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(-) Description

Title :  POLIOVIRUS POLYMERASE ELONGATION COMPLEX WITH 2'-DEOXY-CTP
 
Authors :  P. Gong, O. B. Peersen
Date :  25 Aug 10  (Deposition) - 22 Dec 10  (Release) - 12 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Biol. Unit 3:  I,J,K,L  (1x)
Biol. Unit 4:  M,N,O,P  (1x)
Keywords :  Rna-Dependent Rna Polymerase, Elongation Complex, Virus, Protein-Rna Complex, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Gong, O. B. Peersen
Structural Basis For Active Site Closure By The Poliovirus Rna-Dependent Rna Polymerase.
Proc. Natl. Acad. Sci. Usa V. 107 22505 2010
PubMed-ID: 21148772  |  Reference-DOI: 10.1073/PNAS.1007626107

(-) Compounds

Molecule 1 - POLYMERASE
    Chains: A, E, I, M
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1749-2209
    Gene: 3D
    Mutation: YES
    Organism Scientific: HUMAN POLIOVIRUS 1
    Organism Taxid: 12080
    Strain: MAHONEY
 
Molecule 2 - RNA (5'- R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*CP*GP* GP*AP*AP*A)-3')
    Chains: B, F, J, N
    Engineered: YES
    Other Details: TEMPLATE RNA
    Other Details - Source: RNA PREPARED BY T7 RNA POLYMERASE TRANSCRIPTION FOLLOWED BY GLMS RIBOZYME SELF-CLEAVAGE
    Synthetic: YES
 
Molecule 3 - DNA/RNA (5'-R(*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)- D(P*C)-3')
    Chains: C, G
    Engineered: YES
    Other Details: PRODUCT RNA
    Other Details - Source: 5' PORTION WAS GENERATED BY CHEMICAL SYNTHESIS. THE 3'-PENTANUCLEOTIDE WAS ADDED TO THE RNA CHAIN BY POLIOVIRUS RNA- DEPENDENT RNA POLYMERASE
    Synthetic: YES
 
Molecule 4 - RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
    Chains: D, H, L, P
    Engineered: YES
    Other Details: NONTEMPLATE RNA
    Other Details - Source: RNA WAS PREPARED BY T7 RNA POLYMERASE TRANSCRIPTION FOLLOWED BY GLMS RIBOZYME SELF-CLEAVAGE
    Synthetic: YES
 
Molecule 5 - RNA (5'-R(*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
    Chains: K, O
    Engineered: YES
    Other Details: 5' PORTION WAS GENERATED BY CHEMICAL SYNTHESIS. THE 3'-TETRANUCLEOTIDE WAS ADDED TO THE RNA CHAIN BY POLIOVIRUS RNA- DEPENDENT RNA POLYMERASE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678910111213141516
Asymmetric Unit : ABCDEFGHIJKLMNOP
Biological Unit 1 (1x): ABCD            
Biological Unit 2 (1x):     EFGH        
Biological Unit 3 (1x):         IJKL    
Biological Unit 4 (1x):             MNOP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 21)

