spacer
spacer

PDBsum entry 3lzf
Go to PDB code: 
protein ligands Protein-protein interface(s) links
Viral protein/immune system PDB id
3lzf

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
323 a.a. *
173 a.a. *
216 a.a. *
212 a.a. *
Ligands
NAG-NAG ×2
NAG-NAG-BMA-MAN
NAG
* Residue conservation analysis
PDB id:
3lzf
Name: Viral protein/immune system
Title: Crystal structure of fab 2d1 in complex with the 1918 influenza virus hemagglutinin
Structure: Hemagglutinin, ha1 subunit. Chain: a. Fragment: ectodomain ha1, residues 18-344. Synonym: hemagglutinin ha1 chain, hemagglutinin ha2 chain. Engineered: yes. Hemagglutinin, ha2 subunit. Chain: b. Fragment: ectodomain ha2, residues 345-520. Synonym: hemagglutinin ha1 chain, hemagglutinin ha2 chain.
Source: Influenza a virus. Organism_taxid: 59375. Strain: a/south carolina/1/1918(h1n1). Gene: ha, hemagglutinin. Expressed in: trichoplusia ni. Expression_system_taxid: 7111. Nucleopolyhedrovirus. Homo sapiens. Organism_taxid: 9606.
Resolution:
2.80Å     R-factor:   0.232     R-free:   0.259
Authors: D.C.Ekiert,I.A.Wilson
Key ref: R.Xu et al. (2010). Structural basis of preexisting immunity to the 2009 H1N1 pandemic influenza virus. Science, 328, 357-360. PubMed id: 20339031
Date:
01-Mar-10     Release date:   07-Apr-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9WFX3  (HEMA_I18A0) -  Hemagglutinin from Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)
Seq:
Struc: 		 
Seq:
Struc: 		566 a.a.
323 a.a.
Protein chain
Pfam   ArchSchema ?
Q9WFX3  (HEMA_I18A0) -  Hemagglutinin from Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)
Seq:
Struc: 		 
Seq:
Struc: 		566 a.a.
173 a.a.
Protein chain
No UniProt id for this chain
Struc: 216 a.a.
Protein chain
No UniProt id for this chain
Struc: 212 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
Science 328:357-360 (2010)
PubMed id: 20339031  
 
 
Structural basis of preexisting immunity to the 2009 H1N1 pandemic influenza virus.
R.Xu, D.C.Ekiert, J.C.Krause, R.Hai, J.E.Crowe, I.A.Wilson.
 
  ABSTRACT  
 
The 2009 H1N1 swine flu is the first influenza pandemic in decades. The crystal structure of the hemagglutinin from the A/California/04/2009 H1N1 virus shows that its antigenic structure, particularly within the Sa antigenic site, is extremely similar to those of human H1N1 viruses circulating early in the 20th century. The cocrystal structure of the 1918 hemagglutinin with 2D1, an antibody from a survivor of the 1918 Spanish flu that neutralizes both 1918 and 2009 H1N1 viruses, reveals an epitope that is conserved in both pandemic viruses. Thus, antigenic similarity between the 2009 and 1918-like viruses provides an explanation for the age-related immunity to the current influenza pandemic.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22982990 D.C.Ekiert, A.K.Kashyap, J.Steel, A.Rubrum, G.Bhabha, R.Khayat, J.H.Lee, M.A.Dillon, R.E.O'Neil, A.M.Faynboym, M.Horowitz, L.Horowitz, A.B.Ward, P.Palese, R.Webby, R.A.Lerner, R.R.Bhatt, and I.A.Wilson (2012).
Cross-neutralization of influenza A viruses mediated by a single antibody loop.
  Nature, 489, 526-532.
PDB codes: 4fnk 4fnl 4fp8 4fqr
23007571 P.C.Wilson, and S.F.Andrews (2012).
Tools to therapeutically harness the human antibody response.
  Nat Rev Immunol, 12, 709-719.  
