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- PDB-2kxa: The hemagglutinin fusion peptide (H1 subtype) at pH 7.4 -

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Basic information

Entry
Database: PDB / ID: 2kxa
TitleThe hemagglutinin fusion peptide (H1 subtype) at pH 7.4
ComponentsHaemagglutinin HA2 CHAIN PEPTIDE
KeywordsVIRAL PROTEIN / IMMUNE SYSTEM / fusion peptide / influenza
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
Model detailslowest energy, model 1
AuthorsLorieau, J.L. / Louis, J.M. / Bax, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: The complete influenza hemagglutinin fusion domain adopts a tight helical hairpin arrangement at the lipid:water interface.
Authors: Lorieau, J.L. / Louis, J.M. / Bax, A.
History
DepositionApr 29, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents ..._pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Haemagglutinin HA2 CHAIN PEPTIDE


Theoretical massNumber of molelcules
Total (without water)3,1521
Polymers3,1521
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 60structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Haemagglutinin HA2 CHAIN PEPTIDE


Mass: 3151.596 Da / Num. of mol.: 1
Fragment: RESIDUES 1 TO 23 OF HA2 SUBUNIT (UNP Residues 345-367)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/swine/Scotland/410440/94(H1N2) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9YTC2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1322D 1H-1H NOESY
1413D HNCO
1513D HNCA
1613D HN(CO)CA
1713D 1H-15N NOESY
2812D 1H-15N HSQC
2912D 1H-13C HSQC
21013D HN(CO)CA

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Sample preparation

Details
Solution-IDContentsSolvent system
17 % D2O-1, 25 mM [U-99% 2H] TRIS-2, 130-180 mM [U-99% 2H] DPC-3, 93% H2O/7% D2O93% H2O/7% D2O
225 mM [U-99% 2H] TRIS-4, 130-180 mM [U-99% 2H] DPC-5, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
7 %D2O-11
25 mMTRIS-2[U-99% 2H]1
mMDPC-3[U-99% 2H]130-1801
25 mMTRIS-4[U-99% 2H]2
mMDPC-5[U-99% 2H]130-1802
Sample conditionsIonic strength: 20mM Tris / pH: 7.4 / Pressure: ambient / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE7502
Bruker AvanceBrukerAVANCE6003
Bruker AvanceBrukerAVANCE5004

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddarddata analysis
Sparky3.113Goddardpeak picking
NMRPipe5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipe5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
NMRPipe5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDraw5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRDraw5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
ModelFree4.2Palmerdata analysis
PSVS1.4Bhattacharya and Montelionedata analysis
TALOS1.2009.0721.18Cornilescu, Delaglio and Baxdata analysis
X-PLOR NIH2.24Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.24Schwieters, Kuszewski, Tjandra and Clorestructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 449 / NOE intraresidue total count: 109 / NOE long range total count: 66 / NOE medium range total count: 144 / NOE sequential total count: 130 / Protein chi angle constraints total count: 4 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 18 / Protein psi angle constraints total count: 18
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 1 Å / Maximum torsion angle constraint violation: 0 ° / Maximum upper distance constraint violation: 1 Å
NMR ensemble rmsDistance rms dev: 0.031 Å

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