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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BORNA DISEASE VIRUS NUCLEOPROTEIN
 
Authors :  M. G. Rudolph, I. Kraus, A. Dickmanns, W. Garten, R. Ficner
Date :  22 Nov 02  (Deposition) - 07 Oct 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym. Unit :  X
Biol. Unit 1:  X  (4x)
Keywords :  Rna Virus Nucleoprotein Tetramer, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. G. Rudolph, I. Kraus, A. Dickmanns, M. Eickmann, W. Garten, R. Ficne
Crystal Structure Of The Borna Disease Virus Nucleoprotein
Structure V. 11 1219 2003
PubMed-ID: 14527390  |  Reference-DOI: 10.1016/J.STR.2003.08.011

(-) Compounds

Molecule 1 - P40 NUCLEOPROTEIN
    Chains: X
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMAL-C2G
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: BORNA DISEASE VIRUS
    Organism Taxid: 12455

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : X
Biological Unit 1 (4x): X

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1N93)

(-) Sites  (0, 0)

(no "Site" information available for 1N93)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N93)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser X:217 -Pro X:218

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_NCAP_BDV1_001 *I47TNCAP_BDV1  ---  ---XI47T
2UniProtVAR_NCAP_BDV1_002 *N56SNCAP_BDV1  ---  ---XN56S
3UniProtVAR_NCAP_BDV1_003 *I357VNCAP_BDV1  ---  ---XI357V
4UniProtVAR_NCAP_BDV1_004 *R362KNCAP_BDV1  ---  ---XK362K
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (4, 16)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_NCAP_BDV1_001 *I47TNCAP_BDV1  ---  ---XI47T
2UniProtVAR_NCAP_BDV1_002 *N56SNCAP_BDV1  ---  ---XN56S
3UniProtVAR_NCAP_BDV1_003 *I357VNCAP_BDV1  ---  ---XI357V
4UniProtVAR_NCAP_BDV1_004 *R362KNCAP_BDV1  ---  ---XK362K
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1N93)

(-) Exons   (0, 0)

(no "Exon" information available for 1N93)

(-) 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 X from PDB  Type:PROTEIN  Length:335
 aligned with NCAP_BDV1 | P0C796 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:343
                                    37        47        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   
            NCAP_BDV1    28 KLPGKFLQYTVGGSDPHPGIGHEKDIRQNAVALLDQSRRDMFHTVTPSLVFLCLLIPGLHAAFVHGGVPRESYLSTPVTRGEQTVVKTAKFYGEKTTQRDLTELEISSIFSHCCSLLIGVVIGSSSKIKAGAEQIKKRFKTMMAALNRPSHGETATLLQMFNPHEAIDWINGQPWVGSFVLSLLTTDFESPGKEFMDQIKLVASYAQMTTYTTIKEYLAECMDATLTIPVVAYEIRDFLEVSAKLKEEHADLFPFLGAIRHPDAIKLAPRSFPNLASAAFYWSKKENPTMAGYRASTIQPGASVKETQLARYRRREISRGEDGAELSGEISAIMRMIGVTGLN 370
               SCOP domains d1n93x_ X: P40 nucleoprotein                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1n93X01 X:28-235 borna disease virus nucleoprotein, domain 1                                                                                                                                                    1n93X02 X:236-370 borna disease virus nucleoprotein, domain 2                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhhhhhhhhhh.hhhhhh....hhhhhhhhhhhh.hhhhhhhhh.....eeeeeee......eeee.............hhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhh...hhhhhh.......hhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh--------.........hhhhhhhhhh............hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------T--------S------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V----K-------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n93 X  28 KLPGKFLQYTVGGSDPHPGIGHEKDIRQNAVALLDQSRRDMFHTVTPSLVFLCLLIPGLHAAFVHGGVPRESYLSTPVTRGEQTVVKTAKFYGEKTTQRDLTELEISSIFSHCCSLLIGVVIGSSSKIKAGAEQIKKRFKTMMAALNRPSHGETATLLQMFNPHEAIDWINGQPWVGSFVLSLLTTDFESPGKEFMDQIKLVASYAQMTTYTTIKEYLAECMDATLTIPVVAYEIRDFLEVSAKLKEDHADLFPFLGAIRHPDAIKLAPRSFPNLASAAFYWSKKEN--------STIQPGASVKETQLARYRRREISRGEDGAELSGEISAIMKMIGVTGLN 370
                                    37        47        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      |  -     | 327       337       347       357       367   
                                                                                                                                                                                                                                                                                                                        314      323                                               


