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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE HEV CAPSID PROTEIN, PORF2
 
Authors :  N. Miyazaki, L. Xing, C. -Y. Wang, T. -C. Li, N. Takeda, A. Higashiura, A. Nakagawa, T. Tsukihara, T. Miyamura, R. H. Cheng
Date :  23 Feb 09  (Deposition) - 09 Mar 10  (Release) - 09 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.81
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (60x)
Keywords :  Virus, Viral Capsid Protein, Virus-Like Particle, Hepatitis E Virus, Hev, Cytoplasm, Host-Virus Interaction, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Miyazaki, L. Xing, C. -Y. Wang, T. -C. Li, N. Takeda, A. Higashiura, A. Nakagawa, T. Tsukihara, T. Miyamura, R. H. Cheng
Role Of Protein Domain-Modularity In Designating Capsid Assembly And Antigenicity
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROTEIN ORF3, CAPSID PROTEIN
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: BTL-TN 5B1-4 (TN5)
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 61-114 OF PROTEIN ORF3, UNP RESIDUES 112-608 OF CAPSID PROTEIN
    Gene: ORF3, ORF2
    Organism Common: HEV-1
    Organism Scientific: HEPATITIS E VIRUS
    Organism Taxid: 31769
    Other Details: FUSION PROTEIN COMPRISES N-TERMINAL INITIATING METHIONINE, RESIDUES 58-111 OF STRUCTURAL PROTEIN 1 (PORF3), AND RESIDUES 112-608 OF STRUCTURAL PROTEIN 2 (CAPSID PROTEIN, PORF2)
    Strain: GENOTYPE 1 (ISOLATE HUMAN/BURMA)
    Synonym: PORF3, PORF2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (60x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2ZZQ)

(-) Sites  (0, 0)

(no "Site" information available for 2ZZQ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZZQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZZQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZZQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZZQ)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZZQ)

(-) 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:483
 aligned with CAPSD_HEVBU | P29326 from UniProtKB/Swiss-Prot  Length:660

    Alignment length:489
                                   127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597         
          CAPSD_HEVBU   118 DTPPVPDVDSRGAILRRQYNLSTSPLTSSVATGTNLVLYAAPLSPLLPLQDGTNTHIMATEASNYAQYRVARATIRYRPLVPNAVGGYAISISFWPQTTTTPTSVDMNSITSTDVRILVQPGIASELVIPSERLHYRNQGWRSVETSGVAEEEATSGLVMLCIHGSLVNSYTNTPYTGALGLLDFALELEFRNLTPGNTNTRVSRYSSTARHRLRRGADGTAELTTTAATRFMKDLYFTSTNGVGEIGRGIALTLFNLADTLLGGLPTELISSAGGQLFYSRPVVSANGEPTVKLYTSVENAQQDKGIAIPHDIDLGESRVVIQDYDNQHEQDRPTPSPAPSRPFSVLRANDVLWLSLTAAEYDQSTYGSSTGPVYVSDSVTLVNVATGAQAVARSLDWTKVTLDGRPLSTIQQYSKTFFVLPLRGKLSFWEAGTTKAGYPYNYNTTASDQLLVENAAGHRVAISTYTTSLGAGPVSISAVAVLAPHSA 606
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains SP2-2zzqA01 A:118-606                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Pfam domains
         Sec.struct. author ..............eeeeeeeeeeee........eeeeeeee..........ee.hhhhhhhh...eeeeeeeeeeeee.....ee...eeeeee..........hhhhhhh...eeee.....eeeeehhhhhhhhhh.eee......hhhhhh..eeeeeee...ee...........eeeeeeeeeee...........eeeeeeeeeeeeee.....eeee..hhhhhh.hhhhh............eeeeeeehhhhhh..hhhhhhh....eeeeeee.......eeeee.hhhhhhh.........eeeeeeeeeeee...........................eeeeee.................eee..eeeee............hhhhh.......eeee....eeeee...............------........eeee......eee.............eeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zzq A 118 DTPPVPDVDSRGAILRRQYNLSTSPLTSSVATGTNLVLYAAPLSPLLPLQDGTNTHIMATEASNYAQYRVARATIRYRPLVPNAVGGYAISISFWPQTTTTPTSVDMNSITSTDVRILVQPGIASELVIPSERLHYRNQGWRSVETSGVAEEEATSGLVMLCIHGSPVNSYTNTPYTGALGLLDFALELEFRNLTPGNTNTRVSRYSSTARHRLRRGADGTAELTTTAATRFMKDLYFTSTNGVGEIGRGIALTLFNLADTLLGGLPTELISSAGGQLFYSRPVVSANGEPTVKLYTSVENAQQDKGIAIPHDIDLGESRVVIQDYDNQHEQDRPTPSPAPSRPFSVLRANDVLWLSLTAAEYDQSTYGSSTGPVYVSDSVTLVNVATGAQAVARSLDWTKVTLDGRPLSTIQQYSKTFFVLPLRGKLSFWEAGTTK------YNTTASDQLLVENAAGHRVAISTYTTSLGAGPVSISAVAVLAPHSA 606
                                   127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547      |  -   |   567       577       587       597         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              554    561                                             


