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(-) Description

Title :  CRYSTAL STRUCTURE OF ROTAVIRUS SA11 VP1/RNA (UGUGACC)/MRNA 5'-CAP (M7GPPPG) COMPLEX
 
Authors :  X. Lu, S. C. Harrison, Y. J. Tao, J. T. Patton, M. L. Nibert
Date :  10 Sep 07  (Deposition) - 29 Jul 08  (Release) - 14 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,X
Keywords :  Viral Protein, Rna-Dependent Rna Polymerase, Single Subunit Polymerase Fold, Fingers, Palm, Thumb, Right Hand Configuration, Rna-Directed Rna Polymerase, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Lu, S. M. Mcdonald, M. A. Tortorici, Y. J. Tao, R. Vasquez-Del Carpio, M. L. Nibert, J. T. Patton, S. C. Harrison
Mechanism For Coordinated Rna Packaging And Genome Replication By Rotavirus Polymerase Vp1.
Structure V. 16 1678 2008
PubMed-ID: 19000820  |  Reference-DOI: 10.1016/J.STR.2008.09.006

(-) Compounds

Molecule 1 - RNA-DEPENDENT RNA POLYMERASE
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PCRBAC
    Expression System Strain: SF21
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: GENE 1
    Organism Scientific: SIMIAN ROTAVIRUS
    Organism Taxid: 10922
    Strain: SA11
 
Molecule 2 - RNA (5'-R(*UP*GP*UP*GP*AP*CP*C)-3')
    Chains: X
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AX

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:16 , ASP A:80 , TYR A:82 , SER A:137 , SER A:140 , HIS A:185 , TYR A:189 , GLY A:746 , ARG A:749BINDING SITE FOR RESIDUE GTP A 1201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R7W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R7W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R7W)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RDRP_DSRNA_REOPS50523 RdRp of Reoviridae dsRNA viruses catalytic domain profile.RDRP_ROTSP501-687  1A:501-687

(-) Exons   (0, 0)

(no "Exon" information available for 2R7W)

(-) 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:1073
 aligned with RDRP_ROTSP | O37061 from UniProtKB/Swiss-Prot  Length:1088