Chain X from PDB  Type:PROTEIN  Length:335
 aligned with NCAP_BDVV | P0C797 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:343
                                    37        47        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   
            NCAP_BDVV    28 KLPGKFLQYTVGGSDPHPGIGHEKDIRQNAVALLDQSRRDMFHTVTPSLVFLCLLIPGLHAAFVHGGVPRESYLSTPVTRGEQTVVKTAKFYGEKTTQRDLTELEISSIFSHCCSLLIGVVIGSSSKIKAGAEQIKKRFKTMMAALNRPSHGETATLLQMFNPHEAIDWINGQPWVGSFVLSLLTTDFESPGKEFMDQIKLVASYAQMTTYTTIKEYLAECMDATLTIPVVAYEIRDFLEVSAKLKEDHADLFPFLGAIRHPDAIKLAPRSFPNLASAAFYWSKKENPTMAGYRASTIQPGASVKETQLARYRRREISRGEDGAELSGEISAIMKMIGVTGLN 370
               SCOP domains d1n93x_ X: P40 nucleoprotein                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1n93X01 X:28-235 borna disease virus nucleoprotein, domain 1                                                                                                                                                    1n93X02 X:236-370 borna disease virus nucleoprotein, domain 2                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhhhhhhhhhh.hhhhhh....hhhhhhhhhhhh.hhhhhhhhh.....eeeeeee......eeee.............hhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhh...hhhhhh.......hhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh--------.........hhhhhhhhhh............hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------T--------S------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V----K-------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n93 X  28 KLPGKFLQYTVGGSDPHPGIGHEKDIRQNAVALLDQSRRDMFHTVTPSLVFLCLLIPGLHAAFVHGGVPRESYLSTPVTRGEQTVVKTAKFYGEKTTQRDLTELEISSIFSHCCSLLIGVVIGSSSKIKAGAEQIKKRFKTMMAALNRPSHGETATLLQMFNPHEAIDWINGQPWVGSFVLSLLTTDFESPGKEFMDQIKLVASYAQMTTYTTIKEYLAECMDATLTIPVVAYEIRDFLEVSAKLKEDHADLFPFLGAIRHPDAIKLAPRSFPNLASAAFYWSKKEN--------STIQPGASVKETQLARYRRREISRGEDGAELSGEISAIMKMIGVTGLN 370
                                    37        47        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      |  -     | 327       337       347       357       367   
                                                                                                                                                                                                                                                                                                                        314      323
   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  (1, 1)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1N93)

(-) Gene Ontology  (10, 20)

Asymmetric Unit(hide GO term definitions)
Chain X   (NCAP_BDV1 | P0C796)
biological process
    GO:0060153    modulation by virus of host cell cycle    Any viral process that modulates the rate or extent of progression through the cell cycle.
    GO:0039592    suppression by virus of G2/M transition of host mitotic cell cycle    Any viral process that decreases the rate or extent of progression from G2 phase to M phase of the host mitotic cell cycle.
    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:0075732    viral penetration into host nucleus    The crossing by the virus of the host nuclear membrane, either as naked viral genome or for small viruses as an intact capsid.
    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:0019029    helical viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles; the subunits are arranged to form a protein helix with the genetic material contained within. Tobacco mosaic virus has such a capsid structure.
    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:0019013    viral nucleocapsid    The complete protein-nucleic acid complex that is the packaged form of the genome in a virus particle.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

Chain X   (NCAP_BDVV | P0C797)
biological process
    GO:0060153    modulation by virus of host cell cycle    Any viral process that modulates the rate or extent of progression through the cell cycle.
    GO:0039592    suppression by virus of G2/M transition of host mitotic cell cycle    Any viral process that decreases the rate or extent of progression from G2 phase to M phase of the host mitotic cell cycle.
    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:0075732    viral penetration into host nucleus    The crossing by the virus of the host nuclear membrane, either as naked viral genome or for small viruses as an intact capsid.
    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:0019029    helical viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles; the subunits are arranged to form a protein helix with the genetic material contained within. Tobacco mosaic virus has such a capsid structure.
    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:0019013    viral nucleocapsid    The complete protein-nucleic acid complex that is the packaged form of the genome in a virus particle.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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    Ser X:217 - Pro X:218   [ RasMol ]  
 
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  1n93
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 Related Entries

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

UniProtKB/Swiss-Prot
        NCAP_BDV1 | P0C796: 1pp1
        NCAP_BDVV | P0C797: 1pp1

(-) Related Entries Specified in the PDB File

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