4XHA - JenaLib

Title :   CRYSTAL STRUCTURE OF THOSEA ASIGNA VIRUS RNA-DEPENDENT RNA POLYMERASE (RDRP) COMPLEXED WITH LU3+

Authors :   D. S. Ferrero, M. Buxaderas, J. F. Rodriguez, N. Verdaguer

Date :   05 Jan 15 (Deposition) - 04 Nov 15 (Release) - 09 Dec 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Polymerase, Rdrp, Virus, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. S. Ferrero, M. Buxaderas, J. F. Rodriguez, N. Verdaguer
The Structure Of The Rna-Dependent Rna Polymerase Of A Permutotetravirus Suggests A Link Between Primer-Dependent And Primer-Independent Polymerases.
Plos Pathog. V. 11 05265 2015
PubMed-ID: 26625123 | Reference-DOI: 10.1371/JOURNAL.PPAT.1005265

Compounds

Molecule 1 - RNA-DEPENDENT RNA POLYMERASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Cell Line	:	HIGH FIVE
	Expression System Common	:	CABBAGE LOOPER
	Expression System Plasmid	:	PFASTBAC1-HM
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	UNP RESIDUES 1-674
	Gene	:	RDRP
	Organism Scientific	:	THOSEA ASIGNA VIRUS
	Organism Taxid	:	83810

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Asymmetric/Biological Unit (3, 12)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	LU	2	Ligand/Ion	LUTETIUM (III) ION
3	SO4	8	Ligand/Ion	SULFATE ION

Sites (12, 12)

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:140 , ASP B:140 , ASP B:142 , LU B:701	binding site for residue LU A 701
02	AC2	SOFTWARE	ARG A:269 , ARG A:545 , ARG A:564 , ALA A:610	binding site for residue SO4 A 702
03	AC3	SOFTWARE	VAL A:440 , GLY A:442 , THR A:443 , THR A:444	binding site for residue SO4 A 703
04	AC4	SOFTWARE	SER A:215 , LYS A:264 , TYR A:282	binding site for residue SO4 A 704
05	AC5	SOFTWARE	PRO A:46 , TYR A:628 , TYR A:631	binding site for residue GOL A 705
06	AC6	SOFTWARE	THR A:109 , VAL A:118 , LYS A:119	binding site for residue GOL A 706
07	AC7	SOFTWARE	ARG A:164 , LYS A:278 , ARG A:280 , PHE A:370 , GLN A:372 , LYS A:488	binding site for residue SO4 A 707
08	AC8	SOFTWARE	ASP A:140 , ASP A:142 , LU A:701 , ASP B:142	binding site for residue LU B 701
09	AC9	SOFTWARE	ARG B:269 , PRO B:544 , ARG B:545 , ARG B:564 , ALA B:610	binding site for residue SO4 B 702
10	AD1	SOFTWARE	GLY B:442 , THR B:443 , THR B:444	binding site for residue SO4 B 703
11	AD2	SOFTWARE	SER B:215 , LYS B:264 , TYR B:282	binding site for residue SO4 B 704
12	AD3	SOFTWARE	ARG B:164 , LYS B:278 , ARG B:280 , PHE B:370 , LYS B:371 , GLN B:372	binding site for residue SO4 B 705

