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(-) Description

Title :  CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN FARMINGTON HILLS 2004 IN COMPLEX WITH HBGA TYPE LEB (TETRAGLYCAN)
 
Authors :  B. K. Singh, M. Leuthold, G. S. Hansman
Date :  06 Feb 14  (Deposition) - 17 Dec 14  (Release) - 11 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Norovirus, Viral Capsid Protein, Histo Blood Group Antigen (Hbga), Protruding Domain, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. K. Singh, M. M. Leuthold, G. S. Hansman
Human Noroviruses' Fondness For Histo-Blood Group Antigens.
J. Virol. V. 89 2024 2015
PubMed-ID: 25428879  |  Reference-DOI: 10.1128/JVI.02968-14

(-) Compounds

Molecule 1 - MAJOR CAPSID PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MBP-HTSHP
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: P DOMAIN FARMINGTON HILLS 2004 (RESIDUES 225 TO 530)
    Gene: JQ478408
    Organism Scientific: NOROVIRUS HU/GII.4/FARMINGTON HILLS/2004/USA
    Organism Taxid: 1182143

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2GAL1Ligand/IonBETA-D-GALACTOSE
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:442 , GLY A:443 , SER B:343 , THR B:344 , ARG B:345 , ASP B:374 , GAL B:602 , NAG B:603 , FUC B:604 , HOH B:823BINDING SITE FOR RESIDUE FUC B 601
2AC2SOFTWAREASN A:310 , SER A:442 , FUC B:601 , NAG B:603 , FUC B:604BINDING SITE FOR RESIDUE GAL B 602
3AC3SOFTWAREASP A:289 , FUC B:601 , GAL B:602 , FUC B:604 , HOH B:863BINDING SITE FOR RESIDUE NAG B 603
4AC4SOFTWAREASP A:391 , GLY A:392 , GLY A:443 , HOH A:707 , FUC B:601 , GAL B:602 , NAG B:603BINDING SITE FOR RESIDUE FUC B 604

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:399 -Pro A:400
2Glu B:399 -Pro B:400

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OPS)

(-) 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:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhh..........eeeee.................................eeeeeee.....eeeeee.........................eeeeeeeee......eeeeeeeee......hhhh.eeeeee...........eeeeeeeee.......................................eeeeeeeee..eeee....eeee..hhhhhhhhhhhh......eeeeeeee....eeeeeeeee...eeeee....ee.......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ops A 225 KPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTTQLSPVNICTFRGDVTHIAGTHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGRIQGMLTQTTRGDGSTRGHKATVSTGDVHFTPKLGSIQFNTDTNNDFETGQNTKFTPVGVVQDGNGAHQNEPQQWVLPSYSGRTGHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMNLDCLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLVIPPNGYFRFDSWVNQFYTLAPM 530
                                   234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524      


Chain B from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhh..........eeee..................................eeeeeee.....eeeeee.........................eeeeeeeee......eeeeeeeee......hhhh.eeeeee...........eeeeeeeee.......................................eeeeeeeee..eeee....eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee....ee.......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ops B 225 KPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTTQLSPVNICTFRGDVTHIAGTHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGRIQGMLTQTTRGDGSTRGHKATVSTGDVHFTPKLGSIQFNTDTNNDFETGQNTKFTPVGVVQDGNGAHQNEPQQWVLPSYSGRTGHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMNLDCLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLVIPPNGYFRFDSWVNQFYTLAPM 530
                                   234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524
   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 4OPS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4OPS)

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 Related Entries

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UniProtKB/TrEMBL
        R4I4P2_9CALI | R4I4P2: 4oov 4opv 4x05

(-) Related Entries Specified in the PDB File

4oos
4oov CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN FARMINGTON HILLS 2004
4oox
4op7