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(-) Description

Title :  DODECAHEDRON FORMED OF PENTON BASE PROTEIN FROM ADENOVIRUS AD3
 
Authors :  W. P. Burmeister, E. Szolajska, M. Zochowska, B. Nerlo, I. Andreev, G. S J. -P. Andrieu, P. Fender, A. Naskalska, C. Zubieta, S. Cusack, J. Chro
Date :  20 Apr 12  (Deposition) - 24 Oct 12  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.80
Chains :  Asym. Unit :  A,P
Biol. Unit 1:  A,P  (60x)
Keywords :  Viral Protein, Capsid Protein, Dsdna Virus, Dodecahedron, Virus-Like Particle, Strand Swapping (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Szolajska, W. P. Burmeister, M. Zochowska, B. Nerlo, I. Andreev, G. Schoehn, J. P. Andrieu, P. Fender, A. Naskalska, C. Zubieta, S. Cusack, J. Chroboczek
The Structural Basis For The Integrity Of Adenovirus Ad3 Dodecahedron.
Plos One V. 7 46075 2012
PubMed-ID: 23049939  |  Reference-DOI: 10.1371/JOURNAL.PONE.0046075

(-) Compounds

Molecule 1 - L2 PROTEIN III (PENTON BASE)
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HIGH-FIVE
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: BAC PAC6
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: RESIDUES 1-542
    Organism Scientific: HUMAN ADENOVIRUS 3
    Organism Taxid: 45659
    Strain: UNIDENTIFIED
    Synonym: PENTON PROTEIN
 
Molecule 2 - FIBER PROTEIN
    Chains: P
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HIGH-FIVE
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: BAC PAC6
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: RESIDUES 1-20
    Organism Scientific: HUMAN ADENOVIRUS 3
    Organism Taxid: 45659
    Strain: UNIDENTIFIED
    Synonym: PIV

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AP
Biological Unit 1 (60x): AP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (0, 0)

(no "Site" information available for 4AR2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AR2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AR2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AR2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AR2)

(-) Exons   (0, 0)

(no "Exon" information available for 4AR2)

(-) 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:455
 aligned with Q2Y0H9_ADE03 | Q2Y0H9 from UniProtKB/TrEMBL  Length:544

    Alignment length:495
                                    57        67        77        87        97       107       117       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     
         Q2Y0H9_ADE03    48 PTEGRNSIRYSELSPLYDTTKLYLVDNKSADIASLNYQNDHSNFLTTVVQNNDFTPTEASTQTINFDERSRWGGQLKTIMHTNMPNVNEYMFSNKFKARVMVSRKAPEGVTVNDTYDHKEDILKYEWFEFILPEGNFSATMTIDLMNNAIIDNYLEIGRQNGVLESDIGVKFDTRNFRLGWDPETKLIMPGVYTYEAFHPDIVLLPGCGVDFTESRLSNLLGIRKRHPFQEGFKIMYEDLEGGNIPALLDVTAYEESKKDTTTETTTLAVAEETSEDDDITRGDTYITEKQKREAAAAEVKKELKIQPLEKDSKSRSYNVLEDKINTAYRSWYLSYNYGNPEKGIRSWTLLTTSDVTCGAEQVYWSLPDMMQDPVTFRSTRQVNNYPVVGAELMPVFSKSFYNEQAVYSQQLRQATSLTHVFNRFPENQILIRPPAPTITTVSENVPALTDHGTLPLRSSIRGVQRVTVTDARRRTCPYVYKALGIVAPRVLSSR 542
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eee...hhhhhhhhh.........ee.......hhhhhhhheee......eeeeeeeeeee..............eeeeeeeee................eeeeeeee........hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eee.............................eee....eee....hhhhhh.eee........eee.............hhhhhhhh...----------------------------------------.............................eehhhhhhh..........eee..........eeee........................eeee..eeeeeee...hhhhhh................hhhhh......eeeeeee..eeeeeeeee...eee.ee...eee........eeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ar2 A  48 PTEGRNSIRYSELSPLYDTTKLYLVDNKSADIASLNYQNDHSNFLTTVVQNNDFTPTEASTQTINFDERSRWGGQLKTIMHTNMPNVNEYMFSNKFKARVMVSRKAPEGVTVNDTYDHKEDILKYEWFEFILPEGNFSATMTIDLMNNAIIDNYLEIGRQNGVLESDIGVKFDTRNFRLGWDPETKLIMPGVYTYEAFHPDIVLLPGCGVDFTESRLSNLLGIRKRHPFQEGFKIMYEDLEGGNIPALLDVTAYEESKKD----------------------------------------KKELKIQPLEKDSKSRSYNVLEDKINTAYRSWYLSYNYGNPEKGIRSWTLLTTSDVTCGAEQVYWSLPDMMQDPVTFRSTRQVNNYPVVGAELMPVFSKSFYNEQAVYSQQLRQATSLTHVFNRFPENQILIRPPAPTITTVSENVPALTDHGTLPLRSSIRGVQRVTVTDARRRTCPYVYKALGIVAPRVLSSR 542
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307         -         -         -         -|      357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537     
                                                                                                                                                                                                                                                                                             307                                      348                                                                                                                                                                                                  


Chain P from PDB  Type:PROTEIN  Length:10
 aligned with SPIKE_ADE02 | P03275 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:10
                                    21
          SPIKE_ADE02    12 NPVYPYDTET  21
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4ar2 P  12 NPVYPYDTEC  21
                                    21
   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 4AR2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AR2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AR2)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q2Y0H9_ADE03 | Q2Y0H9)
molecular function
    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.

Chain P   (SPIKE_ADE02 | P03275)
biological process
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0019058    viral life cycle    A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
    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.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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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  SPIKE_ADE02 | P03275
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 Related Entries

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

UniProtKB/Swiss-Prot
        SPIKE_ADE02 | P03275: 1qhv 1qiu 1v1h 1v1i 1x9t 2c9f 4v4u
UniProtKB/TrEMBL
        Q2Y0H9_ADE03 | Q2Y0H9: 4aqq

(-) Related Entries Specified in the PDB File

1qhv HUMAN ADENOVIRUS SEROTYPE 2 FIBRE HEAD
1qiu A TRIPLE BETA-SPIRAL IN THE ADENOVIRUS FIBRE SHAFT REVEALS A NEW STRUCTURAL MOTIF FOR BIOLOGICAL FIBRES
1v1h ADENOVIRUS FIBRE SHAFT SEQUENCE N-TERMINALLY FUSED TO THE BACTERIOPHAGE T4 FIBRITIN FOLDON TRIMERISATION MOTIF WITH A SHORT LINKER
1v1i ADENOVIRUS FIBRE SHAFT SEQUENCE N-TERMINALLY FUSED TO THE BACTERIOPHAGE T4 FIBRITIN FOLDON TRIMERISATION MOTIF WITH A LONG LINKER
2c9f THE QUASI-ATOMIC MODEL OF THE ADENOVIRUS TYPE 3 PENTON DODECAHEDRON
4aqq DODECAHEDRON FORMED OF PENTON BASE PROTEIN FROM ADENOVIRUS AD3