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(-) Description

Title :  STRUCTURAL CHARACTERIZATION OF A GII.4 2004 NOROVIRUS VARIANT (TCH05)
 
Authors :  S. Shanker, J-M. Choi, B. Sankaran, R. L. Atmar, Estes M. K. , Prasad B.
Date :  21 Jun 11  (Deposition) - 13 Jul 11  (Release) - 24 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Capsid Protein, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Shanker, J. M. Choi, B. Sankaran, R. L. Atmar, M. K. Estes, B. V. Prasa
Structural Analysis Of Histo-Blood Group Antigen Binding Specificity In A Norovirus Gii. 4 Epidemic Variant: Implications For Epochal Evolution.
J. Virol. V. 85 8635 2011
PubMed-ID: 21715503  |  Reference-DOI: 10.1128/JVI.00848-11

(-) Compounds

Molecule 1 - CAPSID
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-C2E
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PROTRUDING DOMAIN (UNP RESIDUES 221-531)
    Organism Scientific: NOROVIRUS HU/GII.4/2004/NL
    Organism Taxid: 311380

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric/Biological Unit (1, 7)
No.NameCountTypeFull Name
1ZN7Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:161 , HOH A:162 , HOH A:167 , HIS A:460 , HOH A:549BINDING SITE FOR RESIDUE ZN A 1
2AC2SOFTWAREHOH A:193BINDING SITE FOR RESIDUE ZN A 2
3AC3SOFTWAREHOH A:79 , HOH A:163 , HOH A:177 , ASP A:471 , VAL A:472 , HIS A:492BINDING SITE FOR RESIDUE ZN A 3
4AC4SOFTWAREHOH A:159 , HOH A:169 , GLU A:464 , HOH A:538BINDING SITE FOR RESIDUE ZN A 4
5AC5SOFTWAREHOH A:160 , HOH A:216 , HIS A:347 , ASP A:370BINDING SITE FOR RESIDUE ZN A 5
6AC6SOFTWAREHOH A:117 , HOH A:157 , HOH A:200 , HIS A:292BINDING SITE FOR RESIDUE ZN A 6
7AC7SOFTWAREARG A:339 , ASP A:341 , GLU A:376 , HIS A:414 , VAL A:416BINDING SITE FOR RESIDUE ZN A 7

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SJP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SJP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SJP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SJP)

(-) Exons   (0, 0)

(no "Exon" information available for 3SJP)

(-) 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:294
 aligned with Q5EGK8_9CALI | Q5EGK8 from UniProtKB/TrEMBL  Length:540

    Alignment length:311
                                   230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530 
         Q5EGK8_9CALI   221 ESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTTQLSPVNICTFRGDVTHIAGTQNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVLTQTTRRDGSTRGHKATVSTGSVHFTPKLGSVQFSTDTSNDFETGQNTRFTPVGVVQDGSTTHQNEPQQWVLPDYSGRDSHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMNLDCLLPQEWVQHFYQESAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLVIPPNGYFRFDSWVNQFYTLAPMG 531
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhh..........eeee...........................hhhhh..eeeeeee......eeeee.........................eeeeeeee.........eeeeeee......hhhh.eeeeee...........eeeeeeee..---------.............................eeeeeeee..--------..eee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee....ee.......eeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sjp A 221 ESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGALLGTTQLSPVDICTFRGDVTHIAGTQNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVLTQTTRRDGSTRGHKATVSTGSVHFTPKLGSVQFSTDTSNDFETGQNTRFTPVGVVQ---------PQQWVLPDYSGRDSHNVHLAPAVAPTFPGEQLLFFRSTM--------MNLDCLLPQEWVQHFYQESAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLVIPPNGYFRFDSWVNQFYTLAPMG 531
                                   230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       | -      |450       460       470       480       490       500       510       520       530 
                                                                                                                                                                                                   390       400                                   438      447
   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 3SJP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SJP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SJP)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5EGK8_9CALI | Q5EGK8)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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

UniProtKB/TrEMBL
        Q5EGK8_9CALI | Q5EGK8: 3sej 3skb 3sld 3sln

(-) Related Entries Specified in the PDB File

3sej 3skb 3sld 3sln