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(-) Description

Title :  POLIOVIRUS POLYMERASE ELONGATION COMPLEX (R3_FORM)
 
Authors :  P. Gong, O. B. Peersen
Date :  12 Apr 13  (Deposition) - 22 May 13  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Polymerase, Rna-Dependent Rna Polymerase, Protein-Rna Complex, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Gong, M. G. Kortus, J. C. Nix, R. E. Davis, O. B. Peersen
Structures Of Coxsackievirus, Rhinovirus, And Poliovirus Polymerase Elongation Complexes Solved By Engineering Rna Mediated Crystal Contacts.
Plos One V. 8 60272 2013
PubMed-ID: 23667424  |  Reference-DOI: 10.1371/JOURNAL.PONE.0060272

(-) Compounds

Molecule 1 - RNA-DIRECTED RNA POLYMERASE 3D-POL
    Chains: A, E
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1749-2209
    Mutation: YES
    Organism Scientific: HUMAN POLIOVIRUS 1
    Organism Taxid: 12081
    Strain: MAHONEY
    Synonym: GENOME POLYPROTEIN
 
Molecule 2 - RNA (5'- R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*CP*GP*AP*AP* A)-3')
    Chains: B, F
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - RNA (5'-R(*UP*GP*UP*UP*CP*GP*CP*GP*AP*GP*AP*GP*A)-3')
    Chains: C, G
    Engineered: YES
    Synthetic: YES
 
Molecule 4 - RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
    Chains: D, H
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:270 , HIS A:272 , CYS A:281 , ASP E:146BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREASP A:233 , TYR A:234 , THR A:235 , THR A:355BINDING SITE FOR RESIDUE GOL A 502
3AC3SOFTWAREASP A:233 , ASP A:329 , VAL A:330 , ASP A:358 , THR A:372 , HOH A:629BINDING SITE FOR RESIDUE GOL A 503
4AC4SOFTWAREASN A:132 , GLN A:134 , TYR A:313 , TYR A:334 , HIS A:336 , GLU A:337BINDING SITE FOR RESIDUE GOL A 504
5AC5SOFTWAREASP A:146 , HIS E:270 , HIS E:272 , CYS E:281BINDING SITE FOR RESIDUE ZN E 501
6AC6SOFTWAREASP E:233 , TYR E:234 , THR E:235 , THR E:355BINDING SITE FOR RESIDUE GOL E 502
7AC7SOFTWAREASN E:132 , GLN E:134 , TYR E:313 , ILE E:316 , TYR E:334 , HIS E:336 , GLU E:337BINDING SITE FOR RESIDUE GOL E 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K4S)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:118 -Pro A:119
2Tyr E:118 -Pro E:119

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K4S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K4S)

(-) Exons   (0, 0)

(no "Exon" information available for 4K4S)

(-) 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:462
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4k4sa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.................ee..........eee............hhhhhhhh..........hhhhhhhhhhhhhhhhh........hhhhhhhh...............hhhhhh.hhhhh.......hhhhhhhhhhhh....eeeee...eeehhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhh...........hhhhhh.hhhhhh..eee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeee..eeeeee........hhhhhhhhhhhhhhhhhhhhhh...hhhhheeeee..eeeeee....hhhhhhhhhhhh...eehhhhh................eeee.......eeee.hhhhhhhhhhee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4k4s A   1 GEIQWMRPSKEVGYPIINAPSKTKLEPSAFHYVFEGVKEPAVLTKNDPRLKTDFEEAIFSKYVGNKITEVDEYMKEAVDHYAGQLMSLDINTEQMCLEDAMYGTDGLEALDLSTSAGYPYVAMGKKKRDILNKQTRDTKEMQKLLDTYGINLPLVTYVKDELRSKTKVEQGKSRLIEASSLNDSVAMRMAFGNLYAAFHKNPGVITGSAVGCDPDLFWSKIPVLMEEKLFAFDYTGYDASLSPAWFEALKMVLEKIGFGDRVDYIDYLNHSHHLYKNKTYCVKGGMPSGCSGTSIFNSMINNLIIRTLLLKTYKGIDLDHLKMIAYGDDVIASYPHEVDASLLAQSGKDYGLTMTPADKSATFETVTWENVTFLKRFFRADEKYPFLIHPVMPMKEIHESIRWTKDPRNTQDHVRSLCLLAWHNGEEEYNKFLAKIRSVPIGRALDLPEYSTLYRRWLDSFG 462
                                    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
                                                 
