6GOL | pdb_00006gol

Three dimensional structure of a novel influenza hemagglutinin tri-stalk protein

• PDB DOI: https://doi.org/10.2210/pdb6GOL/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/California/VRDL69/2009(H1N1))
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-06-01 Released: 2018-10-10 
• Deposition Author(s): Kirsteina, A., Kazaks, A., Tars, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.219 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Structure and applications of novel influenza HA tri-stalk protein for evaluation of HA stem-specific immunity.

Lu, I.N., Kirsteina, A., Farinelle, S., Willieme, S., Tars, K., Muller, C.P., Kazaks, A.

(2018) PLoS One 13: e0204776-e0204776

• PubMed: 30261065 
• DOI: https://doi.org/10.1371/journal.pone.0204776
• Primary Citation Related Structures: 
  6GOL


• PubMed Abstract: 
  

  Long alpha helix (LAH) from influenza virus hemagglutinin (HA) stem or stalk domain is one of the most conserved influenza virus antigens. Expression of N-terminally extended LAH in E. coli leads to assembly of α-h elical homotrimer which is structurally nearly identical to the corresponding region of post-fusion form of native HA. This novel tri-stalk protein was able to differentiate between group 1 and 2 influenza in ELISA with virus-infected mice sera. It was also successfully applied for enzyme-linked immunospot assay to estimate the number of HA stem-reactive antibody (Ab)-secreting cells in mice. An in-house indirect ELISA was developed using a HA tri-stalk protein as a coating antigen for evaluation of HA stem-specific Ab levels in human sera collected in Luxembourg from 211 persons with occupational exposure to swine before the pandemic H1N1/09 virus had spread to Western Europe. Our results show that 70% of these pre-pandemic sera are positive for HA stem-specific Abs. In addition, levels of HA stem-specific Abs have positive correlation with the corresponding IgG titers and neutralizing activities against pandemic H1N1/09 virus.

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Organizational Affiliation: 
• Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg.
Latvian Biomedical Research and Study Centre, Riga, Latvia.
Department of Molecular Biology, Faculty of Biology, Riga, Latvia.
Laboratoire National de Santé, Dudelange, Luxembourg.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 8.55 kDa 
• Atom Count: 594 
• Modeled Residue Count: 65 
• Deposited Residue Count: 72 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin tri-stalk	A	72	Influenza A virus (A/California/VRDL69/2009(H1N1))	Mutation(s): 0
UniProt
Find proteins for D3G5J5 (Influenza A virus) Explore D3G5J5  Go to UniProtKB:  D3G5J5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.219 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.8	α = 90
b = 41.8	β = 90
c = 90.12	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-10-10 
Deposition Author(s): Kirsteina, A., Kazaks, A., Tars, K.

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Funding Organization	Location	Grant Number
	Latvia	ERAF 1.1.1.1/16/A/054

Revision History  

• Version 1.0: 2018-10-10
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description