Asymmetric Unit (5, 21)
No.NameCountTypeFull Name
1DCP2Ligand/Ion2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
2GOL2Ligand/IonGLYCEROL
3IPA10Ligand/IonISOPROPYL ALCOHOL
4PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
5ZN4Ligand/IonZINC ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1DCP-1Ligand/Ion2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3IPA3Ligand/IonISOPROPYL ALCOHOL
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1DCP-1Ligand/Ion2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
2GOL-1Ligand/IonGLYCEROL
3IPA3Ligand/IonISOPROPYL ALCOHOL
4PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
5ZN-1Ligand/IonZINC ION
Biological Unit 3 (4, 5)
No.NameCountTypeFull Name
1DCP1Ligand/Ion2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3IPA2Ligand/IonISOPROPYL ALCOHOL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5ZN-1Ligand/IonZINC ION
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
1DCP1Ligand/Ion2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
2GOL-1Ligand/IonGLYCEROL
3IPA2Ligand/IonISOPROPYL ALCOHOL
4PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
5ZN-1Ligand/IonZINC ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS M:270 , HIS M:272 , CYS M:281 , HOH M:518BINDING SITE FOR RESIDUE ZN M 2001
02AC2SOFTWAREHIS I:270 , HIS I:272 , CYS I:281 , GOL I:8001BINDING SITE FOR RESIDUE ZN I 2002
03AC3SOFTWAREHIS E:270 , HIS E:272 , CYS E:281BINDING SITE FOR RESIDUE ZN E 2003
04AC4SOFTWAREHIS A:270 , HIS A:272 , CYS A:281 , GOL A:8002BINDING SITE FOR RESIDUE ZN A 2004
05AC5SOFTWARELYS M:159 , ARG M:174 , GLY M:236 , ASP M:238 , ASP M:328 , HOH M:505 , G N:600 , HOH O:296 , HOH O:493 , A O:701BINDING SITE FOR RESIDUE DCP O 4001
06AC6SOFTWAREARG I:174 , GLY I:236 , ASP I:238 , ASN I:297 , ASP I:328 , HOH I:537 , G J:600 , HOH K:301 , HOH K:489 , A K:701BINDING SITE FOR RESIDUE DCP K 4002
07AC7SOFTWAREPRO E:202 , ASP E:213 , PHE E:217BINDING SITE FOR RESIDUE IPA E 6007
08AC8SOFTWAREALA E:357 , SER E:360 , GLU E:364 , VAL E:366 , ASN E:370 , HOH E:568BINDING SITE FOR RESIDUE IPA E 6008
09AC9SOFTWAREGLU E:227 , LEU E:229 , VAL E:366 , THR E:367BINDING SITE FOR RESIDUE IPA E 6010
10BC1SOFTWAREPRO A:202 , CYS A:212 , ASP A:213 , PHE A:217BINDING SITE FOR RESIDUE IPA A 6013
11BC2SOFTWAREPRO I:202 , ASP I:213 , PHE I:217BINDING SITE FOR RESIDUE IPA I 6014
12BC3SOFTWAREGLU M:227 , LEU M:229 , VAL M:366 , THR M:367 , TRP M:368BINDING SITE FOR RESIDUE IPA M 6015
13BC4SOFTWAREGLU A:227 , LEU A:229 , VAL A:366BINDING SITE FOR RESIDUE IPA A 6016
14BC5SOFTWARETYR A:313 , TYR A:334 , HIS A:336BINDING SITE FOR RESIDUE IPA A 6017
15BC6SOFTWAREALA M:357 , SER M:360 , THR M:362 , GLU M:364 , VAL M:366 , ASN M:370BINDING SITE FOR RESIDUE IPA M 6028
16BC7SOFTWAREALA I:122 , G L:806 , A L:807BINDING SITE FOR RESIDUE IPA I 6029
17BC8SOFTWAREASP A:381 , GLU A:382 , LYS A:383 , HIS A:389 , TYR A:454BINDING SITE FOR RESIDUE PEG A 7001
18BC9SOFTWARELEU I:162 , SER I:400 , TRP I:403 , THR I:404 , LYS I:405 , ASN I:409 , HIS I:413 , HOH I:547 , A K:697 , G K:698 , A K:699BINDING SITE FOR RESIDUE PEG I 7002
19CC1SOFTWARELEU A:25 , SER A:400 , TRP A:403 , THR A:404 , LYS A:405 , ASP A:406 , ASN A:409 , HIS A:413 , HOH A:515 , A C:697 , G C:698 , A C:699BINDING SITE FOR RESIDUE PEG A 7003
20CC2SOFTWARETRP I:5 , HIS I:272 , ZN I:2002BINDING SITE FOR RESIDUE GOL I 8001
21CC3SOFTWARETRP A:5 , HIS A:270 , HIS A:272 , LYS A:283 , ZN A:2004BINDING SITE FOR RESIDUE GOL A 8002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OLA)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:118 -Pro A:119
2Tyr E:118 -Pro E:119
3Tyr I:118 -Pro I:119
4Tyr M:118 -Pro M:119

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OLA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OLA)

(-) Exons   (0, 0)

(no "Exon" information available for 3OLA)

(-) 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:461
 aligned with B3VQP5_9ENTO | B3VQP5 from UniProtKB/TrEMBL  Length:2209

