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(-) Description

Title :  COXSACKIEVIRUS B3 POLYMERASE ELONGATION COMPLEX (R2_FORM), RNA
 
Authors :  P. Gong, O. B. Peersen
Date :  12 Apr 13  (Deposition) - 22 May 13  (Release) - 20 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.37
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 :  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-DEPENDENT RNA POLYMERASE
    Chains: A, E, I, M
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1724-2185
    Organism Scientific: HUMAN COXSACKIEVIRUS B3
    Organism Taxid: 12072
 
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*GP*AP* AP*A)-3')
    Chains: B, F, J, N
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')
    Chains: C, G, K, O
    Engineered: YES
    Synthetic: YES
 
Molecule 4 - RNA (5'-R(P*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
    Chains: D, H, L, P
    Engineered: YES
    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  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:7 , HOH A:710 , PRO M:243 , PHE M:246 , ASP M:267 , CYS M:270 , ASN M:271 , ARG M:284BINDING SITE FOR RESIDUE GOL A 501
2AC2SOFTWAREPRO A:243 , ASP A:267 , ASN A:271 , ARG A:284 , HOH A:750 , GLU M:7 , HOH M:667BINDING SITE FOR RESIDUE GOL A 502
3AC3SOFTWAREASP A:233 , ASP A:330 , HOH A:616 , HOH A:730 , HOH A:756 , HOH A:757 , HOH A:759BINDING SITE FOR RESIDUE MG A 503
4AC4SOFTWAREPRO E:243 , ASP E:267 , CYS E:270 , ASN E:271 , ARG E:284 , HOH E:699 , GLU I:7 , HOH I:753BINDING SITE FOR RESIDUE GOL E 501
5AC5SOFTWAREASP E:330 , HOH E:615 , HOH E:621 , HOH E:703 , HOH E:704 , HOH E:719BINDING SITE FOR RESIDUE MG E 502
6AC6SOFTWAREGLU E:7 , ASP I:267 , ASN I:271 , ARG I:284 , HOH I:711BINDING SITE FOR RESIDUE GOL I 501
7AC7SOFTWAREASP I:330 , HOH I:631 , HOH I:684 , HOH I:732 , HOH I:733 , HOH I:751 , HOH I:752BINDING SITE FOR RESIDUE MG I 502
8AC8SOFTWAREASP M:330 , HOH M:634 , HOH M:697 , HOH M:732 , HOH M:745 , HOH M:751BINDING SITE FOR RESIDUE MG M 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K4X)

(-) 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 4K4X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K4X)

(-) Exons   (0, 0)

(no "Exon" information available for 4K4X)

(-) 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:463
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4k4xa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.................ee..........eee............hhhhhhhh..........hhhhhhhhhhhhhhhhh........hhhhhhhh...............hhhhh..hhhhh.......hhhhhhhhhhhh....eeeee...eeehhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh..eee.eee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhheeeeee..eeeeee........hhhhhhhhhhhhhhhhhhhhhh...hhhhheeeee..eeeeee....hhhhhhhhhhhh...eee.hhh................eeee.......eeee.hhhhhhhhhhee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k4x A   1 GEIEFIESSKDAGFPVINTPSKTKLEPSVFHQVFEGNKEPAVLRSGDPRLKANFEEAIFSKYIGNVNTHVDEYMLEAVDHYAGQLATLDISTEPMKLEDAVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKKTKDLTKLKECMDKYGLNLPMVTYVKDELRSIEKVAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHLNPGVVTGSAVGCDPDLFWSKIPVMLDGHLIAFDYSGYDASLSPVWFACLKMILEKLGYTHKETNYIDYLCNSHHLYRDKHYFVRGGMPSGCSGTSIFNSMINNIIIRTLMLKVYKGIDLDQFRMIAYGDDVIASYPWPIDASLLAEAGKGYGLIMTPADKGECFNEVTWTNVTFLKRYFRADEQYPFLVHPVMPMKDIHESIRWTKDPKNTQDHVRSLCLLAWHNGEHEYEEFIRKIRSVPVGRCLTLPAFSTLRRKWLDSFG 463
                                    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:16
                                                
                 4k4x B 597 CAGGUCUCUCGUCGAA 612
                                   606      


Chain C from PDB  Type:RNA  Length:13
                                             
                 4k4x C 689 GUUCGACGAGAGA 701
                                   698   


Chain D from PDB  Type:RNA  Length:2
                                  
                 4k4x D 804 GG 805


Chain E from PDB  Type:PROTEIN  Length:463
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4k4xe_ E: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.................ee..........eee............hhhhhhhh..........hhhhhhhhhhhhhhhhh........hhhhhhhh...............hhhhh..hhhhh.......hhhhhhhhhhhh....eeeee...eeehhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhh...........hhhhhh.hhhhhh..eee.eee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhheeeeee..eeeeee........hhhhhhhhhhhhhhhhhhhhhh...hhhhheeeee..eeeeee....hhhhhhhhhhhh...eee.hhh...........ee..eeeee.......eeee.hhhhhhhhhhee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k4x E   1 GEIEFIESSKDAGFPVINTPSKTKLEPSVFHQVFEGNKEPAVLRSGDPRLKANFEEAIFSKYIGNVNTHVDEYMLEAVDHYAGQLATLDISTEPMKLEDAVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKKTKDLTKLKECMDKYGLNLPMVTYVKDELRSIEKVAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHLNPGVVTGSAVGCDPDLFWSKIPVMLDGHLIAFDYSGYDASLSPVWFACLKMILEKLGYTHKETNYIDYLCNSHHLYRDKHYFVRGGMPSGCSGTSIFNSMINNIIIRTLMLKVYKGIDLDQFRMIAYGDDVIASYPWPIDASLLAEAGKGYGLIMTPADKGECFNEVTWTNVTFLKRYFRADEQYPFLVHPVMPMKDIHESIRWTKDPKNTQDHVRSLCLLAWHNGEHEYEEFIRKIRSVPVGRCLTLPAFSTLRRKWLDSFG 463
                                    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:16
                                                
