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(-) Description

Title :  CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN SAGA4
 
Authors :  B. K. Singh, G. S. Hansman
Date :  04 Feb 14  (Deposition) - 17 Dec 14  (Release) - 11 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
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
    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 225-530
    Gene: AB447457
    Organism Scientific: NOROVIRUS HU/GII-4/KUMAMOTO5/2006/JP
    Organism Taxid: 546987

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2EDO8Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 20)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2EDO16Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:277 , LEU A:278 , HOH A:801 , HOH A:884BINDING SITE FOR RESIDUE ACT A 601
02AC2SOFTWAREHIS A:505 , LEU A:507 , VAL A:508 , HOH A:875BINDING SITE FOR RESIDUE ACT A 602
03AC3SOFTWARELEU A:272 , LEU A:273 , GLY A:274 , THR A:276 , LEU A:321 , HOH A:841 , HOH A:867BINDING SITE FOR RESIDUE EDO A 603
04AC4SOFTWAREGLN A:260 , TRP A:403 , LEU A:405 , HOH A:734 , HOH A:760 , HOH A:865BINDING SITE FOR RESIDUE EDO A 604
05AC5SOFTWAREGLN A:402 , TRP A:403 , PHE A:433 , ASP A:450 , HOH A:794 , HOH A:985BINDING SITE FOR RESIDUE EDO A 605
06AC6SOFTWAREPHE A:286 , ARG A:287 , LEU A:303 , ALA A:304 , SER A:305 , LEU A:306 , PRO A:320 , HOH A:986BINDING SITE FOR RESIDUE EDO A 606
07AC7SOFTWAREASN A:298 , VAL A:351 , TYR A:352 , SER A:355 , GLN A:366 , PHE A:367 , SER A:368 , HOH A:725BINDING SITE FOR RESIDUE EDO A 607
08AC8SOFTWAREARG A:411 , HOH A:767BINDING SITE FOR RESIDUE EDO A 608
09AC9SOFTWARELYS A:225 , GLN A:463 , GLU A:464BINDING SITE FOR RESIDUE EDO A 609
10BC1SOFTWAREGLY A:354 , LEU A:405 , PRO A:406 , SER A:407 , PRO A:427 , HOH A:720 , HOH A:892BINDING SITE FOR RESIDUE EDO A 610

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:399 -Pro A:400

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OOX)

(-) 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:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh..........eeee...........................hhhhh..eeeeeee.....eeeeee.........................eeeeeeeee......eeeeeeeee......hhhh.eeeeee...........eeeeeeeee.......................................eeeeeeeee..eee.....eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee....ee.......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oox 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
   Legend:   → Mismatch (orange background)
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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 4OOX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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 Related Entries

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UniProtKB/TrEMBL
        B5BTT5_9CALI | B5BTT5: 4opo

(-) Related Entries Specified in the PDB File

4oov 4oox 4op7 4opo 4ops