3JSB - JenaLib

Title :   CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF THE LYMPHOCYTIC CHORIOMENINGITIS VIRUS L PROTEIN

Authors :   B. Morin, S. Jamal, F. P. Ferron, B. Coutard, G. Bricogne, B. Canard, C. V Marseilles Structural Genomics Program @ Afmb (Msgp)

Date :   10 Sep 09 (Deposition) - 15 Sep 10 (Release) - 15 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.13

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (2x)
Biol. Unit 2: B  (2x)

Keywords :   Viral Protein, Vizier, Structural Genomics, Marseilles Structural Genomics Program @ Afmb, Msgp, Nucleotide-Binding, Nucleotidyltransferase, Rna Replication, Rna-Directed Rna Polymerase, Transferase, Virion, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Morin, B. Coutard, M. Lelke, F. P. Ferron, R. Kerber, S. Jamal, A. Frangeul, C. Baronti, R. Charrel, X. De Lamballerie, C. Vonrhein, J. Lescar, G. Bricogne, S. Gunther, B. Canard
The N-Terminal Domain Of The Arenavirus L Protein Is An Rna Endonuclease Essential In Mrna Transcription
Plos Pathog. V. 6 01038 2010
PubMed-ID: 20862324 | Reference-DOI: 10.1371/JOURNAL.PPAT.1001038

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:173
 aligned with L_LYCVA | P14240 from UniProtKB/Swiss-Prot  Length:2210

    Alignment length:173
                             1                                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169   
              L_LYCVA     - -MDEIISELRELCLNYIEQDERLSRQKLNFLGQREPRMVLIEGLKLLSRCIEIDSADKSGCTHNHDDKSVETILVESGIVCPGLPLIIPDGYKLIDNSLILLECFVRSSPASFEKKFIEDTNKLACIREDLAVAGVTLVPIVDGRCDYDNSFMPEWANFKFRDLLFKLLEYSN 172
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..ee.....hhhhhhhh..............eeeee..eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee........hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------T---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jsb A  -1 HHDEIISELRELCLNYIEQDERLSRQKLNFLGQREPRMVLIEGLKLLSRCIEIDSADKSGCTHNHDDKSVETILVESGIVCPGLPLIIPDGYKLIDNSLILLECFVRSTPASFEKKFIEDTNKLACIREDLAVAGVTLVPIVDGRCDYDNSFMPEWANFKFRDLLFKLLEYSN 171
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168

Chain B from PDB  Type:PROTEIN  Length:194
 aligned with L_LYCVA | P14240 from UniProtKB/Swiss-Prot  Length:2210

    Alignment length:194
                              1                                                                                                                                                                                               
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188    
              L_LYCVA     - --MDEIISELRELCLNYIEQDERLSRQKLNFLGQREPRMVLIEGLKLLSRCIEIDSADKSGCTHNHDDKSVETILVESGIVCPGLPLIIPDGYKLIDNSLILLECFVRSSPASFEKKFIEDTNKLACIREDLAVAGVTLVPIVDGRCDYDNSFMPEWANFKFRDLLFKLLEYSNQNEKVFEESEYFRLCESLKT 192
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---Arena_RNA_pol-3jsbB01 B:1-191                                                                                                                                                                   Pfam domains (1)
           Pfam domains (2) ---Arena_RNA_pol-3jsbB02 B:1-191                                                                                                                                                                   Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..ee.....hhhhhhhh..............eeee...eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------T------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jsb B  -2 HHHDEIISELRELCLNYIEQDERLSRQKLNFLGQREPRMVLIEGLKLLSRCIEIDSADKSGCTHNHDDKSVETILVESGIVCPGLPLIIPDGYKLIDNSLILLECFVRSTPASFEKKFIEDTNKLACIREDLAVAGVTLVPIVDGRCDYDNSFMPEWANFKFRDLLFKLLEYSNQDEKVFEESEYFRLCESLKT 191
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (11, 11)

Asymmetric Unit(hide GO term definitions)

Chain A,B (L_LYCVA | P14240)

molecular function
	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.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0039696	RNA-templated viral transcription	A transcription process that uses viral RNA as a template.
	GO:0075526	cap snatching	A transcription initiation process during which a nucleotide sequence between 10 and 20 nucleotides in size is cleaved from the 5' end of host mRNAs by a viral RNA-dependent polymerase. The capped leader sequence obtained is subsequently used to prime transcription on the viral genome, which ultimately leads to the synthesis of capped, translatable viral mRNAs.
	GO:0039689	negative stranded viral RNA replication	A viral genome replication process where the template genome is negative stranded, single stranded RNA ((-)ssRNA).
	GO:0039694	viral RNA genome replication	The replication of a viral RNA genome.
	GO:0019079	viral genome replication	Any process involved directly in viral genome replication, including viral nucleotide metabolism.
cellular component
	GO:0030430	host cell cytoplasm	The cytoplasm of a host cell.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.

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