Research / PDB depositions

Unité de Virologie Structurale

Protein Data Bank depositions


PDB
Crystal Structures Resolution (A) Year




  NON-VIRAL proteins    
 
   
  Eukariotyc cell-cell fusion    
4OJC Wild-type full-length trimeric ectodomain of C. elegans fusion protein EFF-1  2.93 2014
4OJD C-ter truncated trimeric ectodomain of C. elegans fusion protein EFF-1 G260A/D321E/D322E mutant  2.26 2014
4OJE C-ter truncated trimeric ectodomain of C. elegans fusion protein EFF-1  2.57  2014
       




  VIRAL proteins    
 
   
  Flaviviridae family:
   
       
  Pestiviruses
   
  Bovine viral diarrhea virus
   
4DVK Glycoprotein Erns from pestivirus BVDV-1 strain NCP-7 2.20 2012
4DVL Glycoprotein Erns from pestivirus BVDV-1 in complex with 2'-3'-cyclo-UMP 2.75 2012
4DVN Glycoprotein Erns from pestivirus BVDV-1 in complex with 2'-UMP 2.38 2012
4DW3 Glycoprotein Erns from pestivirus BVDV-1 in complex with 5'-CMP 2.35 2012
4DW4 Glycoprotein Erns from pestivirus BVDV-1 in complex with 5'-UMP 2.23 2012
4DW5 Glycoprotein Erns from pestivirus BVDV-1 in complex with a non-cleavable CpU dinucleotide 2.21 2012
4DW7 Active-site mutant (H32K) Erns from pestivirus BVDV-1 in complex with a CpU dinucleotide 3.07 2012
4DWA Active-site mutant (H32K) Erns from pestivirus BVDV-1 in complex with a CpUpC trinucleotide 3.01 2012
4DWC Glycoprotein Erns from the pestivirus BVDV-1 in complex with Zn ions 2.89 2012
       
  Flaviviruses
   
  Dengue virus    
3UZV Domain III of the envelope protein E from DENV 2 with the variable domains of Mab 4E11 2.10 2012
3UZQ Domain III of the envelope protein E from DENV 1 with the variable domains of Mab 4E11 1.60 2012
3UZE Domain III of the envelope protein E from DENV 3 with the variable domains of Mab 4E11 2.04 2012
3UYP Domain III of the envelope protein E from DENV 4 with the variable domains of Mab 4E11 2.00 2012
3UC0 Domain I of the envelope protein E from DENV 4 with Fab of the chimpanzee monoclonal Ab 5H2 2.71 2011
3UAJ Envelope glycoprotein ectodomain E from DENV 4 with Fab of the chimpanzee monoclonal Ab 5H2 3.23 2011
  Tick-Borne Encephalitis Virus    
1URZ Post-fusion form of the envelope glycoprotein E from Tick-Borne Encephalitis virus 2.70 2004
1SVB Pre-fusion form of the envelope glycoprotein E from Tick-Borne Encephalitis virus 1.90 1996
       
  Hepaciviruses    

Hepatitis C Virus    
4JZN Broadly neutralizing human anti-Hepatitis C virus glycoprotein E2 Fab fragment HC84-1 2.05 2013
4JZO Broadly neutralizing human anti-Hepatitis C virus (HCV) glycoprotein E2 Fab fragment HC84-27 2.22 2013
4JVP Broadly neutralizing anti-Hepatitis C virus (HCV) glycoprotein E2 alpaca nanobody D03 1.76 2013
3U6R Broadly neutralizing anti-Hepatitis C virus (HCV) glycoprotein E2 single chain FV fragment 1:7 2.67 2011
1GX5 Hepatitis C virus RNA polymerase in complex with ribonucleotides 1.70 2002
1CSJ RNA-dependent RNA polymerase of Hepatitis C virus 2.80 1999
       
 
   

Togaviridade family:    
       
  Alphaviruses    
  Chikungunya virus
   
3N40 Immature envelope glycoproteins p62-E1 of Chikungunya virus 2.17 2010
3N41 Mature envelope glycoproteins complex (spontaneous cleavage) of Chikungunya virus 3.01 2010
3N42 Mature envelope glycoproteins complex (furin cleavage) of Chikungunya virus 3.00 2010
3N43 Mature envelope glycoproteins complex (trypsin cleavage) of Chikungunya virus 2.58 2010
3N44 Mature envelope glycoproteins complex (trypsin cleavage; osmium soak) of Chikungunya virus 2.35 2010
2XFB Fit of the Chikungunya E2-E1 envelope glycoproteins into Sindbis virus cryo-EM map 9.00 2010
2XFC Fit of the Chikungunya E2-E1 envelope glycoproteins into Semliki Forest virus cryo-EM map 9.00 2010
  Semliki Forest virus    
2V33 Domain III of E1 fusion glycoprotein from Semliki Forest virus 1.55 2008
2ALA Semliki Forest virus envelope protein E1 in its monomeric conformation 3.00 2006
1I9W Pre-fusion form of the envelope glycoprotein E1 from Semliki Forest virus 3.00 2004
1RER Post-fusion form of the envelope glycoprotein E1 from Semliki Forest virus 3.20 2004
       
