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(-) Description

Title :  CRYSTAL STRUCTURE OF APO SWINE FLU INFLUENZA NUCLEOPROTEIN
 
Authors :  H. A. Lewis, E. T. Baldwin, S. Steinbacher, K. Maskos, M. Mortl, R. Kiefe S. Edavettal, P. A. Mcdonnell, B. C. Pearce, D. R. Langley
Date :  29 Feb 12  (Deposition) - 06 Mar 13  (Release) - 06 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. A. Lewis, E. T. Baldwin, S. Steinbacher, K. Maskos, M. Mortl, R. Kiefersauer, S. Edavettal, P. A. Mcdonnell, B. C. Pearce, D. R. Langley
To Be Determined
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NUCLEOCAPSID PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 26-489
    Gene: NP
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 11320
    Synonym: NUCLEOPROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4DYS)

(-) Sites  (0, 0)

(no "Site" information available for 4DYS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4DYS)

(-) Sequences/Alignments

Asymmetric/Biological 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:441
 aligned with G8XKZ6_9INFA | G8XKZ6 from UniProtKB/TrEMBL  Length:498

    Alignment length:473
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486   
         G8XKZ6_9INFA    17 GERQDATEIRASVGRMIGGIGRFYIQMCTELKLSDYDGRLIQNSITIERMVLSAFDERRNKYLEEHPSAGKDPKKTGGPIYRRVDGKWMRELILYDKEEIRRVWRQANNGEDATAGLTHIMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTIAMELIRMIKRGINDRNFWRGENGRRTRVAYERMCNILKGKFQTAAQRAMMDQVRESRNPGNAEIEDLIFLARSALILRGSVAHKSCLPACVYGLAVASGHDFEREGYSLVGIDPFKLLQNSQVVSLMRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGKKVIPRGKLSTRGVQIASNENVEIMDSNTLELRSRYWAIRTRSGGNTNQQKASAGQISVQPTFSVQRNLPFERATVMAAFSGNNEGRTSDMRTEVIRMMESAKPEDLSFQGRGVFELSDEKATNPIVPSFDMSNEGSYFF 489
               SCOP domains d        4dysa_ A: Nucleocapsid protein                                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author h--------hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...-------------..eeeeeeeee....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.............hhhhhhhhhhh..hhhhhh....hhhhhhhhhh...eeee....hhhhhhhhhhhhhhh....hhhhhhhhhh....hhhhh...........hhhhheeee....................-----............ee...hhhhhhhhhh------.hhhhhhhhhhhhhh....ee................................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dys A  31 G--------RASVGRMIGGIGRFYIQMCTELKLSDYDGRLIQNSITIERMVLSAFDERR-------------PKKTGGPIYRRVDGKWMRELILYDKEEIRRVWRQANNGEDATAGLTHIMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTIAMELIRMIKRGINDRNFWRGENGRRTRVAYERMCNILKGKFQTAAQRAMMDQVRESRNPGNAEIEDLIFLARSALILRGSVAHKSCLPACVYGLAVASGHDFEREGYSLVGIDPFKLLQNSQVVSLMRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGKKVIPRGKLSTRGVQIASNENVEIMDSNTLELRSRYWAIRTRSGGNTNQ-----GQISVQPTFSVQRNLPFERATVMAAFS------TSDMRTEVIRMMESAKPEDLSFQGRGVFELSDEKATNPIVPSFDMSNEGSYFF 495
                            |       32        42        52        62        72        |-         -  |    102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402 |     412       422       432   |     -|      452       462       472       482       492   
                            |       32                                               81            95                                                                                                                                                                                                                                                                                                                  404   410                       436    443                                                    
                           31                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:448
 aligned with G8XKZ6_9INFA | G8XKZ6 from UniProtKB/TrEMBL  Length:498

