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(-) Description

Title :  CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN SAGA4 IN COMPLEX WITH HBGA TYPE LEB (TETRAGLYCAN)
 
Authors :  B. K. Singh, G. S. Hansman
Date :  06 Feb 14  (Deposition) - 17 Dec 14  (Release) - 11 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
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 - VP1
    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 SAGA4 (UNP RESIDUES 225-530)
    Gene: AB447457
    Organism Scientific: NOROVIRUS HU/GII-4/KUMAMOTO5/2006/JP
    Organism Taxid: 546987

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric/Biological Unit (5, 15)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3FUC4Ligand/IonALPHA-L-FUCOSE
4GAL2Ligand/IonBETA-D-GALACTOSE
5NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:505 , LEU A:507 , VAL A:508 , MET A:530BINDING SITE FOR RESIDUE ACT A 601
02AC2SOFTWARETHR A:267 , ASP A:269 , VAL A:271 , LYS A:493 , EDO A:603 , HOH A:834 , HOH A:955 , HOH A:969BINDING SITE FOR RESIDUE EDO A 602
03AC3SOFTWARETHR A:267 , LYS A:493 , SER A:494 , EDO A:602 , HOH A:870 , HOH A:955BINDING SITE FOR RESIDUE EDO A 603
04AC4SOFTWAREHIS B:505 , LEU B:507 , VAL B:508 , HOH B:907BINDING SITE FOR RESIDUE ACT B 601
05AC5SOFTWARELEU B:272 , LEU B:273 , GLY B:274 , THR B:276 , LEU B:321 , HOH B:1036 , HOH B:1067BINDING SITE FOR RESIDUE EDO B 602
06AC6SOFTWAREGLU A:235 , GLU A:236 , HOH A:1003 , GLN B:277 , LEU B:278 , LEU B:306 , HOH B:784BINDING SITE FOR RESIDUE EDO B 603
07AC7SOFTWAREHOH A:922 , HOH A:1082 , GLN B:260 , TRP B:403 , VAL B:404 , LEU B:405BINDING SITE FOR RESIDUE EDO B 604
08AC8SOFTWAREGLN B:390 , ASP B:391 , GLY B:392 , SER B:393 , GLY B:443 , NAG B:606 , GAL B:607 , HOH B:1125BINDING SITE FOR RESIDUE FUC B 605
09AC9SOFTWAREGLY B:392 , FUC B:605 , GAL B:607 , FUC B:608 , HOH B:888 , HOH B:939 , HOH B:940 , HOH B:944 , HOH B:960BINDING SITE FOR RESIDUE NAG B 606
10BC1SOFTWARESER B:442 , TRP B:520 , FUC B:605 , NAG B:606 , FUC B:608 , HOH B:931 , HOH B:941 , HOH B:942 , HOH B:1125BINDING SITE FOR RESIDUE GAL B 607
11BC2SOFTWARESER A:343 , THR A:344 , ARG A:345 , ASP A:374 , SER B:442 , GLY B:443 , NAG B:606 , GAL B:607 , HOH B:764 , HOH B:1124BINDING SITE FOR RESIDUE FUC B 608
12BC3SOFTWAREGLN A:390 , ASP A:391 , GLY A:392 , SER A:442 , SER A:519 , HOH A:901 , HOH A:916 , HOH A:917 , NAG B:610 , GAL B:611BINDING SITE FOR RESIDUE FUC B 609
13BC4SOFTWAREFUC B:609 , GAL B:611 , FUC B:612 , HOH B:886 , HOH B:938BINDING SITE FOR RESIDUE NAG B 610
14BC5SOFTWARESER A:442 , HOH A:1006 , FUC B:609 , NAG B:610 , FUC B:612 , HOH B:886 , HOH B:945 , HOH B:1039BINDING SITE FOR RESIDUE GAL B 611
15BC6SOFTWARESER A:442 , GLY A:443 , THR B:344 , ARG B:345 , ASP B:374 , NAG B:610 , GAL B:611 , HOH B:1006 , HOH B:1074BINDING SITE FOR RESIDUE FUC B 612

(-) SS Bonds  (0, 0)

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

(-) 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 4OPO)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OPO)

(-) 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:309
                                                                                                                                                                                                                                                                                                                                                     
               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
                 4opo A 222 TGSKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTTQLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGLLTQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDGSTTHRNEPQQWVLPSYSGRNVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLDCLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLVIPPNGYFRFDSWVNQFYTLAPM 530
                                   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         


Chain B from PDB  Type:PROTEIN  Length:307
                                                                                                                                                                                                                                                                                                                                                   
               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
                 4opo B 224 SKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTTQLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGLLTQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDGSTTHRNEPQQWVLPSYSGRNVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLDCLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLVIPPNGYFRFDSWVNQFYTLAPM 530
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 4OPO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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 Related Entries

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        B5BTT5_9CALI | B5BTT5: 4oox

(-) Related Entries Specified in the PDB File

4oos
4oov
4oox CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN SAGA4
4op7
4ops