21407805 A.Jayaraman, C.Pappas, R.Raman, J.A.Belser, K.Viswanathan, Z.Shriver, T.M.Tumpey, and R.Sasisekharan (2011).
A single base-pair change in 2009 H1N1 hemagglutinin increases human receptor affinity and leads to efficient airborne viral transmission in ferrets.
  PLoS One, 6, e17616.  
21206092 D.M.Tscherne, and A.García-Sastre (2011).
Virulence determinants of pandemic influenza viruses.
  J Clin Invest, 121, 6.  
21390107 G.J.Nabel, C.J.Wei, and J.E.Ledgerwood (2011).
Vaccinate for the next H2N2 pandemic now.
  Nature, 471, 157-158.  
  21477134 G.Neumann, and Y.Kawaoka (2011).
The first influenza pandemic of the new millennium.
  Influenza Other Respi Viruses, 5, 157-166.  
21211019 J.Abdussamad, and S.Aris-Brosou (2011).
The nonadaptive nature of the H1N1 2009 Swine Flu pandemic contrasts with the adaptive facilitation of transmission to a new host.
  BMC Evol Biol, 11, 6.  
  21304166 J.C.Krause, D.C.Ekiert, T.M.Tumpey, P.B.Smith, I.A.Wilson, and J.E.Crowe (2011).
An insertion mutation that distorts antibody binding site architecture enhances function of a human antibody.
  MBio, 2, 0.
PDB codes: 3qhf 3qhz
  21477139 J.D.Easterbrook, J.C.Kash, Z.M.Sheng, L.Qi, J.Gao, E.D.Kilbourne, M.C.Eichelberger, and J.K.Taubenberger (2011).
Immunization with 1976 swine H1N1- or 2009 pandemic H1N1-inactivated vaccines protects mice from a lethal 1918 influenza infection.
  Influenza Other Respi Viruses, 5, 198-205.  
21138535 J.McVernon, K.Laurie, I.Barr, A.Kelso, M.Skeljo, and T.Nolan (2011).
Absence of cross-reactive antibodies to influenza A (H1N1) 2009 before and after vaccination with 2009 Southern Hemisphere seasonal trivalent influenza vaccine in children aged 6 months-9 years: a prospective study.
  Influenza Other Respi Viruses, 5, 7.  
21220454 J.Wrammert, D.Koutsonanos, G.M.Li, S.Edupuganti, J.Sui, M.Morrissey, M.McCausland, I.Skountzou, M.Hornig, W.I.Lipkin, A.Mehta, B.Razavi, C.Del Rio, N.Y.Zheng, J.H.Lee, M.Huang, Z.Ali, K.Kaur, S.Andrews, R.R.Amara, Y.Wang, S.R.Das, C.D.O'Donnell, J.W.Yewdell, K.Subbarao, W.A.Marasco, M.J.Mulligan, R.Compans, R.Ahmed, and P.C.Wilson (2011).
Broadly cross-reactive antibodies dominate the human B cell response against 2009 pandemic H1N1 influenza virus infection.
  J Exp Med, 208, 181-193.  
21353280 K.C.Bradley, C.A.Jones, S.M.Tompkins, R.A.Tripp, R.J.Russell, M.R.Gramer, J.Heimburg-Molinaro, D.F.Smith, R.D.Cummings, and D.A.Steinhauer (2011).
Comparison of the receptor binding properties of contemporary swine isolates and early human pandemic H1N1 isolates (Novel 2009 H1N1).
  Virology, 413, 169-182.  
21333316 L.M.Chen, P.Rivailler, J.Hossain, P.Carney, A.Balish, I.Perry, C.T.Davis, R.Garten, B.Shu, X.Xu, A.Klimov, J.C.Paulson, N.J.Cox, S.Swenson, J.Stevens, A.Vincent, M.Gramer, and R.O.Donis (2011).
Receptor specificity of subtype H1 influenza A viruses isolated from swine and humans in the United States.