    Alignment length:473
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486   
         G8XKZ6_9INFA    17 GERQDATEIRASVGRMIGGIGRFYIQMCTELKLSDYDGRLIQNSITIERMVLSAFDERRNKYLEEHPSAGKDPKKTGGPIYRRVDGKWMRELILYDKEEIRRVWRQANNGEDATAGLTHIMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTIAMELIRMIKRGINDRNFWRGENGRRTRVAYERMCNILKGKFQTAAQRAMMDQVRESRNPGNAEIEDLIFLARSALILRGSVAHKSCLPACVYGLAVASGHDFEREGYSLVGIDPFKLLQNSQVVSLMRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGKKVIPRGKLSTRGVQIASNENVEIMDSNTLELRSRYWAIRTRSGGNTNQQKASAGQISVQPTFSVQRNLPFERATVMAAFSGNNEGRTSDMRTEVIRMMESAKPEDLSFQGRGVFELSDEKATNPIVPSFDMSNEGSYFF 489
               SCOP domains d        4dysb_ B: Nucleocapsid protein                                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--------hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh....------------...ee..eeeee....eeeee..eehhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhh.....hhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhhhh.............hhhhhhhhhhh..hhhhhh.....hhhhhhhhh...eee.....hhhhhhhhhhhhhh.....hhhhhhhhhh....hhhhh.................eee......ee............hhhhhh...........ee...hhhhhhh.....-----.hhhhhhhhhhhhh....ee......ee........................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dys B  31 G--------RASVGRMIGGIGRFYIQMCTELKLSDYDGRLIQNSITIERMVLSAFDERR------------DPKKTGGPIYRRVDGKWMRELILYDKEEIRRVWRQANNGEDATAGLTHIMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTIAMELIRMIKRGINDRNFWRGENGRRTRVAYERMCNILKGKFQTAAQRAMMDQVRESRNPGNAEIEDLIFLARSALILRGSVAHKSCLPACVYGLAVASGHDFEREGYSLVGIDPFKLLQNSQVVSLMRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGKKVIPRGKLSTRGVQIASNENVEIMDSNTLELRSRYWAIRTRSGGNTNQQKASAGQISVQPTFSVQRNLPFERATVMAAFSGN-----SDMRTEVIRMMESAKPEDLSFQGRGVFELSDEKATNPIVPSFDMSNEGSYFF 495
                            |       32        42        52        62        72        |-         - |     102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432     |   - |     452       462       472       482       492   
                           31       32                                               81           94                                                                                                                                                                                                                                                                                                                                                     438   444                                                   


Chain C from PDB  Type:PROTEIN  Length:454
 aligned with G8XKZ6_9INFA | G8XKZ6 from UniProtKB/TrEMBL  Length:498

    Alignment length:473
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486   
         G8XKZ6_9INFA    17 GERQDATEIRASVGRMIGGIGRFYIQMCTELKLSDYDGRLIQNSITIERMVLSAFDERRNKYLEEHPSAGKDPKKTGGPIYRRVDGKWMRELILYDKEEIRRVWRQANNGEDATAGLTHIMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTIAMELIRMIKRGINDRNFWRGENGRRTRVAYERMCNILKGKFQTAAQRAMMDQVRESRNPGNAEIEDLIFLARSALILRGSVAHKSCLPACVYGLAVASGHDFEREGYSLVGIDPFKLLQNSQVVSLMRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGKKVIPRGKLSTRGVQIASNENVEIMDSNTLELRSRYWAIRTRSGGNTNQQKASAGQISVQPTFSVQRNLPFERATVMAAFSGNNEGRTSDMRTEVIRMMESAKPEDLSFQGRGVFELSDEKATNPIVPSFDMSNEGSYFF 489
               SCOP domains d        4dysc_ C: Nucleocapsid protein                                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--------hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh-----------..eeeeeeeeee..eeeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.............hhhhhhhhhh...hhhhhh.....hhhhhhhhh..eeeee....hhhhhhhhhhhhhh.....hhhhhhhhhh.........................eeeee....................................ee...hhhhhhh..........hhhhhhhhhhhhhh....ee................................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dys C  31 G--------RASVGRMIGGIGRFYIQMCTELKLSDYDGRLIQNSITIERMVLSAFDERRNK-----------PKKTGGPIYRRVDGKWMRELILYDKEEIRRVWRQANNGEDATAGLTHIMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTIAMELIRMIKRGINDRNFWRGENGRRTRVAYERMCNILKGKFQTAAQRAMMDQVRESRNPGNAEIEDLIFLARSALILRGSVAHKSCLPACVYGLAVASGHDFEREGYSLVGIDPFKLLQNSQVVSLMRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGKKVIPRGKLSTRGVQIASNENVEIMDSNTLELRSRYWAIRTRSGGNTNQQKASAGQISVQPTFSVQRNLPFERATVMAAFSGNNEGRTSDMRTEVIRMMESAKPEDLSFQGRGVFELSDEKATNPIVPSFDMSNEGSYFF 495
                            |       32        42        52        62        72        82|        -  |    102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492   
                           31       32                                                 83          95
   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, 3)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (G8XKZ6_9INFA | G8XKZ6)
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.
biological process
    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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 Related Entries

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(-) Related Entries Specified in the PDB File

4dya 4dyb 4dyn 4dyp 4dyt