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(-) Description

Title :  ATOMIC RESOLUTION STRUCTURAL CHARACTERIZATION OF RECOGNITION OF HISTO-BLOOD GROUP ANTIGENS BY NORWALK VIRUS
 
Authors :  J. M. Choi, A. M. Huston, M. K. Estes, B. V. V. Prasad
Date :  02 Apr 08  (Deposition) - 22 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Norovirus, Norwalk Virus, Hbga, Histo-Blood Group Antigen, Carbohydrate, Vp1, P-Domain, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Choi, A. M. Hutson, M. K. Estes, B. V. V. Prasad
Atomic Resolution Structural Characterization Of Recognition Of Histo-Blood Group Antigens By Norwalk Virus
Proc. Natl. Acad. Sci. Usa V. 105 9175 2008
PubMed-ID: 18599458  |  Reference-DOI: 10.1073/PNAS.0803275105
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 58 KD CAPSID PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHISMAL-C2ET
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Fragment: P-DOMAIN
    Gene: ORF2
    Organism Scientific: NORWALK VIRUS
    Strain: G.I

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 8)

Asymmetric/Biological Unit (6, 8)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CA1Ligand/IonCALCIUM ION
3FUC1Ligand/IonALPHA-L-FUCOSE
4GAL1Ligand/IonBETA-D-GALACTOSE
5MG2Ligand/IonMAGNESIUM ION
6NGA1Ligand/IonN-ACETYL-D-GALACTOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:380BINDING SITE FOR RESIDUE FUC B 1
2AC2SOFTWAREGLN B:342 , ASP B:344BINDING SITE FOR RESIDUE GAL B 2
3AC3SOFTWAREASP B:327 , HIS B:329 , TRP B:375 , SER B:377 , PRO B:378BINDING SITE FOR RESIDUE NGA B 3
4AC4SOFTWARETHR A:347 , THR A:348 , PRO A:349 , PHE A:352 , ASN A:394BINDING SITE FOR RESIDUE CA A 1
5AC5SOFTWAREPRO A:234 , LEU A:236 , TYR A:441 , PHE A:500BINDING SITE FOR RESIDUE MG A 519
6AC6SOFTWAREPRO B:234 , LEU B:236 , TYR B:441 , PHE B:501BINDING SITE FOR RESIDUE MG B 520
7AC7SOFTWARELEU A:248 , PRO A:249 , LYS B:289 , LEU B:304 , PHE B:335BINDING SITE FOR RESIDUE ACT B 521
8AC8SOFTWARELYS A:289 , LEU A:304 , PHE A:335 , LEU B:248 , PRO B:249BINDING SITE FOR RESIDUE ACT A 520

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZL7)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1His A:381 -Pro A:382
2His B:381 -Pro B:382
3Phe B:414 -Gly B:415

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZL7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZL7)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZL7)

(-) 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:285
 aligned with CAPSD_NVN68 | Q83884 from UniProtKB/Swiss-Prot  Length:530

    Alignment length:286
                                   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      
          CAPSD_NVN68   231 FTLPNLPLSSLSNSRAPLPISSMGISPDNVQSVQFQNGRCTLDGRLVGTTPVSLSHVAKIRGTSNGTVINLTELDGTPFHPFEGPAPIGFPDLGGCDWHINMTQFGHSSQTQYDVDTTPDTFVPHLGSIQANGIGSGNYVGVLSWISPPSHPSGSQVDLWKIPNYGSSITEATHLAPSVYPPGFGEVLVFFMSKMPGPGAYNLPCLLPQEYISHLASEQAPTVGEAALLHYVDPDTGRNLGEFKAYPDGFLTCVPNGASSGPQQLPINGVFVFVSWVSRFYQLKPV 516
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh..........eee............................hhhhh.eeeeee...eeee........hhhhh............eeeeeee.......eeeee.......hhhh.eee......eeeeeeeeeee.......................................eeeeeeeee.....eeeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeee......-hhhhh....eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zl7 A 231 FTLPNLPLSSLSNSRAPLPISSMGISPDNVQSVQFQNGRCTLDGRLVGTTPVSLSHVAKIRGTSNGTVINLTELDGTPFHPFEGPAPIGFPDLGGCDWHINMTQFGHSSQTQYDVDTTPDTFVPHLGSIQANGIGSGNYVGVLSWISPPSHPSGSQVDLWKIPNYGSSITEATHLAPSVYPPGFGEVLVFFMSKMPGPGAYNLPCLLPQEYISHLASEQAPTVGEAALLHYVDPDTGRNLGEFKAYPDGFLTCVPNGAS-GPQQLPINGVFVFVSWVSRFYQLKPV 515
                                   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        |-|      499       509      
                                                                                                                                                                                                                                                                                            489 |                         
                                                                                                                                                                                                                                                                                              490                         


