Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF THE LA CROSSE BUNYAVIRUS POLYMERASE IN COMPLEX WITH THE 3' VIRAL RNA
 
Authors :  J. Reguera, P. Gerlach, S. Cusack
Date :  12 Mar 15  (Deposition) - 03 Jun 15  (Release) - 17 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.57
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Hydrolase, Polymerase, Rnadrnapol, Bunyavirus, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Gerlach, H. Malet, S. Cusack, J. Reguera
Structural Insights Into Bunyavirus Replication And Its Regulation By The Vrna Promoter.
Cell(Cambridge, Mass. ) V. 161 1267 2015
PubMed-ID: 26004069  |  Reference-DOI: 10.1016/J.CELL.2015.05.006

(-) Compounds

Molecule 1 - RNA POLYMERASE L
    Chains: A
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: BTI-TN-5B1-4
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PFASTBAC
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Organism Scientific: BUNYAVIRUS LA CROSSE
    Organism Taxid: 11577
 
Molecule 2 - RNA
    Chains: B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: BTI-TN-5B1-4
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PFASTBAC
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Organism Scientific: BUNYAVIRUS LA CROSSE
    Organism Taxid: 11577
 
Molecule 3 - RNA
    Chains: C
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: BTI-TN-5B1-4
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PFASTBAC
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Organism Scientific: BUNYAVIRUS LA CROSSE
    Organism Taxid: 11577

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5AMR)

(-) Sites  (0, 0)

(no "Site" information available for 5AMR)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AMR)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His A:184 -Gly A:185

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AMR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AMR)

(-) Exons   (0, 0)

(no "Exon" information available for 5AMR)