    Alignment length:461
                                  1758      1768      1778      1788      1798      1808      1818      1828      1838      1848      1858      1868      1878      1888      1898      1908      1918      1928      1938      1948      1958      1968      1978      1988      1998      2008      2018      2028      2038      2048      2058      2068      2078      2088      2098      2108      2118      2128      2138      2148      2158      2168      2178      2188      2198      2208 
        B3VQP5_9ENTO   1749 GEIQWMRPSKEVGYPIINAPSKTKLEPSAFHYVFEGVKEPAVLTKNDPRLKTDFEEAIFSKYVGNKITEVDEYMKEAVDHYAGQLMSLDINTEQMCLEDAMYGTDGLEALDLSTSAGYPYVAMGKKKRDILNKQTRDTKEMQKLLDTYGINLPLVTYVKDELRSKTKVEQGKSRLIEASSLNDSVAMRMAFGNLYAAFHKNPGVITGSAVGCDPDLFWSKIPVLMEEKLFAFDYTGYDASLSPAWFEALKMVLEKIGFGDRVDYIDYLNHSHHLYKNKTYCVKGGMPSGCSGTSIFNSMINNLIIRTLLLKTYKGIDLDHLKMIAYGDDVIASYPHEVDASLLAQSGKDYGLTMTPADKSATFETVTWENVTFLKRFFRADEKYPFLIHPVMPMKEIHESIRWTKDPRNTQDHVRSLCLLAWHNGEEEYNKFLAKIRSVPIGRALLLPEYSTLYRRWLDSF 2209
               SCOP domains d3olaa_ A: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..hhhhhh............ee..........eee............hhhhhhh...........hhhhhhhhhhhhhhhhhhh......hhhhhhhh......................hhhhhh......hhhhhhhhhhhh....eeeee...eeehhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhh...........hhhhhh.........eee..ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhheeeee.....eeee........hhhhhhhhhhhhhhhhhhhhhh...hhhhheeeee..eeeeee....hhhhhhhhhhh....eehhhhh................eeee.......eeee.hhhhhhhhhhee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ola A    1 GEIQWMRPSKEVGYPIINAPSKTKLEPSAFHYVFEGVKEPAVLTKNDPRLKTDFEEAIFSKYVGNKITEVDEYMKEAVDHYAGQLMSLDINTEQMCLEDAMYGTDGLEALDLSTSAGYPYVAMGKKKRDILNKQTRDTKEMQKLLDTYGINLPLVTYVKDELRSKTKVEQGKSRLIEASSLNDSVAMRMAFGNLYAAFHKNPGVITGSAVGCDPDLFWSKIPVLMEEKLFAFDYTGYDASLSPAWFEALKMVLEKIGFGDRVDYIDYLNHSHHLYKNKTYCVKGGMPSGCSGTSIFNSMINNLIIRTLLLKTYKGIDLDHLKMIAYGDDVIASYPHEVDASLLAQSGKDYGLTMTPADKSATFETVTWENVTFLKRFFRADEKYPFLIHPVMPMKEIHESIRWTKDPRNTQDHVRSLCLLAWHNGEEEYNKFLAKIRSVPIGRALDLPEYSTLYRRWLDSF  461
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460 


Chain B from PDB  Type:RNA  Length:17
                                                  
                3ola B  596 CCAGGUCUCUCGUCCGG  612
                                   605       


Chain C from PDB  Type:DNA/RNA  Length:15
                                                
                3ola C  688 GCCCGGACGAGAGAC  702
                                   697     


Chain D from PDB  Type:RNA  Length:3
                                    
                3ola D  805 GGA  807


Chain E from PDB  Type:PROTEIN  Length:461
 aligned with B3VQP5_9ENTO | B3VQP5 from UniProtKB/TrEMBL  Length:2209

