2GEC - JenaLib

Title :   STRUCTURE OF THE N-TERMINAL DOMAIN OF AVIAN INFECTIOUS BRONCHITIS VIRUS NUCLEOCAPSID PROTEIN (STRAIN GRAY) IN A NOVEL DIMERIC ARRANGEMENT

Authors :   H. Jayaram, H. Fan, B. R. Bowman, A. Ooi, J. Jayaram, E. W. Collisson, J. Lescar, B. V. Prasad

Date :   19 Mar 06 (Deposition) - 27 Jun 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.30

Chains :   Asym./Biol. Unit : A,B

Keywords :   Nucleocapsid Protein, N Protein, Coronavirus, Ibv N Protein, Viral, Viral Protein (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. 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
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:138
 aligned with NCAP_IBVG | P32923 from UniProtKB/Swiss-Prot  Length:409

    Alignment length:138
                                    32        42        52        62        72        82        92       102       112       122       132       142       152        
            NCAP_IBVG    23 RPPKVGSSGNASWFQAIKAKKLNSPQPKFEGSGVPDNENFKTSQQHGYWRRQARFKPGKGRRKPVPDAWYFYYTGTGPAADLNWGDSQDGIVWVAAKGADVKSRSNQGTRDPDKFDQYPLRFSDGGPDGNFRWDFIPL 160
               SCOP domains d2geca1 A:23-160 Nucleocapsid protein                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................eee.....................hhhh.eeeeeeeeeee......eeeeeeeeeee.................eeeee...................................ee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2gec A  23 RPPKVGSSGNASWFQAIKAKKLNSPQPKFEGSGVPDNENLKTSQQHGYWRRQARFKPGKGRRKPVPDAWYFYYTGTGPAADLNWGDSQDGIVWVAAKGADVKSRSNQGTRDPDKFDQYPLRFSDGGPDGNFRWDFIPL 160
                                    32        42        52        62        72        82        92       102       112       122       132       142       152

Chain B from PDB  Type:PROTEIN  Length:139
 aligned with NCAP_IBVG | P32923 from UniProtKB/Swiss-Prot  Length:409

    Alignment length:139
                                    31        41        51        61        71        81        91       101       111       121       131       141       151         
            NCAP_IBVG    22 PRPPKVGSSGNASWFQAIKAKKLNSPQPKFEGSGVPDNENFKTSQQHGYWRRQARFKPGKGRRKPVPDAWYFYYTGTGPAADLNWGDSQDGIVWVAAKGADVKSRSNQGTRDPDKFDQYPLRFSDGGPDGNFRWDFIPL 160
               SCOP domains d2gecb_ B: Nucleocapsid protein                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eee.....................hhhh.eeeeeeeeeee......eeeeeeeeeee.................eeeee...................................ee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gec B  22 PRPPKVGSSGNASWFQAIKAKKLNSPQPKFEGSGVPDNENLKTSQQHGYWRRQARFKPGKGRRKPVPDAWYFYYTGTGPAADLNWGDSQDGIVWVAAKGADVKSRSNQGTRDPDKFDQYPLRFSDGGPDGNFRWDFIPL 160
                                    31        41        51        61        71        81        91       101       111       121       131       141       151

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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (NCAP_IBVG | P32923)

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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	Ligands, Modified Residues, Ions
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	Sites
(no "Sites" information available for 2gec)

	Cis Peptide Bonds
		Gly A:80 - Lys A:81	[ RasMol ]
		Lys A:81 - Gly A:82	[ RasMol ]

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