  Virology, 412, 401-410.  
20931251 N.Goñi, G.Moratorio, V.Ramas, L.Coppola, H.Chiparelli, and J.Cristina (2011).
Phylogenetic analysis of pandemic 2009 influenza A virus circulating in the South American region: genetic relationships and vaccine strain match.
  Arch Virol, 156, 87-94.  
21198671 P.R.Dormitzer, G.Galli, F.Castellino, H.Golding, S.Khurana, G.Del Giudice, and R.Rappuoli (2011).
Influenza vaccine immunology.
  Immunol Rev, 239, 167-177.  
21747392 R.A.Medina, and A.García-Sastre (2011).
Influenza A viruses: new research developments.
  Nat Rev Microbiol, 9, 590-603.  
21346794 R.Moss, J.M.McCaw, and J.McVernon (2011).
Diagnosis and antiviral intervention strategies for mitigating an influenza epidemic.
  PLoS One, 6, e14505.  
21295153 S.A.Valkenburg, J.A.Rutigliano, A.H.Ellebedy, P.C.Doherty, P.G.Thomas, and K.Kedzierska (2011).
Immunity to seasonal and pandemic influenza A viruses.
  Microbes Infect, 13, 489-501.  
  21464843 S.Cherian, P.Hil, and A.C.Mishra (2011).
Antigen-Antibody docking reveals the molecular basis for cross-reactivity of the 1918 and 2009 Influenza A/H1N1 pandemic viruses.
  Bioinformation, 6, 35-38.  
21437206 W.Xu, L.Han, and Z.Lin (2011).
Screening of random peptide library of hemagglutinin from pandemic 2009 A(H1N1) influenza virus reveals unexpected antigenically important regions.
  PLoS One, 6, e18016.  
20484500 A.C.Boon, J.deBeauchamp, S.Krauss, A.Rubrum, A.D.Webb, R.G.Webster, J.McElhaney, and R.J.Webby (2010).
Cross-reactive neutralizing antibodies directed against pandemic H1N1 2009 virus are protective in a highly sensitive DBA/2 mouse influenza model.
  J Virol, 84, 7662-7667.  
20519459 A.D.Higgins, C.J.Shaw, J.G.Johnson, A.Navarro, N.A.Chapman, S.D.Ewers, J.W.Stockwell, J.M.Carpenter, P.D.Olivo, and L.Y.Miao (2010).
Monoclonal antibody kit for identification of the novel 2009 H1N1 influenza A virus.
  J Clin Microbiol, 48, 2677-2682.  
20964814 F.Carrat, C.Pelat, D.Levy-Bruhl, I.Bonmarin, and N.Lapidus (2010).
Planning for the next influenza H1N1 season: a modelling study.
  BMC Infect Dis, 10, 301.  
20661476 J.M.Aguilar-Yáñez, R.Portillo-Lara, G.I.Mendoza-Ochoa, S.A.García-Echauri, F.López-Pacheco, D.Bulnes-Abundis, J.Salgado-Gallegos, I.M.Lara-Mayorga, Y.Webb-Vargas, F.O.León-Angel, R.E.Rivero-Aranda, Y.Oropeza-Almazán, G.M.Ruiz-Palacios, M.I.Zertuche-Guerra, R.M.DuBois, S.W.White, S.Schultz-Cherry, C.J.Russell, and M.M.Alvarez (2010).
An influenza A/H1N1/2009 hemagglutinin vaccine produced in Escherichia coli.
  PLoS One, 5, e11694.  
20976194 J.Ye, E.M.Sorrell, Y.Cai, H.Shao, K.Xu, L.Pena, D.Hickman, H.Song, M.Angel, R.A.Medina, B.Manicassamy, A.Garcia-Sastre, and D.R.Perez (2010).
Variations in the hemagglutinin of the 2009 H1N1 pandemic virus: potential for strains with altered virulence phenotype?