Chain B from PDB  Type:PROTEIN  Length:286
 aligned with CAPSD_NVN68 | Q83884 from UniProtKB/Swiss-Prot  Length:530

    Alignment length:286
                                   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      
          CAPSD_NVN68   231 FTLPNLPLSSLSNSRAPLPISSMGISPDNVQSVQFQNGRCTLDGRLVGTTPVSLSHVAKIRGTSNGTVINLTELDGTPFHPFEGPAPIGFPDLGGCDWHINMTQFGHSSQTQYDVDTTPDTFVPHLGSIQANGIGSGNYVGVLSWISPPSHPSGSQVDLWKIPNYGSSITEATHLAPSVYPPGFGEVLVFFMSKMPGPGAYNLPCLLPQEYISHLASEQAPTVGEAALLHYVDPDTGRNLGEFKAYPDGFLTCVPNGASSGPQQLPINGVFVFVSWVSRFYQLKPV 516
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Calici_coat-2zl7B01 B:231-295                                    -----Calici_coat_C-2zl7B03 B:301-516                                                                                                                                                                                          Pfam domains (1)
           Pfam domains (2) Calici_coat-2zl7B02 B:231-295                                    -----Calici_coat_C-2zl7B04 B:301-516                                                                                                                                                                                          Pfam domains (2)
         Sec.struct. author ......hhhhh..........eee............................hhhhh.eeeeee...eeee........hhhhh............eeeeeee.......eeeee.......hhhh.eee......eeeeeeeeeee.......................................ee.eeeeee.....eeeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeee.......hhhhh....eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zl7 B 231 FTLPNLPLSSLSNSRAPLPISSMGISPDNVQSVQFQNGRCTLDGRLVGTTPVSLSHVAKIRGTSNGTVINLTELDGTPFHPFEGPAPIGFPDLGGCDWHINMTQFGHSSQTQYDVDTTPDTFVPHLGSIQANGIGSGNYVGVLSWISPPSHPSGSQVDLWKIPNYGSSITEATHLAPSVYPPGFGEVLVFFMSKMPGPGAYNLPCLLPQEYISHLASEQAPTVGEAALLHYVDPDTGRNLGEFKAYPDGFLTCVPNGASSGPQQLPINGVFVFVSWVSRFYQLKPV 516
                                   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
   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 2ZL7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZL7)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Viral_ssRNA_CP (106)
(-)
Clan: no clan defined [family: Calici_coat_C] (19)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CAPSD_NVN68 | Q83884)
cellular component
    GO:0039617    T=3 icosahedral viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=3 symmetry. The T=3 capsid is composed of 12 pentameric and 20 hexameric capsomeres.
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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  Cis Peptide Bonds
    His A:381 - Pro A:382   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        CAPSD_NVN68 | Q83884: 1ihm 2zl5 2zl6 3by1 3by2 3d26 5kw9 5n7m

(-) Related Entries Specified in the PDB File

2zl5 SAME P-DOMAIN
2zl6 SAME P-DOMAIN WITH H-TYPE HBGA