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(-) Description

Title :  NV POLYMERASE POST-INCORPORATION-LIKE COMPLEX
 
Authors :  D. F. Zamyatkin, F. Parra, P. Grochulski, K. K. S. Ng
Date :  25 Jun 14  (Deposition) - 22 Apr 15  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Rna-Depedent Rna Polymerase, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Zamyatkin, C. Rao, E. Hoffarth, G. Jurca, H. Rho, F. Parra, P. Grochulski, K. K. Ng
Structure Of A Backtracked State Reveals Conformational Changes Similar To The State Following Nucleotide Incorporation In Human Norovirus Polymerase.
Acta Crystallogr. , Sect. D V. 70 3099 2014
PubMed-ID: 25478829  |  Reference-DOI: 10.1107/S1399004714021518

(-) Compounds

Molecule 1 - POLYPROTEIN
    Chains: A
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 331-838
    Organism Scientific: NORWALK VIRUS
    Organism Taxid: 11983
    Synonym: POLYPROTEIN
 
Molecule 2 - RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3')
    Chains: P
    Engineered: YES
    Other Details: RNA OLIGONUCLEOTIDE
    Synthetic: YES
 
Molecule 3 - RNA (5'-R(*U*AP*CP*CP*CP*GP*GP*G)-3')
    Chains: T
    Engineered: YES
    Other Details: RNA OLIGONUCLEOTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : APT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MN3Ligand/IonMANGANESE (II) ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:211 , THR A:212 , LEU A:213 , PRO A:214 , ARG A:216 , ARG A:231 , LEU A:337 , PHE A:338 , HOH A:742BINDING SITE FOR RESIDUE GOL A 601
2AC2SOFTWAREASP A:242 , ASP A:343 , ASP A:344 , MN A:603 , G P:7 , G P:8 , HOH P:219BINDING SITE FOR RESIDUE MN A 602
3AC3SOFTWAREASP A:242 , TYR A:243 , ASP A:343 , MN A:602 , HOH A:960 , G P:8BINDING SITE FOR RESIDUE MN A 603
4AC4SOFTWAREASP A:99 , GLU A:205 , HIS A:209BINDING SITE FOR RESIDUE MN A 604
5AC5SOFTWARELYS A:166 , HOH A:934 , G P:6 , G P:7 , HOH P:214 , HOH P:216 , HOH P:218 , C T:3 , C T:4 , C T:5BINDING SITE FOR RESIDUE GOL P 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His A:121 -Pro A:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QPX)

(-) 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:495
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..eeeeee.........eeeee...........ee..............hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh......hhhhhhhhh............hhhhhh.....hhhhhhhhhhhhhhhhhh.....eeeeee...ee.hhhhhh.....eeee.hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.eeee...eeeee.........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhheeeeee..eeeeee....hhhhhhhhhhhh...ee..................ee..eeeeee..eeeeeehhhhhhh...eeeeeee...........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhh.......hhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qpx A   4 SKGTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDPPDKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKTHCVTLPIRVGMNMNEDGPIIFERHSRYRYHYDADYSRWDSTQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELYVPRQEPMFRWMRFSDLSTWEGDRNLAPSFVN 505
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463  ||   480       490       500     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        466|                               
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         474                               


Chain P from PDB  Type:RNA  Length:8
                                        
                 4qpx P   1 UGCCCGGG   8


Chain T from PDB  Type:RNA  Length:7
                                       
                 4qpx T   2 ACCCGGG   8
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4QPX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    His A:121 - Pro A:122   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        Q70ET3_9CALI | Q70ET3: 1sh0 1sh2 1sh3 3bsn 3bso 3h5x 3h5y 5tsn

(-) Related Entries Specified in the PDB File

1sh0 NV POLYMERASE APOENZYME
3bso NV POLYMERASE PRE-INCORPORATION COMPLEX