(-) 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:1657
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh................eeeee..eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee......eee.hhhhhhhh........hhhhhhhhhhhhhhh..hhhhhhhhh..............hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhheee.hhhhh.................hhhhhhhhhhhhhhh......hhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.............eee..eeeee..eee.hhhhhhhhhhhhhhhh...................eee...hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee......eeeee....eeeeeeeeee...........eeeeeee..eeeeee..eeeehhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh....ee......eehhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.....eeeeehhhhhhhhhhh......hhhhhhhhhhhhh...eeee....eeehhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeee........hhhhhhhhh....hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhh......hhhhhh.......eee.........hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeeeee...hhhhhhhhhhhhhhhhhhhh..ee.....eee..eeee..eeee..eee..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.........hhhhh...hhhhh..........hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhh......hhhhhhhhhh......hhhhhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhhhhhhheeeeeee.....eeee........hhhhhhhhhh......hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5amr A    0 GMDYQEYQQFLARINTARDACVAKDIDVDLLMARHDYFGRELCKSLNIEYRNDVPFIDIILDIRPEVDPLTIDAPHITPDNYLYINNVLYIIDYKVSVSNESSVITYDKYYELTRDISDRLSIPIEIVIIRIDPVSRDLHINSDRFKELYPTIVVDINFNQFFDLKQLLYEKFGDDEEFLLKVAHGDFTLTAPWCKTGCPEFWKHPIYKEFKMSMPVPERRLFEESVKFNAYESERWNTNLVKIREYTKKDYSEHISKSAKNIFLASGFYKQPNKNEISEGWTLMVERVQDQREISKSLHDQKPSIHFIWGAHNPGNSNNATFKLILLSKSLQSIKGISTYTEAFKSLGKMMDIGDKAIEYEEFCMSLKSKARSSWKQIMNKKLEPKQINNALVLWEQQFMINNDLIDKSEKLKLFKNFCGIGKKQFKNKMLEDSKPKILDFDDANMYLASLTMMEQSKKILSKSNGLKPDNFILNEFGSRIKDANKETYDNMHKIFETGYWQCISDFSTLMKNILSVSQYNRHNTFRIAMCANNNVFAIVFPSATVVYSIIVLHKEEENIFNPGCLHGTFKCMNGYISISRAIRLDKERCQRIVSSPGLFLTTCLLFKHDNPTLVMSDIMNFSIYTSLSITKSVLSLTEPARYMIMNSLAISSNVKDYIAEKFSPYTKTLFSVYMTRLIKNACFDAYDQRQRVQLRDIDYDITQKGIKDNRELTSIWFPGSVTLKEYLTQIYLPFYFNAKGLHEKHHVMVDLAKTILEIECEQRENIKEIWSTNCTKQTVNLKILIHSLCKNLLADTSRHNHLRNRIENRNNFRRSITTISTFTSSKSCLKIGDFRKEKELQSVKQKKILEVQSRKMRLANYEMLRNAMPNYTDYISTKVFDRLYELLDKKVLTDKPVIEQIMDMMIDHKKFYFTFFNEIFVGEYEAKMCMYAVERIAKERCKLNPDEMISEPGDGKLKVLEQKSEQEIRFLVETTRQKNREIDEAIEALLGKIEKLSLGKAKGLKMEINADMSKWSAQDVFYKYFWLIALDPILYPQEKERILYFMCNYMDKELILPDELLFNLLDQKVAYQNDIIATMTNQLNSNTVLIKRNWLQGNFNYTSSYVHSCAMSVYKEILKEAITLLDGSILVNSLVHSDDNQTSITIVQDKMENDKIIDFAMKEFERACLTFGCQANMKKTYVTNCIKEFVSLFNLYGEPFSIYGRFLLTSVGDCAYIGPYEDLASRISSAQTAIKHGCPPSLAWVSIAISHWMTSLTYNMLPGQSNDPIDYFPAENRKDIPIELNGVLDAPLSMISTVGLESGNLYFLIKLLSKYTPVMQKRESVVNQIAEVKNWKVEDLTDNEIFRLKILRYLVLDSILTPRKFTGSLRKLYSFSKYQDRLSSPGGMVELFTYLLEKPELLVTKGEDMKDYMESVIFRYNSKRFKESLSIQNPAQLFIEQILFSHKPVIDFSGIRDKYINILGKVTFTEAYRLLMRDLSSLELTNDDIQVIYSYIILNDPMMITIANTHILSIYGSPQRRMGMSCSTMPEFRNHHSPALVLRAYSNNPDIPTEMARDLVHLKEFVENTNLEEKMKVRIAMNEAEKGQRDIVFELKEMTRFYQVCYEYVKSTEHKIKVFILPAKSYTTTDFCSLMQGNLIKDKEWYTVHYLKQIL 1745
                                     9        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   ||  430   ||  443       453       463       473       483       493       503       513       523       533       543   ||  560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873||     900       910       920       930       940       959       969       979       989       999      1009      1019      1029||    1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1167      1177      1187      1197      1207      1217      1227      1237      1247      1257      1267      1277      1287      1297      1307      1317      1327      1337      1347      1357      1367      1377      1387      1397      1425      1437      1447      1457      1467      1477      1487      1497      1507      1517      1527  ||  1549      1559      1569      1579      1589      1599      1609     |1623      1634  ||  1648      1658      1668      1678      1688      1698      1708      1718      1728      1738       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 423|      434|                                                                                                          547|                                                                                                                                                       709|                                                                                                                                                              874|                                                      949|                                                                   1030|                                                                                                                                                                                                                                                                                                                                                                           1406|    1433|                                                                                          1530|                                                                    1615|       1631|   ||                                                                                                       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                  425       438                                                                                                           555                                                                                                                                                        713                                                                                                                                                               892                                                       959                                                                    1039                                                                                                                                                                                                                                                                                                                                                                            1425     1436                                                                                           1543                                                                     1620        1633   ||                                                                                                       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         1637|                                                                                                       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          1642                                                                                                       


Chain B from PDB  Type:RNA  Length:16
                                                 
                5amr B    1 UUGGUAGUACACUACU   16
                                    10      


Chain C from PDB  Type:RNA  Length:8
                                         
                5amr C    9 GCUACCAA   16
   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)

(no "SCOP Domain" information available for 5AMR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AMR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AMR)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

 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 5amr)
 
  Sites
(no "Sites" information available for 5amr)
 
  Cis Peptide Bonds
    His A:184 - Gly A:185   [ 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 ](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
  5amr
    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
  A5HC98_BUNLC | A5HC98
    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)
  2.7.7.48
    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
  A5HC98_BUNLC | A5HC98
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A5HC98_BUNLC | A5HC98: 2xi5 2xi7 5amq

(-) Related Entries Specified in the PDB File

5amq STRUCTURE OF THE LA CROSSE BUNYAVIRUS POLYMERASE IN COMPLEX WITH THE 3' AND 5' VIRAL RNA