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(-) Description

Title :  CRYSTAL STRUCTURE OF NOROVIRUS OIF P DOMAIN IN COMPLEX WITH LEWIS A TRISACCHARIDE
 
Authors :  W. Liu, Y. Chen, M. Tan, M. Xia, X. Li, X. Jiang, Z. Rao
Date :  18 Oct 14  (Deposition) - 24 Jun 15  (Release) - 04 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Mixed Alpha/Beta, Receptor Binding, Hbga, Virus Caspid, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Liu, Y. Chen, X. Jiang, M. Xia, Y. Yang, M. Tan, X. Li, Z. Rao
A Unique Human Norovirus Lineage With A Distinct Hbga Binding Interface.
Plos Pathog. V. 11 05025 2015
PubMed-ID: 26147716  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1005025

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PROTRUSION DOMAIN (UNP RESIDUES 220-527)
    Mutation: YES
    Organism Scientific: NOROVIRUS
    Organism Taxid: 286545
    Strain: OIF

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2GAL2Ligand/IonBETA-D-GALACTOSE
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:295 , TRP A:296 , SER A:354 , THR A:356 , SER A:357 , GLU A:358 , ASN A:392 , ASN A:394 , THR A:395 , ASP A:478 , HOH A:750 , HOH A:841 , ASP B:254 , ARG B:398BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 601 TO 603
2AC2SOFTWAREGLN A:466 , HOH A:946 , TRP B:296 , SER B:354 , THR B:356 , SER B:357 , ASN B:392 , ASN B:394 , THR B:395 , HOH B:767 , HOH B:877BINDING SITE FOR CHAIN B OF POLYSACCHARIDE RESIDUES 601 TO 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RM0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4RM0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RM0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RM0)

(-) Exons   (0, 0)

(no "Exon" information available for 4RM0)

(-) 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:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh..........eeeee..........................hhhhh..eeeee..........eeeeee........................eeeeeee.............eeeeee......hhhh.eeeeeeee.......eeeeeeeeee...................................eeeeeeeeee.eee....eeeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee....eee......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rm0 A 221 KTKPFTLPILTIGELTNSRFPAPIDQLYTSPNADVVVQPQNGRCSLDGELQGTTQLLTTAICSYRGMTSNPTRDYWDGHLLHLVHPNGATYDPTEDVPAPFGTQDFRGILYGVLTQNPRASGDEAANSQGVYISSTSEKFTPKLGTIGLHQVQGNIASNQQSKFTPVGIAVNGNTPFRQWELPNYSGALTLNTNLAPAVGPNFPGEQILFFRSNVPSVQGGQPIEIDCLIPQEWVSHFYQESAPSQSDVALVRYVNPDTGRTIFEAKLHRQGFITIAATGSNPVVVPPNGYFRFDSWVNQFYALAPM 527
                                   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       


Chain B from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhh..........eeeee..........................hhhhh..eeeee..........eeeeee........................eeeeeee.............eeeeee......hhhh.eeeeeeee.......eeeeeeeeee...................................eeeeeeeeee.eee....eeeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee....eee......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rm0 B 222 TKPFTLPILTIGELTNSRFPAPIDQLYTSPNADVVVQPQNGRCSLDGELQGTTQLLTTAICSYRGMTSNPTRDYWDGHLLHLVHPNGATYDPTEDVPAPFGTQDFRGILYGVLTQNPRASGDEAANSQGVYISSTSEKFTPKLGTIGLHQVQGNIASNQQSKFTPVGIAVNGNTPFRQWELPNYSGALTLNTNLAPAVGPNFPGEQILFFRSNVPSVQGGQPIEIDCLIPQEWVSHFYQESAPSQSDVALVRYVNPDTGRTIFEAKLHRQGFITIAATGSNPVVVPPNGYFRFDSWVNQFYALAPM 527
                                   231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521
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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 4RM0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RM0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RM0)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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 Related Entries

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

UniProtKB/TrEMBL
        Q6B7R3_9CALI | Q6B7R3: 4rlz

(-) Related Entries Specified in the PDB File

4rlz