  PLoS Pathog, 6, e1001145.  
20502705 M.C.Johns, A.A.Eick, D.L.Blazes, S.E.Lee, C.L.Perdue, R.Lipnick, K.G.Vest, K.L.Russell, R.F.DeFraites, and J.L.Sanchez (2010).
Seasonal influenza vaccine and protection against pandemic (H1N1) 2009-associated illness among US military personnel.
  PLoS One, 5, e10722.  
20863352 M.Roriz-Cruz, I.Rosset, and M.Montero-Odasso (2010).
Lower mortality from H1N1 influenza in older Argentineans: men more affected.
  J Am Geriatr Soc, 58, 1813-1815.  
20812310 P.D.Griffiths (2010).
Back to the future with influenza.
  Rev Med Virol, 20, 263-264.  
20852645 Q.Li, J.Qi, W.Zhang, C.J.Vavricka, Y.Shi, J.Wei, E.Feng, J.Shen, J.Chen, D.Liu, J.He, J.Yan, H.Liu, H.Jiang, M.Teng, X.Li, and G.F.Gao (2010).
The 2009 pandemic H1N1 neuraminidase N1 lacks the 150-cavity in its active site.
  Nat Struct Mol Biol, 17, 1266-1268.
PDB code: 3nss
  20975689 R.A.Medina, B.Manicassamy, S.Stertz, C.W.Seibert, R.Hai, R.B.Belshe, S.E.Frey, C.F.Basler, P.Palese, and A.García-Sastre (2010).
Pandemic 2009 H1N1 vaccine protects against 1918 Spanish influenza virus.
  Nat Commun, 1, 1-6.  
  21040570 R.T.Lee, C.L.Santos, T.M.de Paiva, L.Cui, F.L.Sirota, F.Eisenhaber, and S.Maurer-Stroh (2010).
All that glitters is not gold--founder effects complicate associations of flu mutations to disease severity.
  Virol J, 7, 297.  
20616031 S.Gras, L.Kedzierski, S.A.Valkenburg, K.Laurie, Y.C.Liu, J.T.Denholm, M.J.Richards, G.F.Rimmelzwaan, A.Kelso, P.C.Doherty, S.J.Turner, J.Rossjohn, and K.Kedzierska (2010).
Cross-reactive CD8+ T-cell immunity between the pandemic H1N1-2009 and H1N1-1918 influenza A viruses.
  Proc Natl Acad Sci U S A, 107, 12599-12604.
PDB codes: 3lkn 3lko 3lkp 3lkq 3lkr 3lks
20937163 S.J.Turner, P.C.Doherty, and A.Kelso (2010).
Q&A: H1N1 pandemic influenza--what's new?
  BMC Biol, 8, 130.  
  20535229 S.Maurer-Stroh, R.T.Lee, F.Eisenhaber, L.Cui, S.P.Phuah, and R.T.Lin (2010).
A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus.
  PLoS Curr, 2, RRN1162.  
  20930526 S.Maurer-Stroh, S.S.Paing, R.T.Lee, and F.Eisenhaber (2010).
Sporadic human cases of swine-origin influenza before 2009 share the Sa epitope.
  Cell Cycle, 9, 3826-3828.  
20649513 T.Merry, and S.Astrautsova (2010).
Alternative approaches to antiviral treatments: focusing on glycosylation as a target for antiviral therapy.
  Biotechnol Appl Biochem, 56, 103-109.  
20809098 X.Ding, L.Jiang, C.Ke, Z.Yang, C.Lei, K.Cao, J.Xu, L.Xu, X.Yang, Y.Zhang, P.Huang, W.Huang, X.Zhu, Z.He, L.Liu, J.Li, J.Yuan, J.Wu, X.Tang, and M.Li (2010).
Amino acid sequence analysis and identification of mutations under positive selection in hemagglutinin of 2009 influenza A (H1N1) isolates.
  Virus Genes, 41, 329-340.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

spacer
spacer