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(-) Description

Title :  CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN SAGA4 IN COMPLEX WITH HBGA TYPE LEA (TRIGLYCAN)
 
Authors :  B. K. Singh, G. S. Hansman
Date :  20 Nov 14  (Deposition) - 17 Dec 14  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Viral Capsid Protein, 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 - VP1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: MBP-HTSHP
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: P DOMAIN (UNP RESIDUES 225-530)
    Organism Scientific: NOROVIRUS HU/GII-4/SAGA4/2006/JP
    Organism Taxid: 546981

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 19)

Asymmetric/Biological Unit (5, 19)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2EDO9Ligand/Ion1,2-ETHANEDIOL
3FUC2Ligand/IonALPHA-L-FUCOSE
4GAL2Ligand/IonBETA-D-GALACTOSE
5NDG2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:402 , TRP A:403 , PHE A:433 , ASP A:450 , HOH A:857 , HOH A:909binding site for residue EDO A 601
02AC2SOFTWARELEU A:272 , LEU A:273 , GLY A:274 , THR A:276 , HOH A:885binding site for residue EDO A 602
03AC3SOFTWAREPHE A:286 , ARG A:287 , LEU A:303 , ALA A:304 , LEU A:306 , HOH A:833binding site for residue EDO A 603
04AC4SOFTWAREGLN A:260 , TRP A:403 , VAL A:404 , LEU A:405 , HOH A:726binding site for residue EDO A 604
05AC5SOFTWAREGLN A:277 , LEU A:278 , HOH A:910 , HOH A:961 , HOH B:894binding site for residue ACT A 605
06AC6SOFTWARELEU A:486 , HIS A:505 , LEU A:507 , VAL A:508binding site for residue ACT A 606
07AC7SOFTWAREGLN B:402 , TRP B:403 , PHE B:433 , ASP B:450 , HOH B:851 , HOH B:899binding site for residue EDO B 601
08AC8SOFTWAREPHE B:286 , ARG B:287 , LEU B:303 , ALA B:304 , LEU B:306 , HOH B:819binding site for residue EDO B 602
09AC9SOFTWARELEU B:272 , LEU B:273 , GLY B:274 , THR B:276 , HOH B:875binding site for residue EDO B 603
10AD1SOFTWAREGLN B:260 , TRP B:403 , VAL B:404 , LEU B:405 , HOH B:723binding site for residue EDO B 604
11AD2SOFTWARELEU B:405 , PRO B:406 , SER B:407 , HOH B:709 , HOH B:812binding site for residue EDO B 605
12AD3SOFTWAREHOH A:889 , GLN B:277 , LEU B:278 , HOH B:908 , HOH B:954binding site for residue ACT B 606
13AD4SOFTWAREHIS B:505 , LEU B:507 , VAL B:508binding site for residue ACT B 607
14AD5SOFTWARESER A:343 , THR A:344 , ARG A:345 , ASP A:374 , SER B:442 , GLY B:443 , TYR B:444 , SER B:519 , HOH B:980binding site for Poly-Saccharide residues FUC A 607 through GAL A 609
15AD6SOFTWARESER A:442 , GLY A:443 , TYR A:444 , SER A:519 , FUC A:607 , HOH A:980 , SER B:343 , THR B:344 , ARG B:345 , ASP B:374 , SER B:442 , TYR B:444 , SER B:519 , HOH B:980binding site for Poly-Saccharide residues FUC B 608 through GAL B 610

(-) SS Bonds  (0, 0)

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

(-) 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 4WZL)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WZL)

(-) 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:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh..........eeeee..........................hhhhh..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
                 4wzl A 223 GSKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTTQLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGLLTQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDGSTTHRNEPQQWVLPSYSGRNVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLDCLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLVIPPNGYFRFDSWVNQFYTLAPM 530
                                   232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522        


Chain B from PDB  Type:PROTEIN  Length:308
                                                                                                                                                                                                                                                                                                                                                    
               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
                 4wzl B 223 GSKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTTQLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGLLTQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDGSTTHRNEPQQWVLPSYSGRNVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLDCLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLVIPPNGYFRFDSWVNQFYTLAPM 530
                                   232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522
   Legend:   → Mismatch (orange background)
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    → 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 4WZL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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 Related Entries

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

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        B5BTR7_9CALI | B5BTR7: 4wze 4wzk 4x06 4x07

(-) Related Entries Specified in the PDB File

4oox CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN SAGA4
4wze CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN SAGA4 IN COMPLEX WITH HBGA TYPE LEY (TETRAGLYCAN)
4wzk CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN SAGA4 IN COMPLEX WITH HBGA TYPE H2 (TRIGLYCAN)