  Rubiviridae    
  Rubella virus    
4ADI Post-fusion form of the envelope fusion protein E1 from Rubella virus (Na+) 1.78 2013
4ADG Post-fusion form of the envelope fusion protein E1 from Rubella virus (Ca+, soak Gal3S)  2.18 2013
4ADJ Post-fusion form of the envelope fusion protein E1 from Rubella virus (Ca+ 1mM)  1.94 2013
4B3V Post-fusion form of the envelope fusion protein E1 from Rubella virus (Ca+, 20mM)  1.98 2013
       
 
   
  Retroviridae family:
   
       
  Human immunodeficiency virus (HIV-1)    
2XT1 HIV-1 capsid protein C-terminal domain (146-231) in complex with a camelid VHH 1.32 2011
2XV6 HIV-1 capsid protein C-terminal domain (146-220) in complex with a camelid VHH 1.90 2011
2XXC Camelid VHH raised against the HIV-1 capsid protein C-terminal domain 1.67 2011
2XXM HIV-1 capsid C-terminal domain in complex with a Camelid VHH and the CAI peptide 1.65 2011
3DPH HIV-1 capsid C-terminal domain mutant (L211S) 2.01 2008
3DS0 HIV-1 capsid C-terminal domain mutant (N183A) in complex with an inhibitor of particle assembly 1.60 2008
3DS1 HIV-1 capsid C-terminal domain mutant (E187A) in complex with an inhibitor of particle assembly 1.60 2008
3DS2 HIV-1 capsid C-terminal domain mutant (Y169A) 1.20 2008
3DS3 HIV-1 capsid C-terminal domain mutant (Y169A) in complex with an inhibitor of particle assembly 2.70 2008
3DS4 HIV-1 capsid C-terminal domain mutant (L211S) in complex with an Inhibitor of particle assembly 1.12 2008
3DS5 HIV-1 capsid C-terminal domain mutant (N183A) 2.40 2008
3DTJ HIV-1 capsid C-terminal domain mutant (E187A) 4.00 2008
2BUO HIV-1 capsid C-terminal domain in complex with an inhibitor of particle assembly 1.70 2005
  Endogenous retrovirus    
1Y4M Human endogenous retrovirus HERV-FRD envelope protein (syncitin-2) 1.60 2005
 
   
  Arenaviridae family (arenavirus):
   
  Lymphocytic Choriomeningitis virus    
3MKO Lymphocytic Choriomeningitis virus membrane fusion glycoprotein GP2 in post-fusion form
1.80 2011
 
   
  Herpesviridae family:    
  Pseudorabies virus
   
2XQY Pseudorabies core fragment of glycoprotein H in complex with Fab D6.3 2.05 2010
 
   
  Paramyxoviridae family:    
  Respiratory Syncitial Virus    
2WJ8 Respiratory Syncitial virus nucleocapsid-RNA decameric rings 3.29 2009
 
   
  Rhabdoviridae family:    
  Vesicular Stomatitis Virus    
2J6J Pre-fusion form of the Vesicular Stomatitis virus glycoprotein G ectodomain 3.00 2007
2CMZ VSV-Indiana glycoprotein in its acidic conformation 2.40 2006
 
   
  Coronaviridae family:
   
  Coronavirus    
1WYY Post-fusion hairpin conformation of the SARS Coronavirus spike glycoprotein 2.20 2005
 
   
  Other viruses
   
       
  Dicistroviridae family:
   
3NAP Triatoma virus (TrV) 2.50 2010
  Picornaviridae family:    
2VF1 Capsid of the Picobirnavirus 3.40 2005
  Birnaviridae family:
   
3IDE Aquabirnavirus (IPNV) subviral particle 3.35 2009
1WCD Birnavirus IBDV T1 virus-like particle 3.00 2005
1WCE Birnavirus IBDV T13 viral particle 7.00 2005
  Reoviridae family:
   
1QHD Major capsid protein VP6 of group A rotavirus 1.95 2001
 
   
  Non-viral structures    
       
4ACQ Alpha-2 macroglobulin
4.20 2012
2J6E Autoimmune complex between a human IGM rheumatoid factor and IGG1 Fc 3.00 2007