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(-) Description

Title :  CRYO-EM STRUCTURE OF HUMAN AICHI VIRUS
 
Authors :  L. Zhu, X. X. Wang, J. S. Ren, T. J. Tuthill, E. E. Fry, Z. H. Rao, D. I. Stuar
Date :  04 Jul 16  (Deposition) - 21 Sep 16  (Release) - 26 Apr 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  3.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (60x)
Keywords :  Picornavirus, Entry, Receptor Binding, Gastroenteritis, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Zhu, X. Wang, J. Ren, A. Kotecha, T. S. Walter, S. Yuan, T. Yamashita, T. J. Tuthill, E. E. Fry, Z. Rao, D. I. Stuart
Structure Of Human Aichi Virus And Implications For Recepto Binding
Nat Microbiol V. 1 16150 2016
PubMed-ID: 27595320  |  Reference-DOI: 10.1038/NMICROBIOL.2016.150

(-) Compounds

Molecule 1 - CAPSID PROTEIN VP1
    Chains: A
    Engineered: YES
    Expression System: CHLOROCEBUS AETHIOPS
    Expression System Taxid: 9534
    Organism Common: AICHI VIRUS (STRAIN A846/88)
    Organism Scientific: AICHI VIRUS (STRAIN HUMAN/A846/88/1989)
    Organism Taxid: 650132
 
Molecule 2 - CAPSID PROTEIN VP0
    Chains: B
    Engineered: YES
    Expression System: CHLOROCEBUS AETHIOPS
    Expression System Taxid: 9534
    Organism Common: AICHI VIRUS (STRAIN A846/88)
    Organism Scientific: AICHI VIRUS (STRAIN HUMAN/A846/88/1989)
    Organism Taxid: 650132
 
Molecule 3 - GENOME POLYPROTEIN
    Chains: C
    Engineered: YES
    Expression System: CHLOROCEBUS AETHIOPS
    Expression System Cell: GREEN MONKEY KIDNEY (VERO) CELLS
    Expression System Taxid: 9534
    Organism Common: AICHI VIRUS (STRAIN A846/88)
    Organism Scientific: AICHI VIRUS (STRAIN HUMAN/A846/88/1989)
    Organism Taxid: 650132

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (60x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5GKA)

(-) Sites  (0, 0)

(no "Site" information available for 5GKA)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GKA)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ala A:60 -Pro A:61
2Pro A:126 -Gly A:127
3Pro B:52 -Pro B:53
4Pro B:170 -Ser B:171
5Phe B:209 -Pro B:210
6Ser B:222 -Pro B:223

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GKA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GKA)

(-) Exons   (0, 0)

(no "Exon" information available for 5GKA)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................................hhhhhh...ee..........eeee.........hhhhhhh.....hhhhhhhhh.eee...eeeeeee......eeeeeee...........hhhhhhh...eeeee....................ee........................eeeeee.........eeeeeeeee....ee............................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gka A   1 TLTEDLDAPQDTGNIENGAADNSPQPRTTFDYTGNPLPPDTKLENFFSFYRLLPMGGSGAPSLSFPADEGTIIPLDPINWLKGADVSGIAAMLSCFTYIAADLRITLRFSNPNDNPATMLVAFAPPGATIPLKPTRQMLSNFYMAEVPVSAATSTMVSFSIPYTSPLSAIPTSYFGWEDWSGTNFGQLSSGSWGNLMLIPSLSVDSAIPFDFQLSCWVAFGNFKAWVPRPPPPLPPLPTPAANAERTVAVIKQ 253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   


Chain B from PDB  Type:PROTEIN  Length:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................................................................................eee......eee..................................ee....ee.................hhhhh....................eehhhhhhh....hhhhhh......eeeeeeeeee...........ee..ee..hhhhhh.....hhhhh...........eeeeee................eee.ee..............ee.eeeeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gka B   5 TNIYGNGNNVNTDVGANGWAPTVSTGLGDGPVSCTPPTPSPGDTEVPPPRKPFTFPAPPTKSGSRFSKWWEPAAAPSSTANPQPSLIALNPSATQSGNASILTGSTAPSLLAYPTATPVPLPNPDEPSQPGPSGDRTWLLDTVTWSQEFTRGWNIAGSNGMQWTGLESLIFPVSTDTNWTSTSSPTAYPLPFSFVRAYPDSSWAAMYNTHSMWNCGWRVQVTVNGSQFHAGALILYMVPEATTHAIQTARDNAGFVFPYVILNLYESNTATIEVPYISPTPNTSSGLHAPWTFYLQVLSPLNPPPSLPTSLSCSIYVTPVDSSFHGLRYLAPQ 371
                                    14        24        34        44        54        64        74    || 118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368   
                                                                                                     79|                                                                                                                                                                                                                                                                 
                                                                                                     114                                                                                                                                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............ee.............................hhhhhh..eeeeeeeee.......eee....hhhhhhh....hhhhhhheeeee..eeeeee.......eeeeeeeee........hhhhhh...eeeee.....eee...........ee..............eeeeeeeeeee.......eeeeeeeeee....eeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5gka C   2 HWKTRAVPGAGTFGSAVAGQELPLCGVRAYYPPNAYIPAQVRDWLEFAHRPGLMATVPWTMADEPAERLGIFPVSPSAIAGTGAPISYVISLFSQWRGELAAHLLFTGSAQHYGRLVVCYTPAAPQPPSTMQEAMRGTYTVWDVNAASTLEFTIPFISNSYWKTVDVNNPDALLSTTGYVSIWVQNPLVGPHTAPASALVQAFISAGESFNVRLMQNPALTS 223
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5GKA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GKA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GKA)

(-) Gene Ontology  (35, 35)

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  Ligands, Modified Residues, Ions
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  Sites
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  Cis Peptide Bonds
    Ala A:60 - Pro A:61   [ RasMol ]  
    Phe B:209 - Pro B:210   [ RasMol ]  
    Pro A:126 - Gly A:127   [ RasMol ]  
    Pro B:170 - Ser B:171   [ RasMol ]  
    Pro B:52 - Pro B:53   [ RasMol ]  
    Ser B:222 - Pro B:223   [ RasMol ]  
 
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        O91464_AIV | O91464: 5lvc 5lz3

(-) Related Entries Specified in the PDB File

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