 26, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Feb 20, 2013Group: Refinement description
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 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

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Assembly

Deposited unit
A: HEMAGGLUTININ FUSION PEPTIDE G8A MUTANT
B: HEMAGGLUTININ FUSION PEPTIDE G8A MUTANT
C: HEMAGGLUTININ FUSION PEPTIDE G8A MUTANT


Theoretical massNumber of molelcules
Total (without water)9,4973
Polymers9,4973
Non-polymers00
Water0
1
A: HEMAGGLUTININ FUSION PEPTIDE G8A MUTANT


Theoretical massNumber of molelcules
Total (without water)3,1661
Polymers3,1661
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HEMAGGLUTININ FUSION PEPTIDE G8A MUTANT


Theoretical massNumber of molelcules
Total (without water)3,1661
Polymers3,1661
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: HEMAGGLUTININ FUSION PEPTIDE G8A MUTANT


Theoretical massNumber of molelcules
Total (without water)3,1661
Polymers3,1661
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 480structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide HEMAGGLUTININ FUSION PEPTIDE G8A MUTANT


Mass: 3165.622 Da / Num. of mol.: 3 / Mutation: G8A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Hong Kong/1035/1998(H1N1) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q91IJ0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The 3-conformer ensemble for the G8A mutant of the hemagglutinin fusion peptide refined with chemical shift dihedral restraints, RDCs and NOEs.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-13C HSQC
1212D 1H-15N HSQC
1313D HNCA
1413D 1H-15N NOESY
1512D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.3-0.6 mM [U-100% 13C; U-100% 15N] Hemagglutinin Fusion Peptide G8A mutant, 25 mM TRIS, 130-160 mM [U-100% 2H] DPC, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMHemagglutinin Fusion Peptide G8A mutant-1[U-100% 13C; U-100% 15N]0.3-0.61
25 mMTRIS-21
mMDPC-3[U-100% 2H]130-1601
Sample conditionsIonic strength: 0 / pH: 7.3 / Pressure: ambient / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE5003
Bruker AvanceBrukerAVANCE7504

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe7.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.113Goddardchemical shift assignment
X-PLOR NIH2.31Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE ENTRY CONSISTS OF 20 SETS OF 3 MODELS, WHERE EACH INDIVIDUAL SET REPRESENTS THREE CONFORMERS THAT ARE IN FAST EXCHANGE WITH ONE ANOTHER, AND EACH SET OF THREE WHEN TAKEN TOGETHER AT ...Details: THE ENTRY CONSISTS OF 20 SETS OF 3 MODELS, WHERE EACH INDIVIDUAL SET REPRESENTS THREE CONFORMERS THAT ARE IN FAST EXCHANGE WITH ONE ANOTHER, AND EACH SET OF THREE WHEN TAKEN TOGETHER AT POPULATIONS OF 15% (CHAIN A), 42.5% (CHAIN B) AND 42.5% (CHAIN C) SATISFIES THE EXPERIMENTAL DATA.
NMR constraintsNOE constraints total: 316 / NOE intraresidue total count: 118 / NOE long range total count: 22 / NOE medium range total count: 92 / NOE sequential total count: 84 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 20 / Protein psi angle constraints total count: 20
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 480 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.35 Å / Maximum upper distance constraint violation: 0.35 Å
NMR ensemble rmsDistance rms dev error: 0.045 Å

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