    Alignment length:461
                                  1758      1768      1778      1788      1798      1808      1818      1828      1838      1848      1858      1868      1878      1888      1898      1908      1918      1928      1938      1948      1958      1968      1978      1988      1998      2008      2018      2028      2038      2048      2058      2068      2078      2088      2098      2108      2118      2128      2138      2148      2158      2168      2178      2188      2198      2208 
        B3VQP5_9ENTO   1749 GEIQWMRPSKEVGYPIINAPSKTKLEPSAFHYVFEGVKEPAVLTKNDPRLKTDFEEAIFSKYVGNKITEVDEYMKEAVDHYAGQLMSLDINTEQMCLEDAMYGTDGLEALDLSTSAGYPYVAMGKKKRDILNKQTRDTKEMQKLLDTYGINLPLVTYVKDELRSKTKVEQGKSRLIEASSLNDSVAMRMAFGNLYAAFHKNPGVITGSAVGCDPDLFWSKIPVLMEEKLFAFDYTGYDASLSPAWFEALKMVLEKIGFGDRVDYIDYLNHSHHLYKNKTYCVKGGMPSGCSGTSIFNSMINNLIIRTLLLKTYKGIDLDHLKMIAYGDDVIASYPHEVDASLLAQSGKDYGLTMTPADKSATFETVTWENVTFLKRFFRADEKYPFLIHPVMPMKEIHESIRWTKDPRNTQDHVRSLCLLAWHNGEEEYNKFLAKIRSVPIGRALLLPEYSTLYRRWLDSF 2209
               SCOP domains d3olae_ E: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..hhhhhh............ee..........eee............hhhhhhh...........hhhhhhhhhhhhhhhhh........hhhhhhhh......................hhhhhh......hhhhhhhhhhhh....eeeee...eeehhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhh...........hhhhhh.........eee..ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhheeeee.....eeee........hhhhhhhhhhhhhhhhhhhhhh...hhhhheeeee..eeeeee....hhhhhhhhhhh....eehhhhh................eeee.......eeee.hhhhhhhhhhee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ola E    1 GEIQWMRPSKEVGYPIINAPSKTKLEPSAFHYVFEGVKEPAVLTKNDPRLKTDFEEAIFSKYVGNKITEVDEYMKEAVDHYAGQLMSLDINTEQMCLEDAMYGTDGLEALDLSTSAGYPYVAMGKKKRDILNKQTRDTKEMQKLLDTYGINLPLVTYVKDELRSKTKVEQGKSRLIEASSLNDSVAMRMAFGNLYAAFHKNPGVITGSAVGCDPDLFWSKIPVLMEEKLFAFDYTGYDASLSPAWFEALKMVLEKIGFGDRVDYIDYLNHSHHLYKNKTYCVKGGMPSGCSGTSIFNSMINNLIIRTLLLKTYKGIDLDHLKMIAYGDDVIASYPHEVDASLLAQSGKDYGLTMTPADKSATFETVTWENVTFLKRFFRADEKYPFLIHPVMPMKEIHESIRWTKDPRNTQDHVRSLCLLAWHNGEEEYNKFLAKIRSVPIGRALDLPEYSTLYRRWLDSF  461
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460 


Chain F from PDB  Type:RNA  Length:17
                                                  
                3ola F  596 CCAGGUCUCUCGUCCGG  612
                                   605       


Chain G from PDB  Type:DNA/RNA  Length:15
                                                
                3ola G  688 GCCCGGACGAGAGAC  702
                                   697     


Chain H from PDB  Type:RNA  Length:3
                                    
                3ola H  805 GGA  807


Chain I from PDB  Type:PROTEIN  Length:461
 aligned with B3VQP5_9ENTO | B3VQP5 from UniProtKB/TrEMBL  Length:2209

