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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CAPSID P DOMAIN FROM NORWALK VIRUS STRAIN HIROSHIMA/1999 IN COMPLEX WITH HBGA TYPE B (TRIGLYCAN)
 
Authors :  G. S. Hansman, C. Biertumpfel, J. S. Mclellan, I. Georgiev, L. Chen, T. Z K. Katayama, P. D. Kwong
Date :  21 Mar 11  (Deposition) - 11 May 11  (Release) - 02 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Norovirus, P-Domain, Capsid, Receptor, Histo Blood Group Antigen (Hbga), Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. S. Hansman, C. Biertumpfel, I. Georgiev, J. S. Mclellan, L. Chen, T. Zhou, K. Katayama, P. D. Kwong
Crystal Structures Of Gii. 10 And Gii. 12 Norovirus Protrudin Domains In Complex With Histo-Blood Group Antigens Reveal Details For A Potential Site Of Vulnerability.
J. Virol. V. 85 6687 2011
PubMed-ID: 21525337  |  Reference-DOI: 10.1128/JVI.00246-11

(-) Compounds

Molecule 1 - VP1 PROTEIN
    Chains: A
    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: UNP RESIDUES 225-525
    Gene: CAPSID PROTEIN
    Organism Scientific: NORWALK-LIKE VIRUS
    Organism Taxid: 95340
    Strain: HIROSHIMA/1999/JP

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2FUC1Ligand/IonALPHA-L-FUCOSE
3GAL1Ligand/IonBETA-D-GALACTOSE
4GLA1Ligand/IonALPHA D-GALACTOSE
Biological Unit 1 (4, 10)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2FUC2Ligand/IonALPHA-L-FUCOSE
3GAL2Ligand/IonBETA-D-GALACTOSE
4GLA2Ligand/IonALPHA D-GALACTOSE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGAL A:2 , GLA A:3 , CYS A:345 , ARG A:346 , ASP A:375 , GLY A:438BINDING SITE FOR RESIDUE FUC A 1
2AC2SOFTWAREFUC A:1 , GLA A:3BINDING SITE FOR RESIDUE GAL A 2
3AC3SOFTWAREFUC A:1 , GAL A:2 , HIS A:348 , LYS A:436 , GLY A:437 , HOH A:536BINDING SITE FOR RESIDUE GLA A 3
4AC4SOFTWAREHOH A:89 , HOH A:134 , SER A:285 , PHE A:286 , THR A:306 , ASN A:307 , ILE A:308 , PRO A:322 , LEU A:323BINDING SITE FOR RESIDUE EDO A 526
5AC5SOFTWAREHOH A:8 , HOH A:27 , GLU A:451 , HIS A:455 , GLN A:458BINDING SITE FOR RESIDUE EDO A 527

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R6K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3R6K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R6K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R6K)

(-) Exons   (0, 0)

(no "Exon" information available for 3R6K)

(-) 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:301
 aligned with Q54AD6_9CALI | Q54AD6 from UniProtKB/TrEMBL  Length:535

    Alignment length:301
                                   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 
         Q54AD6_9CALI   225 KPFTLPILTIGELTNSRFPVPIDELYTSPNESLVVQPQNGRCALDGELQGTTQLLPTAICSFRGRINQKVSGENHVWNMQVTNINGTPFDPTEDVPAPLGTPDFSGKLFGVLSQRDHDNACRSHDAVIATNSAKFTPKLGAIQIGTWEEDDVHINQPTKFTPVGLFEDGGFNQWTLPNYSGALTLNMGLAPPVAPTFPGEQILFFRSHIPLKGGVADPVIDCLLPQEWIQHLYQESAPSQSDVALIRFTNPDTGRVLFEAKLHRSGYITVANTGSRPIVVPANGYFRFDSWVNQFYSLAPM 525
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Calici_coat-3r6kA01 A:225-291                                      -------------Calici_coat_C-3r6kA02 A:305-525                                                                                                                                                                                               Pfam domains
         Sec.struct. author ........hhhhh..........eeee..................................eeeeeeee......eeeeeee........................eeeeeeeee.....eeeeeeeee......hhhh.eeeeee..........eeeeeeeee..................................eeeeeeeee..........eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee....ee.......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r6k A 225 KPFTLPILTIGELTNSRFPVPIDELYTSPNESLVVQPQNGRCALDGELQGTTQLLPTAICSFRGRINQKVSGENHVWNMQVTNINGTPFDPTEDVPAPLGTPDFSGKLFGVLSQRDHDNACRSHDAVIATNSAKFTPKLGAIQIGTWEEDDVHINQPTKFTPVGLFEDGGFNQWTLPNYSGALTLNMGLAPPVAPTFPGEQILFFRSHIPLKGGVADPVIDCLLPQEWIQHLYQESAPSQSDVALIRFTNPDTGRVLFEAKLHRSGYITVANTGSRPIVVPANGYFRFDSWVNQFYSLAPM 525
                                   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
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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 3R6K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R6K)

(-) Pfam Domains  (2, 2)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3R6K)

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 Related Entries

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        Q54AD6_9CALI | Q54AD6: 3r6j

(-) Related Entries Specified in the PDB File

3onu 3ony 3pa1 3pa2 3q38 3q39 3q3a 3q6q 3q6r 3r6j