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(-) Description

Title :  MURINE NOROVIRUS RDRP IN COMPLEX WITH PPNDS
 
Authors :  R. Croci, D. Tarantino, M. Milani, M. Pezzullo, M. Bolognesi, E. Mastra
Date :  19 Dec 13  (Deposition) - 05 Nov 14  (Release) - 05 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Rna-Dependent-Rna-Polymerase, Rna Binding, Viral Protein-Replication Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Croci, D. Tarantino, M. Milani, M. Pezzullo, J. Rohayem, M. Bolognesi, E. Mastrangelo
Ppnds Inhibits Murine Norovirus Rna-Dependent Rna-Polymeras Mimicking Two Rna Stacking Bases.
Febs Lett. V. 588 1720 2014
PubMed-ID: 24657439  |  Reference-DOI: 10.1016/J.FEBSLET.2014.03.021

(-) Compounds

Molecule 1 - RNA-DEPENDENT-RNA-POLYMERASE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1181-1687
    Organism Scientific: MURINE NOROVIRUS 1
    Organism Taxid: 223997
    Synonym: RDRP

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric Unit (2, 16)
No.NameCountTypeFull Name
120V6Ligand/Ion3-[(E)-{4-FORMYL-5-HYDROXY-6-METHYL-3-[(PHOSPHONOOXY)METHYL]PYRIDIN-2-YL}DIAZENYL]-7-NITRONAPHTHALENE-1,5-DISULFONIC ACID
2SO410Ligand/IonSULFATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
120V2Ligand/Ion3-[(E)-{4-FORMYL-5-HYDROXY-6-METHYL-3-[(PHOSPHONOOXY)METHYL]PYRIDIN-2-YL}DIAZENYL]-7-NITRONAPHTHALENE-1,5-DISULFONIC ACID
2SO46Ligand/IonSULFATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
120V2Ligand/Ion3-[(E)-{4-FORMYL-5-HYDROXY-6-METHYL-3-[(PHOSPHONOOXY)METHYL]PYRIDIN-2-YL}DIAZENYL]-7-NITRONAPHTHALENE-1,5-DISULFONIC ACID
2SO44Ligand/IonSULFATE ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
120V2Ligand/Ion3-[(E)-{4-FORMYL-5-HYDROXY-6-METHYL-3-[(PHOSPHONOOXY)METHYL]PYRIDIN-2-YL}DIAZENYL]-7-NITRONAPHTHALENE-1,5-DISULFONIC ACID
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:219 , MET A:221 , TYR A:341 , LEU A:391 , ARG A:392 , ARG A:393 , GLN A:414 , LYS A:419 , 20V A:602 , HOH A:718BINDING SITE FOR RESIDUE 20V A 601
02AC2SOFTWAREPHE A:29 , LYS A:166 , LEU A:169 , TYR A:341 , ARG A:392 , SER A:410 , ARG A:413 , GLN A:414 , LYS A:419 , 20V A:601 , HOH A:718 , HOH A:724 , HOH A:896BINDING SITE FOR RESIDUE 20V A 602
03AC3SOFTWAREGLY A:48 , SER A:49 , SER A:58 , LEU A:59 , HOH A:733 , HOH A:745 , HOH A:779BINDING SITE FOR RESIDUE SO4 A 603
04AC4SOFTWAREMET A:360 , ARG A:363 , HOH A:713BINDING SITE FOR RESIDUE SO4 A 604
05AC5SOFTWARETHR A:117 , LYS A:127 , MET A:192 , HOH A:771 , HOH A:773BINDING SITE FOR RESIDUE SO4 A 605
06AC6SOFTWAREGLN A:61 , ARG A:64BINDING SITE FOR RESIDUE SO4 A 606
07AC7SOFTWARELYS A:68 , SO4 A:608 , HOH A:937 , HOH A:958 , HOH A:968BINDING SITE FOR RESIDUE SO4 A 607
08AC8SOFTWARETHR A:8 , ALA A:10 , GLY A:11 , LYS A:68 , SO4 A:607 , HOH A:720 , HOH A:958BINDING SITE FOR RESIDUE SO4 A 608
09AC9SOFTWAREMET B:219 , MET B:221 , TYR B:341 , LEU B:391 , ARG B:392 , ARG B:393 , LEU B:406 , GLN B:414 , LYS B:419 , 20V B:602BINDING SITE FOR RESIDUE 20V B 601
10BC1SOFTWAREMET B:28 , PHE B:29 , LEU B:169 , TYR B:341 , ARG B:392 , SER B:410 , ARG B:413 , GLN B:414 , LYS B:419 , 20V B:601 , HOH B:724BINDING SITE FOR RESIDUE 20V B 602
11BC2SOFTWAREGLY B:48 , SER B:49 , SER B:58 , LEU B:59 , HOH B:762 , HOH B:774 , HOH B:782BINDING SITE FOR RESIDUE SO4 B 603
12BC3SOFTWARETHR B:8 , ALA B:10 , GLY B:11 , SO4 B:605BINDING SITE FOR RESIDUE SO4 B 604
13BC4SOFTWARESO4 B:604 , HOH B:701 , HOH B:936BINDING SITE FOR RESIDUE SO4 B 605
14BC5SOFTWAREASP B:407 , ARG B:408 , HIS B:450BINDING SITE FOR RESIDUE SO4 B 606
15BC6SOFTWAREMET C:219 , MET C:221 , TYR C:341 , LEU C:391 , ARG C:392 , ARG C:393 , GLN C:414 , LYS C:419 , 20V C:602 , HOH C:863BINDING SITE FOR RESIDUE 20V C 601
16BC7SOFTWAREPHE C:29 , LYS C:166 , LEU C:169 , TYR C:341 , ARG C:392 , SER C:410 , ARG C:413 , GLN C:414 , LYS C:419 , 20V C:601 , HOH C:720 , HOH C:795 , HOH C:893BINDING SITE FOR RESIDUE 20V C 602