    Alignment length:461
                                  1758      1768      1778      1788      1798      1808      1818      1828      1838      1848      1858      1868      1878      1888      1898      1908      1918      1928      1938      1948      1958      1968      1978      1988      1998      2008      2018      2028      2038      2048      2058      2068      2078      2088      2098      2108      2118      2128      2138      2148      2158      2168      2178      2188      2198      2208 
        B3VQP5_9ENTO   1749 GEIQWMRPSKEVGYPIINAPSKTKLEPSAFHYVFEGVKEPAVLTKNDPRLKTDFEEAIFSKYVGNKITEVDEYMKEAVDHYAGQLMSLDINTEQMCLEDAMYGTDGLEALDLSTSAGYPYVAMGKKKRDILNKQTRDTKEMQKLLDTYGINLPLVTYVKDELRSKTKVEQGKSRLIEASSLNDSVAMRMAFGNLYAAFHKNPGVITGSAVGCDPDLFWSKIPVLMEEKLFAFDYTGYDASLSPAWFEALKMVLEKIGFGDRVDYIDYLNHSHHLYKNKTYCVKGGMPSGCSGTSIFNSMINNLIIRTLLLKTYKGIDLDHLKMIAYGDDVIASYPHEVDASLLAQSGKDYGLTMTPADKSATFETVTWENVTFLKRFFRADEKYPFLIHPVMPMKEIHESIRWTKDPRNTQDHVRSLCLLAWHNGEEEYNKFLAKIRSVPIGRALLLPEYSTLYRRWLDSF 2209
               SCOP domains d3olai_ I: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhh............ee...........ee............hhhhhhh...........hhhhhhhhhhhhhhhhh........hhhhhhhh...............hhhhhh.hhhhhh......hhhhhhhhhhhh....eeeee...ee.hhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhh...........hhhhhh.hhhhhh..eee.eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeee..eeeeee........hhhhhhhhhhhhhhhhhhhhh....hhhhheeeee..eeeeee....hhhhhhhhh......eee....................eeee.......eeee.hhhhhhhhhhee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ola I    1 GEIQWMRPSKEVGYPIINAPSKTKLEPSAFHYVFEGVKEPAVLTKNDPRLKTDFEEAIFSKYVGNKITEVDEYMKEAVDHYAGQLMSLDINTEQMCLEDAMYGTDGLEALDLSTSAGYPYVAMGKKKRDILNKQTRDTKEMQKLLDTYGINLPLVTYVKDELRSKTKVEQGKSRLIEASSLNDSVAMRMAFGNLYAAFHKNPGVITGSAVGCDPDLFWSKIPVLMEEKLFAFDYTGYDASLSPAWFEALKMVLEKIGFGDRVDYIDYLNHSHHLYKNKTYCVKGGMPSGCSGTSIFNSMINNLIIRTLLLKTYKGIDLDHLKMIAYGDDVIASYPHEVDASLLAQSGKDYGLTMTPADKSATFETVTWENVTFLKRFFRADEKYPFLIHPVMPMKEIHESIRWTKDPRNTQDHVRSLCLLAWHNGEEEYNKFLAKIRSVPIGRALDLPEYSTLYRRWLDSF  461
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460 


Chain J from PDB  Type:RNA  Length:18
                                                   
                3ola J  595 UCCAGGUCUCUCGUCCGG  612
                                   604        


Chain K from PDB  Type:RNA  Length:14
                                               
                3ola K  688 GCCCGGACGAGAGA  701
                                   697    


Chain L from PDB  Type:RNA  Length:4
                                     
                3ola L  805 GGAG  808


Chain M from PDB  Type:PROTEIN  Length:461
 aligned with B3VQP5_9ENTO | B3VQP5 from UniProtKB/TrEMBL  Length:2209

