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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MURINE NOROVIRUS NS6 PROTEASE (INACTIVE C139A MUTANT) WITH A C-TERMINAL EXTENSION TO INCLUDE RESIDUE P1 PRIME OF NS7
 
Authors :  H. Fernandes, E. N. Leen, S. Curry
Date :  27 Nov 14  (Deposition) - 18 Feb 15  (Release) - 18 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  Murine Norovirus Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Fernandes, E. N. Leen, H. Cromwell, M. P. Pfeil, S. Curry
Structure Determination Of Murine Norovirus Ns6 Proteases With C-Terminal Extensions Designed To Probe Protease-Substrate Interactions.
Peerj V. 3 E798 2015
PubMed-ID: 25755927  |  Reference-DOI: 10.7717/PEERJ.798
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NS6 PROTEASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PETM-11
    Expression System Taxid: 469008
    Expression System Variant: CODONPLUS
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 995-1178
    Mutation: YES
    Organism Scientific: MURINE NOROVIRUS 1
    Organism Taxid: 223997
 
Molecule 2 - NS6 PROTEASE
    Chains: E
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PETM-11
    Expression System Taxid: 469008
    Expression System Variant: CODONPLUS
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1174-1178
    Organism Scientific: MURINE NOROVIRUS 1
    Organism Taxid: 223997
 
Molecule 3 - NS6 PROTEASE
    Chains: F
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PETM-11
    Expression System Taxid: 469008
    Expression System Variant: CODONPLUS
    Expression System Vector Type: PLASMID
    Organism Scientific: MURINE NOROVIRUS 1
    Organism Taxid: 223997
    Strain: CW1

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    D  
Biological Unit 5 (1x):     E 
Biological Unit 6 (1x):      F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1IMD1Ligand/IonIMIDAZOLE
2UNK7Mod. Amino Acid
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1IMD-1Ligand/IonIMIDAZOLE
2UNK-1Mod. Amino Acid
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1IMD-1Ligand/IonIMIDAZOLE
2UNK-1Mod. Amino Acid
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1IMD-1Ligand/IonIMIDAZOLE
2UNK-1Mod. Amino Acid
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1IMD1Ligand/IonIMIDAZOLE
2UNK-1Mod. Amino Acid
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1IMD-1Ligand/IonIMIDAZOLE
2UNK-1Mod. Amino Acid
Biological Unit 6 (0, 0)
No.NameCountTypeFull Name
1IMD-1Ligand/IonIMIDAZOLE
2UNK-1Mod. Amino Acid

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:124 , SER A:125 , ARG B:100 , SER C:125 , ARG D:100binding site for residue IMD D 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4X2V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4X2V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X2V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X2V)

(-) Exons   (0, 0)

(no "Exon" information available for 4X2V)

(-) 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:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhh.eeee..eeeee....eeeee.hhh..............eeeeee..eeeeee...........ee........eeeeeee....eeeeeeeeeeeee..........eeeeee....................eeeeee..eeeeeeeeeee.....eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4x2v A   1 APVSIWSRVVQFGTGWGFWVSGHVFITAKHVAPPKGTEIFGRKPGDFTVTSSGDFLKYYFTSAVRPDIPAMVLENGCQEGVVASVLVKRASGEMLALAVRMGSQAAIKIGSAVVHGQTGMLLTGSNAKAQDLGTIPGDAGCPYVYKKGNTWVVIGVHVAATRSGNTVIAATHGE 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    


Chain B from PDB  Type:PROTEIN  Length:185
                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhh.eeee..eeeee....eeeee.hhh..............eeeeee..eeeeee...........ee........eeeeeee.....eeeeeeeeeeeeeeee..eeeeeeeeee....................eeeeee..eeeeeeeeeee.....eeeee.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x2v B   0 SAPVSIWSRVVQFGTGWGFWVSGHVFITAKHVAPPKGTEIFGRKPGDFTVTSSGDFLKYYFTSAVRPDIPAMVLENGCQEGVVASVLVKRASGEMLALAVRMGSQAAIKIGSAVVHGQTGMLLTGSNAKAQDLGTIPGDAGCPYVYKKGNTWVVIGVHVAATRSGNTVIAATHGEPTLEALEFQG 184
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179     


Chain C from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh.eeee..eeeee....eeeee.hhh..............eeeeee..eeeeee...........ee........eeeeeee....eeeeeeeeeeeeeeee....eeeeeeeee....................eeeeee..eeeeeeeeeee.....eeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x2v C   3 VSIWSRVVQFGTGWGFWVSGHVFITAKHVAPPKGTEIFGRKPGDFTVTSSGDFLKYYFTSAVRPDIPAMVLENGCQEGVVASVLVKRASGEMLALAVRMGSQAAIKIGSAVVHGQTGMLLTGSNAKAQDLGTIPGDAGCPYVYKKGNTWVVIGVHVAATRSGNTVIAATHGE 174
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172  


Chain D from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh.eeee..eeeee....eeeee.hhh..............eeeeee..eeeeee...........ee........eeeeeee.....eeeeeeeeeeeee........eeeeeee....................eeeeee..eeeeeeeeeee.....eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x2v D   3 VSIWSRVVQFGTGWGFWVSGHVFITAKHVAPPKGTEIFGRKPGDFTVTSSGDFLKYYFTSAVRPDIPAMVLENGCQEGVVASVLVKRASGEMLALAVRMGSQAAIKIGSAVVHGQTGMLLTGSNAKAQDLGTIPGDAGCPYVYKKGNTWVVIGVHVAATRSGNTVIAATHG 173
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172 


Chain E from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4x2v E 180 LEFQG 184


Chain F from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 4x2v F   1 xxxxxxx   7
                            |||||||
                            1-UNK||
                             2-UNK|
                              3-UNK
                               4-UNK
                                5-UNK
                                 6-UNK
                                  7-UNK
   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 4X2V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X2V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X2V)

(-) Gene Ontology  (18, 35)

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 Related Entries

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        Q80J95_9CALI | Q80J95: 2m4g 2mcd 2mch 3nah 3nai 3qid 3sfg 3sfu 3upf 3uqs 3ur0 4ash 4nru 4o4r 4x2w 4x2x 4x2y

(-) Related Entries Specified in the PDB File

4ash THIS ENTRY CONTAINS C TERMINAL EXTENSION TO INCLUDE RESIDUE P1PRIME OF NS7 IN ADDITION TO 4ASH
4x2w