                 4k4s B 595 UCCAGGUCUCUCGCGAA 611
                                   604       


Chain C from PDB  Type:RNA  Length:13
                                             
                 4k4s C 689 UGUUCGCGAGAGA 701
                                   698   


Chain D from PDB  Type:RNA  Length:4
                                    
                 4k4s D   1 GGAG   4


Chain E from PDB  Type:PROTEIN  Length:462
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4k4se_ E: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.................ee..........eee............hhhhhhhh..........hhhhhhhhhhhhhhhhh........hhhhhhhh...............hhhhhh.hhhhh.......hhhhhhhhhhhh....eeeee...eeehhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhh...........hhhhhh.hhhhhh..eee..ee.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhheeeeee..eeeeee........hhhhhhhhhhhhhhhhhhhhhh...hhhhheeeee..eeeeee....hhhhhhhhhhhh...eehhhhh................eeee.......eeee.hhhhhhhhhhee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4k4s E   1 GEIQWMRPSKEVGYPIINAPSKTKLEPSAFHYVFEGVKEPAVLTKNDPRLKTDFEEAIFSKYVGNKITEVDEYMKEAVDHYAGQLMSLDINTEQMCLEDAMYGTDGLEALDLSTSAGYPYVAMGKKKRDILNKQTRDTKEMQKLLDTYGINLPLVTYVKDELRSKTKVEQGKSRLIEASSLNDSVAMRMAFGNLYAAFHKNPGVITGSAVGCDPDLFWSKIPVLMEEKLFAFDYTGYDASLSPAWFEALKMVLEKIGFGDRVDYIDYLNHSHHLYKNKTYCVKGGMPSGCSGTSIFNSMINNLIIRTLLLKTYKGIDLDHLKMIAYGDDVIASYPHEVDASLLAQSGKDYGLTMTPADKSATFETVTWENVTFLKRFFRADEKYPFLIHPVMPMKEIHESIRWTKDPRNTQDHVRSLCLLAWHNGEEEYNKFLAKIRSVPIGRALDLPEYSTLYRRWLDSFG 462
                                    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
                                                 
                 4k4s F 595 UCCAGGUCUCUCGCGAA 611
                                   604       


Chain G from PDB  Type:RNA  Length:13
                                             
                 4k4s G 689 UGUUCGCGAGAGA 701
                                   698   


Chain H from PDB  Type:RNA  Length:3
                                   
                 4k4s H   1 GGA   3
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K4S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K4S)

(-) Gene Ontology  (48, 48)

Asymmetric Unit(hide GO term definitions)

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  POLG_POL1M | P03300
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 Related Entries

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

UniProtKB/Swiss-Prot
        POLG_POL1M | P03300: 1al2 1ar6 1ar7 1ar8 1ar9 1asj 1dgi 1fpt 1hxs 1l1n 1ng7 1nn8 1po1 1po2 1pov 1ra6 1ra7 1raj 1rdr 1tql 1vbd 1xyr 2bbl 2bbp 2ijd 2ijf 2ily 2ilz 2im0 2im1 2im2 2im3 2plv 3epc 3iyb 3iyc 3j3o 3j3p 3j48 3j8f 3j9f 3jbc 3jbd 3jbe 3jbf 3jbg 3ol7 4dcd 4k4t 4k4u 4k4v 4k4w 4nlo 4nlp 4nlq 4nlr 4nls 4nlt 4nlu 4nlv 4nlw 4nlx 4nly 4r0e 5ktz 5ku0 5ku2 5kwl

(-) Related Entries Specified in the PDB File

1ra6 3ol6 4k4t 4k4u 4k4v 4k4w 4k4x 4k4y 4k4z 4k50