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(-) Description

Title :  ENTEROVIRUS 71 POLYMERASE ELONGATION COMPLEX (C1S4 FORM)
 
Authors :  B. Shu, P. Gong
Date :  09 Dec 15  (Deposition) - 22 Jun 16  (Release) - 03 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.68
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Polymerase-Rna Complex, Elongation, Nucleotide Addition Cycle, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Shu, P. Gong
Structural Basis Of Viral Rna-Dependent Rna Polymerase Catalysis And Translocation
Proc. Natl. Acad. Sci. Usa V. 113 E4005 2016
PubMed-ID: 27339134  |  Reference-DOI: 10.1073/PNAS.1602591113

(-) Compounds

Molecule 1 - GENOME POLYPROTEIN
    Chains: A
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Taxid: 562
    Expression System Vector Type: BL21(DE3) PCG1
    Fragment: UNP RESIDUES 1732-2193
    Organism Scientific: ENTEROVIRUS A71
    Organism Taxid: 39054
 
Molecule 2 - RNA (35-MER)
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - RNA (5'- R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*GP*AP*C)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric/Biological Unit (5, 7)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG2Ligand/IonMAGNESIUM ION
3POP1Ligand/IonPYROPHOSPHATE 2-
4SO42Ligand/IonSULFATE ION
5ZN1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:233 , TYR A:234 , ASP A:329 , POP A:1007 , HOH A:1173 , C C:702binding site for residue MG A 1001
2AC2SOFTWAREASP A:233 , ASP A:329 , ASP A:330 , A C:701 , C C:702 , HOH C:806binding site for residue MG A 1002
3AC3SOFTWAREHIS A:271 , HIS A:273 , CYS A:282 , GLU A:343binding site for residue ZN A 1003
4AC4SOFTWAREARG A:163 , SER A:164 , LYS A:167 , HOH A:1127binding site for residue SO4 A 1004
5AC5SOFTWARECYS A:212 , ASN A:213 , THR A:216 , PHE A:217 , LYS A:220 , HOH A:1130binding site for residue SO4 A 1005
6AC6SOFTWAREGLY A:211 , CYS A:212 , TYR A:327 , LEU A:375 , ARG A:377 , U B:603 , C B:604 , G C:700binding site for residue GOL A 1006
7AC7SOFTWAREARG A:163 , ARG A:174 , TYR A:234 , GLY A:236 , TYR A:237 , ASP A:329 , MG A:1001 , HOH A:1102 , HOH A:1173 , C C:702binding site for residue POP A 1007

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F8J)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:118 -Pro A:119

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F8J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F8J)

(-) Exons   (0, 0)

(no "Exon" information available for 5F8J)

(-) 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:462
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee...eehhhhh............ee...........ee............hhhhhhhh..........hhhhhhhhhhhhhhhhh........hhhhhhhh......................hhhhh.......hhhhhhhhhhhh....eeeee...eehhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhheeeeee..eeeeee........hhhhhhhhhhhhhhhhhhhhhh...hhhhheeeee..eeeeee....hhhhhhhhhhhh...ee................ee..eeeee.......eeee.hhhhhhhhhhee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5f8j A   1 GEIQWVKPNKETGRLNINGPTRTKLEPSVFHDVFEGNKEPAVLHSKDPRLEVDFEQALFSKYVGNTLYEPDEYIKEAALHYANQLKQLDIDTSQMSMEEACYGTENLEAIDLHTSAGYPYSALGIKKRDILDSTTRDVSKMKFYMDKYGLDLPYSTYVKDELRSIDKIKKGKSRLIEASSLNDSVYLRMTFGHLYETFHANPGTVTGSAVGCNPDTFWSKLPILLPGSLFAFDYSGYDASLSPVWFRALELVLREIGYSEEAVSLVEGINHTHHVYRNKTYCVLGGMPSGCSGTSIFNSMINNIIIRALLIKTFKGIDLDELNMVAYGDDVLASYPFPIDCLELARTGKEYGLTMTPADKSPCFNEVNWDNATFLKRGFLPDEQFPFLIHPTMPMKEIHESIRWTKDARNTQDHVRSLCLLAWHNGKQEYEKFVSAIRSVPVGKALAIPNYENLRRNWLELF 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:12
                                            
                 5f8j B 599 GGUCUCUCUCGU 610
                                   608  


Chain C from PDB  Type:RNA  Length:11
                                           
                 5f8j C 692 ACGAGAGAGAC 702
                                   701
   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 5F8J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F8J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F8J)

(-) Gene Ontology  (36, 36)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Tyr A:118 - Pro A:119   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        E5RPG2_9ENTO | E5RPG2: 5f8h 5f8i 5f8l 5f8m 5f8n

(-) Related Entries Specified in the PDB File

5f8g 5f8h 5f8i 5f8l 5f8m 5f8n 5f8o