Chain A from PDB  Type:PROTEIN  Length:483
 aligned with ORF3_HEVBU | P69616 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:483
                                                                                                                             1             16         17           30  31                                                                  100                                                                                                 101   107                  108   114                                                                                                                                            
                                     -         -         -         -         -         -         -         -         -       | 3        13  |      -   |    23      |  -|       40        50        60        70        80        90       100         -         -         -         -         -         -         -         -         -       101     |   -         -      |111  |      -         -         -         -         -         -         -         -         -         -         -         -         -         -   
           ORF3_HEVBU     - -------------------------------------------------------------------------------------------------MGSRPCALGLFCCCSS----------CFCLCCPRHRPVSR---LAAVVGGAAAVPAVVSGVTGLILSPSQSPIFIQPTPSPPMSPLRPGLDLVFANPPDHSAPLGVTRPSAPP---------------------------------------------------------------------------------------------------LPHVVDL--------------------PQLGPRR--------------------------------------------------------------------------------------------------------------------------------------------   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains SP2-2zzqA01 A:118-606                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Pfam domains
         Sec.struct. author ..............eeeeeeeeeeee........eeeeeeee..........ee.hhhhhhhh...eeeeeeeeeeeee.....ee...eeeeee..........hhhhhhh...eeee.....eeeeehhhhhhhhhh.eee......hhhhhh..eeeeeee...ee...........eeeeeeeeeee...........eeeeeeeeeeeeee.....eeee..hhhhhh.hhhhh............eeeeeeehhhhhh..hhhhhhh....eeeeeee.......eeeee.hhhhhhh.........eeeeeeeeeeee...........................eeeeee.................eee..eeeee............hhhhh.......eeee....eeeee.......................eeee......eee.............eeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zzq A 118 DTPPVPDVDSRGAILRRQYNLSTSPLTSSVATGTNLVLYAAPLSPLLPLQDGTNTHIMATEASNYAQYRVARATIRYRPLVPNAVGGYAISISFWPQTTTTPTSVDMNSITSTDVRILVQPGIASELVIPSERLHYRNQGWRSVETSGVAEEEATSGLVMLCIHGSPVNSYTNTPYTGALGLLDFALELEFRNLTPGNTNTRVSRYSSTARHRLRRGADGTAELTTTAATRFMKDLYFTSTNGVGEIGRGIALTLFNLADTLLGGLPTELISSAGGQLFYSRPVVSANGEPTVKLYTSVENAQQDKGIAIPHDIDLGESRVVIQDYDNQHEQDRPTPSPAPSRPFSVLRANDVLWLSLTAAEYDQSTYGSSTGPVYVSDSVTLVNVATGAQAVARSLDWTKVTLDGRPLSTIQQYSKTFFVLPLRGKLSFWEAGTTKYNTTASDQLLVENAAGHRVAISTYTTSLGAGPVSISAVAVLAPHSA 606
                                   127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547      |563       573       583       593       603   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              554|                                             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                               561
   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 2ZZQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZZQ)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Viral_ssRNA_CP (106)

(-) Gene Ontology  (8, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (ORF3_HEVBU | P69616)
biological process
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.

Chain A   (CAPSD_HEVBU | P29326)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
cellular component
    GO:0039615    T=1 icosahedral viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=1 symmetry. The T=1 capsid is composed of 12 pentameric capsomeres.
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0044228    host cell surface    The external part of the host cell wall and/or host plasma membrane.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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