1T6O - JenaLib

Title :   NUCLEOCAPSID-BINDING DOMAIN OF THE MEASLES VIRUS P PROTEIN (AMINO ACIDS 457-507) IN COMPLEX WITH AMINO ACIDS 486-505 OF THE MEASLES VIRUS N PROTEIN

Authors :   R. L. Kingston, D. J. Hamel, L. S. Gay, F. W. Dahlquist, B. W. Matthews

Date :   06 May 04 (Deposition) - 03 Aug 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Four Helix Bundle, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. L. Kingston, D. J. Hamel, L. S. Gay, F. W. Dahlquist, B. W. Matthews
Structural Basis For The Attachment Of A Paramyxoviral Polymerase To Its Template.
Proc. Natl. Acad. Sci. Usa V. 101 8301 2004
PubMed-ID: 15159535 | Reference-DOI: 10.1073/PNAS.0402690101
(for further references see the PDB file header)

Compounds

Molecule 1 - PHOSPHOPROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET41A(+)
	Expression System Strain	:	BL21-STAR(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 457-507
	Gene	:	P/V
	Mutation	:	YES
	Organism Scientific	:	MEASLES VIRUS
	Organism Taxid	:	11234
	Other Details	:	CHIMERIC MOLECULE ENCOMPASSING AMINO ACIDS 457-507 OF MEASLES P (CHAIN A) AND 486-505 OF MEASLES N (CHAIN B). THEY ARE CONNECTED BY A FLEXIBLE 8 AMINO ACID LINKER (GS)4 (CHAIN L)
	Strain	:	MORATEN VACCINE STRAIN

Molecule 2 - LINKER
	Chains	:	L
	Engineered	:	YES
	Other Details	:	SYNTHETIC LINKER
	Synthetic	:	YES

Molecule 3 - PHOSPHOPROTEIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET41A(+)
	Expression System Strain	:	BL21-STAR(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 486-505
	Gene	:	N
	Organism Scientific	:	MEASLES VIRUS
	Organism Taxid	:	11234
	Strain	:	MORATEN VACCINE STRAIN

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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:49
 aligned with Q77M42_MEASM | Q77M42 from UniProtKB/TrEMBL  Length:507

    Alignment length:50
                                   466       476       486       496       506
         Q77M42_MEASM   457 GPASRSVIRSIIKSSRLEEDRKRYLMTLLDDIKGANDLAKFHQMLMKIIM 506
               SCOP domains d 1t6oa_ A: RNA polymerase alpha subunit           SCOP domains
               CATH domains 1 t6oA00 A:458-506                                 CATH domains
               Pfam domains --Paramyx_P_V_C-1t6oA01 A:459-502             ---- Pfam domains
         Sec.struct. author .-.hhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                 1t6o A 458 G-ASRSVIRSIIKSSRLEEDRKRYLMTLLDDIKGANDLAKFHQMLMKIIM 506
                            | |    466       476       486       496       506
                          458 |                                               
                            459

Chain B from PDB  Type:PROTEIN  Length:19
 aligned with NCAP_MEASM | Q77M43 from UniProtKB/Swiss-Prot  Length:525

    Alignment length:19
                                   495         
           NCAP_MEASM   486 QDSRRSADALLRLQAMAGI 504
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains Paramyxo_ncap-1t6oB Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                 1t6o B 486 QDSRRSADALLRLQAMAGI 504
                                   495

Chain L from PDB  Type:PROTEIN  Length:2
                                  
               SCOP domains -- SCOP domains
               CATH domains -- CATH domains
               Pfam domains -- Pfam domains
         Sec.struct. author .. Sec.struct. author
                 SAPs(SNPs) -- SAPs(SNPs)
                    PROSITE -- PROSITE
                 Transcript -- Transcript
                 1t6o L 484 GS 485

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)

CATH Domains (1, 1)

Pfam Domains (2, 2)

Gene Ontology (12, 13)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q77M42_MEASM | Q77M42)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003968	RNA-directed 5'-3' RNA polymerase activity	Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
biological process
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0001172	transcription, RNA-templated	The cellular synthesis of RNA on a template of RNA.
	GO:0019079	viral genome replication	Any process involved directly in viral genome replication, including viral nucleotide metabolism.

Chain B (NCAP_MEASM | Q77M43)

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: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:0030430	host cell cytoplasm	The cytoplasm of a host cell.
	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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1t6o)

	Sites
(no "Sites" information available for 1t6o)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1t6o)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1t6o
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	NCAP_MEASM \| Q77M43
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	Q77M42_MEASM \| Q77M42
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	NCAP_MEASM \| Q77M43
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	Q77M42_MEASM \| Q77M42
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description