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(-) Description

Title :  X-RAY STRUCTURE OF THE N AND C-TERMINAL DOMAIN OF CORONAVIRUS NUCLEOCAPSID PROTEIN.
 
Authors :  H. Jayaram, H. Fan, B. R. Bowman, A. Ooi, J. Jayaram, E. W. Collinson, J. Lescar, B. V. V. Prasad
Date :  02 Dec 05  (Deposition) - 21 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Nucleocapsid Protein, Phosphorylation, Rna-Binding, Viral Nucleoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Jayaram, H. Fan, B. R. Bowman, A. Ooi, J. Jayaram, E. W. Collisson, J. Lescar, B. V. V. Prasad
X-Ray Structures Of The N- And C-Terminal Domains Of A Coronavirus Nucleocapsid Protein: Implications For Nucleocapsid Formation.
J. Virol. V. 80 6612 2006
PubMed-ID: 16775348  |  Reference-DOI: 10.1128/JVI.00157-06

(-) Compounds

Molecule 1 - NUCLEOCAPSID PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET16B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: N-TERMINAL DOMAIN, RESIDUES 29-160
    Mutation: YES
    Organism Scientific: AVIAN INFECTIOUS BRONCHITIS VIRUS
    Organism Taxid: 11120
    Strain: BEAUDETTE US
    Synonym: IBV NUCLEOCAPSID, N STRUCTURAL PROTEIN, NC

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2C86)

(-) Sites  (0, 0)

(no "Site" information available for 2C86)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C86)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Gly A:31 -Asn A:32
2Asp A:135 -Lys A:136
3Asp B:135 -Lys B:136
4Asp B:138 -Gln B:139
5Gln B:139 -Tyr B:140

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C86)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2C86)

(-) Exons   (0, 0)

(no "Exon" information available for 2C86)

(-) 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:134
 aligned with NCAP_IBVBU | P69598 from UniProtKB/Swiss-Prot  Length:409

    Alignment length:134
                                    36        46        56        66        76        86        96       106       116       126       136       146       156    
           NCAP_IBVBU    27 VGSSGNASWFQAIKAKKLNTPPPKFEGSGVPDNENIKPSQQHGYWRRQARFKPGKGGRKPVPDAWYFYYTGTGPAADLNWGDTQDGIVWVAAKGADTKSRSNQGTRDPDKFDQYPLRFSDGGPDGNFRWDFIPL 160
               SCOP domains d2c86a_ A: Nucleocapsid protein                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee.........ee..........hhhh.eeeeee................eeeeee.................eeeee..............................ee...ee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c86 A  27 HMSSGNASWFQAIKAKKLNTPPPKFEGSGVPDNENIKPSQQHGYWRRQARFKPGKGGRCPVPDAWYFYYTGTGPAADLNWGDTQDGIVWVAAKGADTKSRSNQGTRDPDKFDQYPLRFSDGGPDGNFRWDFIPL 160
                                    36        46        56        66        76        86        96       106       116       126       136       146       156    


Chain B from PDB  Type:PROTEIN  Length:134
 aligned with NCAP_IBVBU | P69598 from UniProtKB/Swiss-Prot  Length:409

    Alignment length:134
                                    36        46        56        66        76        86        96       106       116       126       136       146       156    
           NCAP_IBVBU    27 VGSSGNASWFQAIKAKKLNTPPPKFEGSGVPDNENIKPSQQHGYWRRQARFKPGKGGRKPVPDAWYFYYTGTGPAADLNWGDTQDGIVWVAAKGADTKSRSNQGTRDPDKFDQYPLRFSDGGPDGNFRWDFIPL 160
               SCOP domains d2c86b_ B: Nucleocapsid protein                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee..........................eeeeee..eeeee..eeeee..eeeee..................eeeee...................................ee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c86 B  27 HMSSGNASWFQAIKAKKLNTPPPKFEGSGVPDNENIKPSQQHGYWRRQARFKPGKGGRCPVPDAWYFYYTGTGPAADLNWGDTQDGIVWVAAKGADTKSRSNQGTRDPDKFDQYPLRFSDGGPDGNFRWDFIPL 160
                                    36        46        56        66        76        86        96       106       116       126       136       146       156
   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 beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2C86)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C86)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NCAP_IBVBU | P69598)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
cellular component
    GO:0044177    host cell Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic host cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack.
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0044172    host cell endoplasmic reticulum-Golgi intermediate compartment    A complex system of membrane-bounded compartments located between host cell endoplasmic reticulum (ER) and the host Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi transport.
    GO:0044196    host cell nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic host cells.
    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:0044220    host cell perinuclear region of cytoplasm    The host cell cytoplasm situated near, or occurring around, the host nucleus.
    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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  Cis Peptide Bonds
    Asp A:135 - Lys A:136   [ RasMol ]  
    Asp B:135 - Lys B:136   [ RasMol ]  
    Asp B:138 - Gln B:139   [ RasMol ]  
    Gln B:139 - Tyr B:140   [ RasMol ]  
    Gly A:31 - Asn A:32   [ RasMol ]  
 
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  2c86
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 Related Entries

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

UniProtKB/Swiss-Prot
        NCAP_IBVBU | P69598: 2btl 2bxx

(-) Related Entries Specified in the PDB File

2btl CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF IBV CORONAVIRUS NUCLEOCAPSID
2bxx CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF IBV CORONAVIRUS NUCLEOCAPSID. NATIVE CRYSTAL FORM