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:302 -A:304

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Tyr A:121 -Pro A:122
2Cys A:302 -Pro A:303
3Arg A:371 -Ala A:372
4His A:433 -Ala A:434
5Tyr B:121 -Pro B:122
6Arg B:436 -Pro B:437
7Pro C:39 -Gly C:40
8Tyr C:121 -Pro C:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O4R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O4R)

(-) Exons   (0, 0)

(no "Exon" information available for 4O4R)

(-) 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:476
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..eeeeee.........eeeee...........ee.............hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh........hhhhhhhhh............hhhhhh.....hhhhhhhhhhhhhhhhh......eeeeee...ee.hhhhhh.....eeee.hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.eeee...eeeee.........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhheeeeee..eeeeee....hhhhhhhhhhhh...................ee..eeeee....eeeeehhhhhhhhhheeeeeee............hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o4r A   4 RPSGTYAGLPIADYGDAPPLSTKTMFWRTSPEKLPPGAWEPAYLGSKDERVDGPSLQQVMRDQLKPYSEPRGLLPPQEILDAVCDAIENRLENTLEPQKPWTFKKACESLDKNTSSGYPYHKQKSKDWTGSAFIGDLGDQATHANNMYEMGKSMRPIYTAALKDELVKPDKIYGKIKKRLLWGSDLGTMIRAARAFGPFCDALKETCIFNPIRVGMSMNEDGPFIFARHANFRYHMDADYTRWDSTQQRAILKRAGDIMVRLSPEPDLARVVMDDLLAPSLLDVGDYKIVVEEGLPSGCPCTTQLNSLAHWILTLCAMVEVTRVDPDIVMQESEFSFYGDDEVVSTNLELDMVKYTMALRRYGLLPTRADPLERRQTLQGISFLRRAIVGDQFGWYGRLDRASIDRQLLWTKGPNHQNPFETLPGHAQRPSQLMALLGEAAMHGEKYYRTVASRVSKEAAQVVPRHRSVLRWVRFG 488
                                    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|      387       397       407       417       427       437       447       457       467||     482      
                                                                                                                                                                                                                                                                                                                                                                                                           373|                                                                                       468|              
                                                                                                                                                                                                                                                                                                                                                                                                            378                                                                                        474              