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:663
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhhhhhhhhh.hhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhh.........ee......................ee..ee............hhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhh.........hhhhhhhhh..hhhhh......hhhhhh..ee............hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhheeeee..eeee.hhh.....eeee.hhhhhhhhhhhhhhhhh.....................hhhhhhhhhhh..........eeeee..eeeeeeee..eeeee.....hhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...ee.....eee............hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..........ee...................eeeeeee..eeeeeee.hhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhh........................hhhhhhhhhh............hhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xha A  10 PTRLSLEAMLAERAMVARQDLAGLKRKLAGADRVLAPQSPEQCGRESAQAQARSVTSELKSAVKEAQGLEHQTLDFLEQLGEYPVCGILHGDHPVHPSGTHNNNGKVSVKRQFAAGVNTSDALTCAFRFEDSDLVRETALKTTYTDGTWAGFVQRLKMQTTRKCVQEKVSRKLLKQLFPYDPQKLVDVSGELSELVLGIKTNAIASAGPPYWRTKRDALPDMLDCVLPLLYDHIVRKDLTTLRNKHPELFLAECKNKTDRYEVESLGEKTRPYFSHPFHLSALVSVLSQSFSGALKIMTEDSTSFNAYGFSWTNGGAEDLAIWARQAGEAGKKPPRIACYGDDTDIYYRKDGKLYRICPDFKQMDGSVDATTIEAVVDYVVDAHVKQYPTARQFWEEVGKLWVEMATQSPFLIDGTKVYRKMQKDGLMTGVVGTTLFDTVKSALAYNDWADQLMFGSLNLLEEKYAIEFFKNKHGLVIKEGTWKPALVNEDPGFGELWTEQKFLGLQLKVVRRENEKVYVPNLPFEDWLTMWVTPRSKYRSKETETMRERTLFDRARGLLVTGAVFDERARGLMGAVINSTAPEVVCMRVQEGGGRGAPPAYAFLTRDGVFEFPISDGYPSYDWVVSLYSRDHPCDMPRVFPEAATLIASYRKQVMDTRVVIK 672
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669

Chain B from PDB  Type:PROTEIN  Length:662
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhhhhhhhhh.hhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee......ee..ee.........................hhhhhhhhhhhhhhhhhhhhhheeee..hhhhhhhhhhhh..........hhhhhhhhh..hhhhh.....hhhhhhhh.ee................hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhheeeee..eeee.hhh.....eeee.hhhhhhhhhhhhhhhhh.....................hhhhhhhhhhh..........eeeee..eeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..ee....eeeee...........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..........ee...................eeeeee....eeeeee.hhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhh........................hhhhhhhhhh............hhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xha B  10 PTRLSLEAMLAERAMVARQDLAGLKRKLAGADRVLAPQSPEQCGRESAQAQARSVTSELKSAVKEAQGLEHQTLDFLEQLGEYPVCGILHGDHPVHPSGTHNNNGKVSVKRQFAAGVNTSDALTCAFRFEDSDLVRETALKTTYTDGTWAGFVQRLKMQTTRKCVQEKVSRKLLKQLFPYDPQKLVDVSGELSELVLGIKTNAIASAGPPYWRTKRDALPDMLDCVLPLLYDHIVRKDLTTLRNKHPELFLAECKNKTDRYEVESLGEKTRPYFSHPFHLSALVSVLSQSFSGALKIMTEDSTSFNAYGFSWTNGGAEDLAIWARQAGEAGKKPPRIACYGDDTDIYYRKDGKLYRICPDFKQMDGSVDATTIEAVVDYVVDAHVKQYPTARQFWEEVGKLWVEMATQSPFLIDGTKVYRKMQKDGLMTGVVGTTLFDTVKSALAYNDWADQLMFGSLNLLEEKYAIEFFKNKHGLVIKEGTWKPALVNEDPGFGELWTEQKFLGLQLKVVRRENEKVYVPNLPFEDWLTMWVTPRSKYRSKETETMRERTLFDRARGLLVTGAVFDERARGLMGAVINSTAPEVVCMRVQEGGGRGAPPAYAFLTRDGVFEFPISDGYPSYDWVVSLYSRDHPCDMPRVFPEAATLIASYRKQVMDTRVVI 671
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669

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 (0, 0)

Gene Ontology (2, 2)

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
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		LU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		AD1	[ RasMol ]	+environment [ RasMol ]
		AD2	[ RasMol ]	+environment [ RasMol ]
		AD3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Pro A:218 - Pro A:219	[ RasMol ]
		Pro B:218 - Pro B:219	[ RasMol ]

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	4xha
		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
	Q6A562_9VIRU \| Q6A562
		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
	Q6A562_9VIRU \| Q6A562
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description