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(-) Description

Title :  INFLUENZA A NEP M1-BINDING DOMAIN
 
Authors :  F. Baudin
Date :  19 May 03  (Deposition) - 16 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Biol. Unit 4:  A (1x),B (1x)
Keywords :  Influenza Virus A, Nep/Ns2, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Akarsu, W. P. Burmeister, C. Petosa, I. Petit, C. W. Muller, R. W. Ruigrok, F. Baudin
Crystal Structure Of The M1 Protein-Binding Domain Of The Influenza A Virus Nuclear Export Protein (Nep/Ns2).
Embo J. V. 22 4646 2003
PubMed-ID: 12970177  |  Reference-DOI: 10.1093/EMBOJ/CDG449

(-) Compounds

Molecule 1 - NONSTRUCTURAL PROTEIN NS2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 59-116
    Gene: NS2
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 11320
    Other Details: M1-BINDING DOMAIN OF NEP

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB
Biological Unit 4 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1PD3)

(-) Sites  (0, 0)

(no "Site" information available for 1PD3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PD3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PD3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PD3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PD3)

(-) Exons   (0, 0)

(no "Exon" information available for 1PD3)

(-) 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:54
 aligned with NEP_I34A1 | P03508 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:64
                                    62        72        82        92       102       112    
            NEP_I34A1    53 GDLHSLQNRNEKWREQLGQKFEEIRWLIEEVRHKLKITENSFEQITFMQALHLLLEVEQEIRTF 116
               SCOP domains d          1pd3a_ A:                                             SCOP domains
               CATH domains 1          pd3A00 A:63-116  [code=1.10.287.230, no name defined] CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .----------.............................hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 1pd3 A  63 G----------KWREQLGQKFEEIRWLIEEVRHRLKITENSFEQITFMQALQLLLEVEQEIRTF 116
                            |        - |      72        82        92       102       112    
                            |         64                                                    
                           63                                                               


Chain B from PDB  Type:PROTEIN  Length:54
 aligned with NEP_I34A1 | P03508 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:64
                                    62        72        82        92       102       112    
            NEP_I34A1    53 GDLHSLQNRNEKWREQLGQKFEEIRWLIEEVRHKLKITENSFEQITFMQALHLLLEVEQEIRTF 116
               SCOP domains d          1pd3b_ B:                                             SCOP domains
               CATH domains 1          pd3B00 B:63-116  [code=1.10.287.230, no name defined] CATH domains
           Pfam domains (1) -----------Flu_NS2-1pd3B01 B:64-116                              Pfam domains (1)
           Pfam domains (2) -----------Flu_NS2-1pd3B02 B:64-116                              Pfam domains (2)
         Sec.struct. author .----------hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 1pd3 B  63 G----------KWREQLGQKFEEIRWLIEEVRHRLKITENSFEQITFMQALQLLLEVEQEIRTF 116
                            |        - |      72        82        92       102       112    
                           63         64
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Flu_NS2] (1)

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NEP_I34A1 | P03508)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006405    RNA export from nucleus    The directed movement of RNA from the nucleus to the cytoplasm.
    GO:0019064    fusion of virus membrane with host plasma membrane    Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
    GO:0075733    intracellular transport of virus    The directed movement of a virus, or part of a virus, within the host cell.
    GO:0019065    receptor-mediated endocytosis of virus by host cell    Any receptor-mediated endocytosis that is involved in the uptake of a virus into a host cell; successive instances of virus endocytosis result in the accumulation of virus particles within the cell.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0019061    uncoating of virus    The process by which an incoming virus is disassembled in the host cell to release a replication-competent viral genome.
    GO:0046761    viral budding from plasma membrane    A viral budding that starts with formation of a membrane curvature in the host plasma membrane.
    GO:0019072    viral genome packaging    The encapsulation of the viral genome within the 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.
    GO:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
    GO:0019083    viral transcription    The process by which a viral genome, or part of a viral genome, is transcribed within the host cell.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030666    endocytic vesicle membrane    The lipid bilayer surrounding an endocytic vesicle.
    GO:0031904    endosome lumen    The volume enclosed by the membrane of an endosome.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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