Chain B from PDB  Type:PROTEIN  Length:480
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......ee..eeeeee.........eeeee...........ee.............hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh........hhhhhhhhh............hhhhhh.....hhhhhhhhhhhhhhhhh......eeeeee...ee.hhhhhh.....eeee.hhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhh..eee..ee..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.eeee...eeeee.........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhheeeeee..eeeeee....hhhhhhhhhhhh...ee.................ee..eeeeee..eeeeeehhhhhhhhhheeeeeee..........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4o4r B   2 LPRPSGTYAGLPIADYGDAPPLSTKTMFWRTSPEKLPPGAWEPAYLGSKDERVDGPSLQQVMRDQLKPYSEPRGLLPPQEILDAVCDAIENRLENTLEPQKPWTFKKACESLDKNTSSGYPYHKQKSKDWTGSAFIGDLGDQATHANNMYEMGKSMRPIYTAALKDELVKPDKIYGKIKKRLLWGSDLGTMIRAARAFGPFCDALKETCIFNPIRVGMSMNEDGPFIFARHANFRYHMDADYTRWDSTQQRAILKRAGDIMVRLSPEPDLARVVMDDLLAPSLLDVGDYKIVVEEGLPSGCPCTTQLNSLAHWILTLCAMVEVTRVDPDIVMQESEFSFYGDDEVVSTNLELDMVKYTMALRRYGLLPTRADKEGPLERRQTLQGISFLRRAIVGDQFGWYGRLDRASIDRQLLWTKGPNHQNPFETLPGRPSQLMALLGEAAMHGEKYYRTVASRVSKEAAQSGVVPRHRSVLRWVRFG 488
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371   ||  382       392       402       412       422       432|      445       455       465    || 478       488
                                                                                                                                                                                                                                                                                                                                                                                                               375|                                                    432|                               470|              
                                                                                                                                                                                                                                                                                                                                                                                                                377                                                     436                                474              


Chain C from PDB  Type:PROTEIN  Length:474
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee..eeeeee.........eeeee...........ee..hhhhh......hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh........hhhhhhhhh............hhhhhh.....hhhhhhhhhhhhhhhhhh.....eeeeee...eehhhhh.......eeee.hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh..eee..ee.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.eeee...eeeee.........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhheeeeee..eeeeee....hhhhhhhhhhhh...ee.............ee..eeeeee..eeeeeehhhhhhhhhheeeeeee............hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4o4r C   5 PSGTYAGLPIADYGDAPPLSTKTMFWRTSPEKLPPGAWEPAYLGSKDERVDGPSLQQVMRDQLKPYSEPRGLLPPQEILDAVCDAIENRLENTLEPQKPWTFKKACESLDKNTSSGYPYHKQKSKDWTGSAFIGDLGDQATHANNMYEMGKSMRPIYTAALKDELVKPDKIYGKIKKRLLWGSDLGTMIRAARAFGPFCDALKETCIFNPIRVGMSMNEDGPFIFARHANFRYHMDADYTRWDSTQQRAILKRAGDIMVRLSPEPDLARVVMDDLLAPSLLDVGDYKIVVEEGLPSGCPCTTQLNSLAHWILTLCAMVEVTRVDPDIVMQESEFSFYGDDEVVSTNLELDMVKYTMALRRYGLLPTRGPLERRQTLQGISFLRRAIVGDQFGWYGRLDRASIDRQLLWTKGPNHQNPFETLPGHAQRPSQLMALLGEAAMHGEKYYRTVASRVSKEAAQVVPRHRSVLRWVRFG 488
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364      |379       389       399       409       419       429       439       449       459       474       484    
                                                                                                                                                                                                                                                                                                                                                                                                        371|                                                                                        468|              
                                                                                                                                                                                                                                                                                                                                                                                                         377                                                                                         474
   Legend:   → Mismatch (orange background)
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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 4O4R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O4R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O4R)

(-) Gene Ontology  (18, 35)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        S4V9Y7_9CALI | S4V9Y7: 4nru
UniProtKB/TrEMBL
        Q80J95_9CALI | Q80J95: 2m4g 2mcd 2mch 3nah 3nai 3qid 3sfg 3sfu 3upf 3uqs 3ur0 4ash 4nru 4x2v 4x2w 4x2x 4x2y

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4O4R)