    Alignment length:1087
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011      1021      1031      1041      1051      1061      1071      1081       
          RDRP_ROTSP      2 GKYNLILSEYLSFIYNSQSAVQIPIYYSSNSELENRCIEFHSKCLENSKNGLSLRKLFVEYNDVIENATLLSILSYSYDKYNAVERKLVKYAKGKPLEADLTVNELDYENNKMTSELFPTAEEYTDSLMDPAILTSLSSNLNAVMFWLEKHENDVAEKLKVYKRRLDLFTIVASTINKYGVPRHNAKYRYEYDVMKDKPYYLVTWANSSIEMLMSVFSHDDYLIAKELIVLSYSNRSTLAKLVSSPMSILVALVDINGTFITNEELELEFSNKYVRAIVPDQTFDELNQMLDNMRKAGLVDIPKMIQDWLVDRSIEKFPLMAKIYSWSFHVGFRKQKMLDAALDQLKTEYTENVDDEMYREYTMLIRDEVVKMLEEPVKHDDHLLRDSELAGLLSMSSASNGESRQLKFGRKTIFSTKKNMHVMDDMANERYTPGIIPPVNVDKPIPLGRRDVPGRRTRIIFILPYEYFIAQHAVVEKMLIYAKHTREYAEFYSQSNQLLSYGDVTRFLSNNTMVLYTDVSQWDSSQHNTQPFRKGIIMGLDILANMTNDAKVLQTLNLYKQTQINLMDSYVQIPDGNVIKKIQYGAVASGEKQTKAANSIANLALIKTVLSRISNKHSFATKIIRVDGDDNYAVLQFNTEVTKQMIQDVSNDVRETYARMNAKVKALVSTVGIEIAKRYIAGGKIFFRAGINLLNNEKRGQSTQWDQAAILYSNYIVNRLRGFETDREFILTKIMQMTSVAITGSLRLFPSERVLTTNSTFKVFDSEDFIIEYGTTVDEVYIQRAFMSLSSQKSGIADEIAASSTFKNYVTRLSEQLLFSKNNIVSRGIALTEKAKLNSYAPISLEKRRAQISALLTMLQKPVTFKSSKITINDILRDIKPFFTVSDAHLPIQYQKFMPTLPDNVQYIIQCIGSRTYQIEDDGSKSAISRLISKYSVYKPSIEELYKVISLHENEIQLYLISLGIPKIDADTYVGSKIYSRDKYRILESYVYNLLSINYGCYQLFDFNSPDLEKLIRIPFKGKIPAVTFILHLYAKLEVINYAIKNGSWISLFCNYPKSEMIKLWKKMWNITSLRSPYTNANFFQE 1088
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------   ---RdRP_4-2r7wA01 A:25-748                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             -------------------------------------------------------------------------------Rotavirus_VP1-2r7wA02 A:828-878                    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..---.eeeeee..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhheeeeeeee......hhhhhhhhhh.............hhhhh..hhhhhh......hhhhh......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh....eeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.......hhhhhhhhhhhhhhh....hhhhhhhh.-----------..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...eeeeeeeeee..eeeeeeehhhhhhhhhh.................eeeeee.......eeee...hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhheeeeee....eeeeee........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee....hhhhhhhhhhhhhhhhhh.....eeeee...ee....eee..eee................hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhee....eeeeehhhhhhh..................hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eehhhhhhhhh..eeeeee.............hhhhhhhhhhhh............hhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.............hhhhhhhee......hhhhhhhhhhhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhh.ee...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RDRP_DSRNA_REO  PDB: A:501-687 UniProt: 501-687                                                                                                                                            ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2r7w A    2 GKYNLILSEYLSFIYNS---VQIPIYYSSNSELENRCIEFHSKCLENSKNGLSLRKLFVEYNDVIENATLLSILSYSYDKYNAVERKLVKYAKGKPLEADLTVNELDYENNKMTSELFPTAEEYTDSLMDPAILTSLSSNLNAVMFWLEKHENDVAEKLKVYKRRLDLFTIVASTINKYGVPRHNAKYRYEYDVMKDKPYYLVTWANSSIEMLMSVFSHDDYLIAKELIVLSYSNRSTLAKLVSSPMSILVALVDINGTFITNEELELEFSNKYVRAIVPDQTFDELNQMLDNMRKAGLVDIPKMIQDWLVDRSIEKFPLMAKIYSWSFHVGFRKQKMLDAALDQ-----------EMYREYTMLIRDEVVKMLEEPVKHDDHLLRDSELAGLLSMSSASNGESRQLKFGRKTIFSTKKNMHVMDDMANERYTPGIIPPVNVDKPIPLGRRDVPGRRTRIIFILPYEYFIAQHAVVEKMLIYAKHTREYAEFYSQSNQLLSYGDVTRFLSNNTMVLYTDVSQWDSSQHNTQPFRKGIIMGLDILANMTNDAKVLQTLNLYKQTQINLMDSYVQIPDGNVIKKIQYGAVASGEKQTKAANSIANLALIKTVLSRISNKHSFATKIIRVDGDDNYAVLQFNTEVTKQMIQDVSNDVRETYARMNAKVKALVSTVGIEIAKRYIAGGKIFFRAGINLLNNEKRGQSTQWDQAAILYSNYIVNRLRGFETDREFILTKIMQMTSVAITGSLRLFPSERVLTTNSTFKVFDSEDFIIEYGTTVDEVYIQRAFMSLSSQKSGIADEIAASSTFKNYVTRLSEQLLFSKNNIVSRGIALTEKAKLNSYAPISLEKRRAQISALLTMLQKPVTFKSSKITINDILRDIKPFFTVSDAHLPIQYQKFMPTLPDNVQYIIQCIGSRTYQIEDDGSKSAISRLISKYSVYKPSIEELYKVISLHENEIQLYLISLGIPKIDADTYVGSKIYSRDKYRILESYVYNLLSINYGCYQLFDFNSPDLEKLIRIPFKGKIPAVTFILHLYAKLEVINYAIKNGSWISLFCNYPKSEMIKLWKKMWNITSLRSPYTNANFFQE 1088
                                    11      |  -|       31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341    |    -      |361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011      1021      1031      1041      1051      1061      1071      1081       
                                           18  22                                                                                                                                                                                                                                                                                                                                 346         358                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          


Chain X from PDB  Type:RNA  Length:7
                                        
                2r7w X 1101 UGUGACC 1107
   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 2R7W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2R7W)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: RdRP (210)
(-)
Clan: no clan defined [family: Rotavirus_VP1] (7)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RDRP_ROTSP | O37061)
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.
    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: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.
cellular component
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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  2r7w
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 Related Entries

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

UniProtKB/Swiss-Prot
        RDRP_ROTSP | O37061: 2r7o 2r7q 2r7r 2r7s 2r7t 2r7u 2r7v 2r7x 4f5x

(-) Related Entries Specified in the PDB File

2r7o 2r7q 2r7r 2r7s 2r7t 2r7u 2r7v 2r7x