    Alignment length:461
                                  1758      1768      1778      1788      1798      1808      1818      1828      1838      1848      1858      1868      1878      1888      1898      1908      1918      1928      1938      1948      1958      1968      1978      1988      1998      2008      2018      2028      2038      2048      2058      2068      2078      2088      2098      2108      2118      2128      2138      2148      2158      2168      2178      2188      2198      2208 
        B3VQP5_9ENTO   1749 GEIQWMRPSKEVGYPIINAPSKTKLEPSAFHYVFEGVKEPAVLTKNDPRLKTDFEEAIFSKYVGNKITEVDEYMKEAVDHYAGQLMSLDINTEQMCLEDAMYGTDGLEALDLSTSAGYPYVAMGKKKRDILNKQTRDTKEMQKLLDTYGINLPLVTYVKDELRSKTKVEQGKSRLIEASSLNDSVAMRMAFGNLYAAFHKNPGVITGSAVGCDPDLFWSKIPVLMEEKLFAFDYTGYDASLSPAWFEALKMVLEKIGFGDRVDYIDYLNHSHHLYKNKTYCVKGGMPSGCSGTSIFNSMINNLIIRTLLLKTYKGIDLDHLKMIAYGDDVIASYPHEVDASLLAQSGKDYGLTMTPADKSATFETVTWENVTFLKRFFRADEKYPFLIHPVMPMKEIHESIRWTKDPRNTQDHVRSLCLLAWHNGEEEYNKFLAKIRSVPIGRALLLPEYSTLYRRWLDSF 2209
               SCOP domains d3olam_ M: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------RdRP_1-3olaM01 M:17-460                                                                                                                                                                                                                                                                                                                                                                                                                                     - Pfam domains (1)
           Pfam domains (2) ----------------RdRP_1-3olaM02 M:17-460                                                                                                                                                                                                                                                                                                                                                                                                                                     - Pfam domains (2)
           Pfam domains (3) ----------------RdRP_1-3olaM03 M:17-460                                                                                                                                                                                                                                                                                                                                                                                                                                     - Pfam domains (3)
           Pfam domains (4) ----------------RdRP_1-3olaM04 M:17-460                                                                                                                                                                                                                                                                                                                                                                                                                                     - Pfam domains (4)
         Sec.struct. author .eeeee.hhhhhh............ee...........ee............hhhhhhh...........hhhhhhhhhhhhhhhhh........hhhhhhhh...............hhhhhh.hhhhhh......hhhhhhhhhhhh....eeeee...ee.hhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhh...........hhhhhh.hhhhhh..eee.eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeee..eeeeee........hhhhhhhhhhhhhhhhhhhhh....hhhhheeeee..eeeeee....hhhhhhhhh......eee....................eeee.......eeee.hhhhhhhhhhee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ola M    1 GEIQWMRPSKEVGYPIINAPSKTKLEPSAFHYVFEGVKEPAVLTKNDPRLKTDFEEAIFSKYVGNKITEVDEYMKEAVDHYAGQLMSLDINTEQMCLEDAMYGTDGLEALDLSTSAGYPYVAMGKKKRDILNKQTRDTKEMQKLLDTYGINLPLVTYVKDELRSKTKVEQGKSRLIEASSLNDSVAMRMAFGNLYAAFHKNPGVITGSAVGCDPDLFWSKIPVLMEEKLFAFDYTGYDASLSPAWFEALKMVLEKIGFGDRVDYIDYLNHSHHLYKNKTYCVKGGMPSGCSGTSIFNSMINNLIIRTLLLKTYKGIDLDHLKMIAYGDDVIASYPHEVDASLLAQSGKDYGLTMTPADKSATFETVTWENVTFLKRFFRADEKYPFLIHPVMPMKEIHESIRWTKDPRNTQDHVRSLCLLAWHNGEEEYNKFLAKIRSVPIGRALDLPEYSTLYRRWLDSF  461
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460 


Chain N from PDB  Type:RNA  Length:18
                                                   
                3ola N  595 UCCAGGUCUCUCGUCCGG  612
                                   604        


Chain O from PDB  Type:RNA  Length:14
                                               
                3ola O  688 GCCCGGACGAGAGA  701
                                   697    


Chain P from PDB  Type:RNA  Length:4
                                     
                3ola P  805 GGAG  808
   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, 4)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OLA)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: RdRP (210)
(-)
Family: RdRP_1 (44)
(-)
Human poliovirus 1 (6)
1aRdRP_1-3olaM01M:17-460
1bRdRP_1-3olaM02M:17-460
1cRdRP_1-3olaM03M:17-460
1dRdRP_1-3olaM04M:17-460

(-) Gene Ontology  (37, 37)

Asymmetric Unit(hide GO term definitions)
Chain A,E,I,M   (B3VQP5_9ENTO | B3VQP5)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003724    RNA helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a RNA helix.
    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:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0005216    ion channel activity    Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0017111    nucleoside-triphosphatase activity    Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate.
    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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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.
    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:0018144    RNA-protein covalent cross-linking    The formation of a covalent cross-link between RNA and a protein.
    GO:0034220    ion transmembrane transport    A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0039707    pore formation by virus in membrane of host cell    The aggregation, arrangement and bonding together of a set of components by a virus to form a pore complex in a membrane of a host organism.
    GO:0051259    protein oligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    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:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0039694    viral RNA genome replication    The replication of a viral RNA genome.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    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.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0044161    host cell cytoplasmic vesicle    A vesicle formed of membrane or protein, found in the cytoplasm of a host cell.
    GO:0044162    host cell cytoplasmic vesicle membrane    The lipid bilayer surrounding a host cell cytoplasmic vesicle.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0044385    integral to membrane of host cell    Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane. Occurring in a host cell.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0019012    virion    The complete fully infectious extracellular virus particle.

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  3ola
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  B3VQP5_9ENTO | B3VQP5
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  2.7.7.48
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 Related Entries

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

UniProtKB/Swiss-Prot
        B3VQP5_9ENTO | B3VQP5: 3ol7
UniProtKB/TrEMBL
        B3VQP5_9ENTO | B3VQP5: 3ol6 3ol8 3ol9 3olb

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3OLA)