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(-) Description

Title :  CRYO-EM STRUCTURE FOR HEPATITIS A VIRUS COMPLEXED WITH FAB
 
Authors :  X. Wang, L. Zhu, M. Dang, Z. Hu, Q. Gao, S. Yuan, Y. Sun, B. Zhang, J. Ren, T. J. Wang, E. E. Fry, D. I. Stuart, Z. Rao
Date :  12 Dec 16  (Deposition) - 25 Jan 17  (Release) - 08 Feb 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  4.20
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B,C,D,E  (60x)
Keywords :  Hav, Neutralizing Mechanism, Receptor Recognition, Viral Entry, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Wang, L. Zhu, M. Dang, Z. Hu, Q. Gao, S. Yuan, Y. Sun, B. Zhang, J. Ren, A. Kotecha, T. S. Walter, J. Wang, E. E. Fry, D. I. Stuart, Z. Rao
Potent Neutralization Of Hepatitis A Virus Reveals A Receptor Mimic Mechanism And The Receptor Recognition Site
Proc. Natl. Acad. Sci. V. 114 770 2017 U. S. A.
PubMed-ID: 28074040  |  Reference-DOI: 10.1073/PNAS.1616502114

(-) Compounds

Molecule 1 - POLYPROTEIN
    Chains: A
    Fragment: UNP RESIDUES 20-289
    Organ: HOMO SAPIENS
    Organism Scientific: HEPATOVIRUS A
    Organism Taxid: 12092
 
Molecule 2 - VP2
    Chains: B
    Organ: HOMO SAPIENS
    Organism Scientific: HEPATITIS A VIRUS
    Organism Taxid: 12092
 
Molecule 3 - VP3
    Chains: C
    Organ: HOMO SAPIENS
    Organism Scientific: HEPATITIS A VIRUS
    Organism Taxid: 12092
 
Molecule 4 - FAB LIGHT CHAIN
    Chains: D
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 5 - FAB HEAVY CHAIN
    Chains: E
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (60x): ABCDE

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5WTH)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1D:23 -D:87
2D:132 -D:192
3E:22 -E:96
4E:148 -E:203

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:119 -Pro A:120
2Asn C:92 -Pro C:93
3Tyr D:138 -Pro D:139
4Trp E:196 -Pro E:197

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5WTH)

(-) 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:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................................hhhhh....hhhhhhh....................hhhhhhhh.eeee.........eeeeeee...........hhhhhhhhh.eeeee..eeeeeeee.....eeeeeee..........eee....hhhhhhh..eeeee.....eeeeee...............hhhhh..eeeeeeeeee.........eeeeeee.....eeeee....hhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wth A   3 DDSGGFSTTVSTEQNVPDPQVGITTMRMDVSGVQAPVGAITTIEDPVLAKKVPETFPELKPGESRHTSDHMSIYKFMGRSHFLCTFTFNSNNKEYTFPITLSSTSNPPHGLPSTLRWFFNLFQLYRGPLDLTIIITGATDVDGMAWFTPVGLAVDTPWVEKESALQIDYKTALGAVRFNTRRTGNIQIRLPWYSYLYAVSGALDGLGDKTDSTFGLVSIQIANYNHSDEYLSFSCYLSVTEQSEFYFPRAPLNSNAMLST 272
                                    12        22      ||42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272
                                                     29|                                                                                                                                                                                                                                        
                                                      40                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeee....eeee..................................eeeee.............eeeehhhhhh.....hhhhhhheeeeeeeeeeeeee......eeeeeeeeee......hhhhhhhh.eeeee.....eeeeee........ee........eeeeeeeeeeee..........eeeeeeeeeeeeeee.hhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wth B   5 EQMIQSVDRTAVTGASYFTSVDQSSVHTAEVGSHQIEPLKTSVDKPGSKKTQGEKFFLIHSARWLTTHALFHEVAKLDVVKLLYNEQFAVQGLLRYHTYARFGIEIQVQINPTPFQQGGLICAMVPGDQSYGSIASLTVYPHGLLNCNINNVVRIKVPFIYTRGAYHFKDPQYPVWELTIRVWSELNIGTGTSAYTSLNVLARFTDLELHGLTPLST 221
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       


Chain C from PDB  Type:PROTEIN  Length:246
                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhh.....hhhhh................hhhhhhh.eeeeee..........eeeeee..................hhhhhhhh.eeeeeeeeeeeeee........eeeeeeee...........hhhhhh..eeeee......eeeeee........ee................eeeeeee...............eeeeeeeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5wth C   1 MMRNETRVSTTENVVNLSNYEDARAKMSFALDQEDWKSDPSQGGGIKITHFTTWTSIPTLAAQFPFNASDSVGQQIKVIPVDPYFFQMTNTNPDQKCITALASICQMFCFWRGDLVFDFQVFPTKYHSGRLLFCFVPGNELIDVTGITLKQATTAPCAVMDIAGVQSTLRFRVPWISDTPYRVNRYTKEAHQKGEYTAIGKLIVYCYNRLTSPSNVAHHVRVNVYLSAINLECFAPLYHAMDVTTQ 246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      


Chain D from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeee.....eeeeeee.......eeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeee.....ee....eeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.........eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wth D   1 DIVLTQSPAIMSASPGEKVTMTCSASSSVSYIHWYQQKSGTSPKRWIYDTSRLAFGVPGRFSGSGSGTSYSLTISSMEAEDAATYYCQQWSSNYTFGGGTNLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  


Chain E from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeee...eeeeeeee......ee........eeeeee....eeeeee...hhhhheeeeeeeeee....eeeeee...eeeee........eeeee......eee.eeeeeee.....eeee.hhhhhh.eeeeeeeee..eeeeeeeeeee.........eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wth E   1 EVKLVESGGGSVKPGGSLKLSCAASGFSFSTYGMSWVRQTPEKRLEWVATISGGGGYTYYPDSVKGRFTISRDNARNILYLQMSSLRSGDTAMYYCARRVTTVAEYYFDYWGQGTTLTVSSPKTTPPSVYPLAPAAASMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    || 144       154       164       174       184       194       204       214       
                                                                                                                                                                135|                                                                                 
                                                                                                                                                                 140
   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 5WTH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (43, 43)

Asymmetric Unit(hide GO term definitions)

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  Sites
(no "Sites" information available for 5wth)
 
  Cis Peptide Bonds
    Asn C:92 - Pro C:93   [ RasMol ]  
    Pro A:119 - Pro A:120   [ RasMol ]  
    Trp E:196 - Pro E:197   [ RasMol ]  
    Tyr D:138 - Pro D:139   [ RasMol ]  
 
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  5wth
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  POLG_HAVHM | P08617
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 Related Entries

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

UniProtKB/Swiss-Prot
        POLG_HAVHM | P08617: 1hav 1qa7 2h6m 2h9h 2hal 4wzn 5wte 5wtf

(-) Related Entries Specified in the PDB File

5wte
5wtf RELATED ID: EMD-6687 RELATED DB: EMDB RELATED ID: EMD-6686 RELATED DB: EMDB