                 4k4x F 597 CAGGUCUCUCGUCGAA 612
                                   606      


Chain G from PDB  Type:RNA  Length:13
                                             
                 4k4x G 689 GUUCGACGAGAGA 701
                                   698   


Chain H from PDB  Type:RNA  Length:2
                                  
                 4k4x H 804 GG 805


Chain I from PDB  Type:PROTEIN  Length:463
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4k4xi_ I: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.................ee..........eee............hhhhhhhh..........hhhhhhhhhhhhhhhhh........hhhhhhhh...............hhhhh..hhhhh.......hhhhhhhhhhhh....eeeee...eeehhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh..eee.eee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhheeeeee..eeeeee........hhhhhhhhhhhhhhhhhhhhhh...hhhhheeeee..eeeeee....hhhhhhhhhhhh...eee.hhh...........ee..eeeee.......eeee.hhhhhhhhhhee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k4x I   1 GEIEFIESSKDAGFPVINTPSKTKLEPSVFHQVFEGNKEPAVLRSGDPRLKANFEEAIFSKYIGNVNTHVDEYMLEAVDHYAGQLATLDISTEPMKLEDAVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKKTKDLTKLKECMDKYGLNLPMVTYVKDELRSIEKVAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHLNPGVVTGSAVGCDPDLFWSKIPVMLDGHLIAFDYSGYDASLSPVWFACLKMILEKLGYTHKETNYIDYLCNSHHLYRDKHYFVRGGMPSGCSGTSIFNSMINNIIIRTLMLKVYKGIDLDQFRMIAYGDDVIASYPWPIDASLLAEAGKGYGLIMTPADKGECFNEVTWTNVTFLKRYFRADEQYPFLVHPVMPMKDIHESIRWTKDPKNTQDHVRSLCLLAWHNGEHEYEEFIRKIRSVPVGRCLTLPAFSTLRRKWLDSFG 463
                                    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:16
                                                
                 4k4x J 597 CAGGUCUCUCGUCGAA 612
                                   606      


Chain K from PDB  Type:RNA  Length:13
                                             
                 4k4x K 689 GUUCGACGAGAGA 701
                                   698   


Chain L from PDB  Type:RNA  Length:2
                                  
                 4k4x L 804 GG 805


Chain M from PDB  Type:PROTEIN  Length:463
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4k4xm_ M: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.................ee..........eee............hhhhhhhh..........hhhhhhhhhhhhhhhhh........hhhhhhhh...............hhhhh..hhhhh.......hhhhhhhhhhhh....eeeee...eeehhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhh............hhhhhh.hhhhhh..eee.eee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhheeeeee..eeeeee........hhhhhhhhhhhhhhhhhhhhhh...hhhhheeeee..eeeeee....hhhhhhhhhhhh...eee.hhh...........ee..eeeee.......eeee.hhhhhhhhhhee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k4x M   1 GEIEFIESSKDAGFPVINTPSKTKLEPSVFHQVFEGNKEPAVLRSGDPRLKANFEEAIFSKYIGNVNTHVDEYMLEAVDHYAGQLATLDISTEPMKLEDAVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKKTKDLTKLKECMDKYGLNLPMVTYVKDELRSIEKVAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHLNPGVVTGSAVGCDPDLFWSKIPVMLDGHLIAFDYSGYDASLSPVWFACLKMILEKLGYTHKETNYIDYLCNSHHLYRDKHYFVRGGMPSGCSGTSIFNSMINNIIIRTLMLKVYKGIDLDQFRMIAYGDDVIASYPWPIDASLLAEAGKGYGLIMTPADKGECFNEVTWTNVTFLKRYFRADEQYPFLVHPVMPMKDIHESIRWTKDPKNTQDHVRSLCLLAWHNGEHEYEEFIRKIRSVPVGRCLTLPAFSTLRRKWLDSFG 463
                                    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:16
                                                
                 4k4x N 597 CAGGUCUCUCGUCGAA 612
                                   606      


Chain O from PDB  Type:RNA  Length:13
                                             
                 4k4x O 689 GUUCGACGAGAGA 701
                                   698   


Chain P from PDB  Type:RNA  Length:2
                                  
                 4k4x P 804 GG 805
   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 4K4X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K4X)

(-) Gene Ontology  (36, 72)

Asymmetric Unit(hide GO term definitions)

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  4k4x
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  Q5UEA2_9ENTO | Q5UEA2
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  Q66338_9ENTO | Q66338
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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
        Q66338_9ENTO | Q66338: 3ddk 4k4y 4k4z
UniProtKB/TrEMBL
        Q5UEA2_9ENTO | Q5UEA2: 3ddk 3zyd 3zye 3zz3 3zz4 3zz5 3zz6 3zz7 3zz8 3zz9 3zza 3zzb 3zzc 3zzd 4k4y 4k4z 4y34 4zp6 4zp7 4zp8 4zp9 4zpa 4zpb 4zpc 4zpd

(-) Related Entries Specified in the PDB File

3ddk 3ol6 4k4s 4k4t 4k4u 4k4v 4k4w 4k4y 4k4z 4k50