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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CAPSID P DOMAIN FROM NORWALK VIRUS STRAIN HIROSHIMA/1999
 
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 :  1.75
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  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:9 , HOH A:24 , LEU A:232 , GLU A:451 , HIS A:455BINDING SITE FOR RESIDUE EDO A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R6J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3R6J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R6J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R6J)

(-) Exons   (0, 0)

(no "Exon" information available for 3R6J)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:305
 aligned with Q54AD6_9CALI | Q54AD6 from UniProtKB/TrEMBL  Length:535

    Alignment length:336
                                   199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519      
         Q54AD6_9CALI   190 GSGDDVFTVSCRVLTRPSPDFDFNYLVPPTVESKTKPFTLPILTIGELTNSRFPVPIDELYTSPNESLVVQPQNGRCALDGELQGTTQLLPTAICSFRGRINQKVSGENHVWNMQVTNINGTPFDPTEDVPAPLGTPDFSGKLFGVLSQRDHDNACRSHDAVIATNSAKFTPKLGAIQIGTWEEDDVHINQPTKFTPVGLFEDGGFNQWTLPNYSGALTLNMGLAPPVAPTFPGEQILFFRSHIPLKGGVADPVIDCLLPQEWIQHLYQESAPSQSDVALIRFTNPDTGRVLFEAKLHRSGYITVANTGSRPIVVPANGYFRFDSWVNQFYSLAPM 525
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------------------------------Calici_coat-3r6jA01 A:225-291                                      -------------Calici_coat_C-3r6jA02 A:305-525                                                                                                                                                                                               Pfam domains
         Sec.struct. author ...-------------------------------.........hhhhh..........eeeee.................................eeeeeeee......eeeeeee........................eeeeeeeee.....eeeeeeeee......hhhh.eeeeee..........eeeeeeeee..................................eeeeeeeee..........eeee..hhhhhhhhhhhh......eeeeeeee....eeeeeeeee...eeeee....eee......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3r6j A 221 GPG-------------------------------SKPFTLPILTIGELTNSRFPVPIDELYTSPNESLVVQPQNGRCALDGELQGTTQLLPTAICSFRGRINQKVSGENHVWNMQVTNINGTPFDPTEDVPAPLGTPDFSGKLFGVLSQRDHDNACRSHDAVIATNSAKFTPKLGAIQIGTWEEDDVHINQPTKFTPVGLFEDGGFNQWTLPNYSGALTLNMGLAPPVAPTFPGEQILFFRSHIPLKGGVADPVIDCLLPQEWIQHLYQESAPSQSDVALIRFTNPDTGRVLFEAKLHRSGYITVANTGSRPIVVPANGYFRFDSWVNQFYSLAPM 525
                              |      -         -         -    |  229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519      
                              |                             224                                                                                                                                                                                                                                                                                                             
                            223
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  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 3R6J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R6J)

(-) 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)
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(-) Related Entries Specified in the PDB File

3onu 3ony 3pa1 3pa2 3q38 3q39 3q3a 3q6q 3q6r 3r6k