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(-) Description

Title :  PROTRUDING DOMAIN OF GII.4 HUMAN NOROVIRUS CHDC2094 IN COMPLEX WITH HBGA TYPE A (TRIGLYCAN)
 
Authors :  B. K. Singh, G. S. Hansman
Date :  24 Mar 16  (Deposition) - 05 Apr 17  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.27
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Norovirus, Virus Capsid, Protruding Domain, Hbga, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. K. Singh, G. S. Hansman
Four Decades Of Structural Evolution Of Gii. 4 Norovirus
To Be Published
PubMed: search

(-) 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/CHDC2094/1974/US
    Organism Taxid: 660656

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 14)

Asymmetric/Biological Unit (5, 14)
No.NameCountTypeFull Name
1A2G2Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2EDO7Ligand/Ion1,2-ETHANEDIOL
3FLC1Ligand/IonCITRATE ANION
4FUC2Ligand/IonALPHA-L-FUCOSE
5GLA2Ligand/IonALPHA D-GALACTOSE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:504 , MET A:529 , HOH A:716 , ASN B:309 , ASN B:310binding site for residue EDO A 601
02AC2SOFTWARETHR A:233 , VAL A:234 , GLU A:235 , PHE A:476 , ILE A:508 , PRO A:509 , PRO A:510 , GLY A:512 , HOH A:704 , HOH A:723binding site for residue EDO A 602
03AC3SOFTWARELEU A:272 , LEU A:273 , GLY A:274 , THR A:276 , LEU A:321 , HOH A:725 , HOH A:850binding site for residue EDO A 603
04AC4SOFTWARELEU A:272 , LEU A:278 , LEU A:321 , HOH A:949 , GLU B:236binding site for residue EDO A 604
05AC5SOFTWARESER A:279 , ALA A:280 , GLN A:454 , HOH A:744 , SER B:279 , ALA B:280 , GLN B:454 , HOH B:752binding site for residue EDO A 605
06AC6SOFTWARELEU A:485 , PHE A:486 , TYR A:504 , LEU A:506 , VAL A:507 , HOH A:748binding site for residue EDO A 606
07AC7SOFTWARESER B:355 , VAL B:356 , HIS B:357 , HIS B:394 , ASN B:397 , HOH B:713 , HOH B:956binding site for residue FLC B 601
08AC8SOFTWARELEU B:272 , LEU B:273 , GLY B:274 , THR B:276 , LEU B:321 , HOH B:797binding site for residue EDO B 602
09AC9SOFTWARESER A:343 , THR A:344 , ARG A:345 , HIS A:347 , ASP A:374 , HOH A:707 , HOH A:727 , HOH A:739 , HOH A:827 , HOH A:920 , HOH A:985 , HOH A:994 , SER B:441 , GLY B:442binding site for Poly-Saccharide residues FUC A 607 through A2G A 609
10AD1SOFTWARELEU A:272 , LEU A:273 , GLY A:274 , THR A:276 , LEU A:278 , SER A:279 , ALA A:280 , LEU A:321 , HIS A:347 , LYS A:348 , ASP A:374 , SER A:441 , GLY A:442 , GLN A:454 , FUC A:607 , HOH A:707 , HOH A:725 , HOH A:727 , HOH A:739 , HOH A:744 , HOH A:827 , HOH A:850 , HOH A:920 , HOH A:949 , GLU B:236 , SER B:279 , ALA B:280 , SER B:343 , THR B:344 , ARG B:345 , HIS B:347 , ASP B:374 , SER B:441 , GLN B:454 , HOH B:701 , HOH B:752 , HOH B:803 , HOH B:928 , HOH B:975binding site for Poly-Saccharide residues FUC B 603 through A2G B 605

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5IYP)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:398 -Pro A:399
2Glu B:398 -Pro B:399

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IYP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IYP)

(-) Exons   (0, 0)

(no "Exon" information available for 5IYP)

(-) 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:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhh...........eeee............................hhh...eeeeeee.....eeeeee.........................eeeeeeeee......eeeeeeeee.......hhh.eeeee............eeeeeeeee.................hhh................eeeeeeeee.eeee.....eeee...hhhhhhhhhh.......eeeeeeee....eeeeeeeee...eeeee.............eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iyp A 225 KPFTVPILTVEEMSNSRFPIPLEKLYTGPSSAFVVQPQNGRCTTDGVLLGTTQLSAVNICNFRGDVTRVGISHDYTMNLVSQNWNNYDPTEEIPAPLGTPDFVGKIQGLLTQTTRADGSTRAHKATVSTGSVHFTPKLGSVQFTTDTNNDFQTGQNTKFTPVGVIQDGHQNEPQQWVLPNYSGTSGHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMNLDCLLPQEWVSHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYITVAHTGPYDLVIPPNGYFRFDSWVNQFYTLAPM 529
                                   234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       396       406       416       426       436       446       456       466       476       486       496       506       516       526   
                                                                                                                                                                                                 392|                                                                                                                                      
                                                                                                                                                                                                  395                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhh...........eeee............................hhh...eeeeeee.....eeeeee.........................eeeeeeeee......eeeeeeeee.......hhh.eeeee............eeeeeeeee......................................eeeeeeeee.eeee.....eeee...hhhhhhhhhh.......eeeeeee......eeeeeeee...eeeee.............eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5iyp B 224 SKPFTVPILTVEEMSNSRFPIPLEKLYTGPSSAFVVQPQNGRCTTDGVLLGTTQLSAVNICNFRGDVTRVGISHDYTMNLVSQNWNNYDPTEEIPAPLGTPDFVGKIQGLLTQTTRADGSTRAHKATVSTGSVHFTPKLGSVQFTTDTNNDFQTGQNTKFTPVGVIQDGDHHQNEPQQWVLPNYSGTSGHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMNLDCLLPQEWVSHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYITVAHTGPYDLVIPPNGYFRFDSWVNQFYTLAPM 529
                                   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)
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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 5IYP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IYP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IYP)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5IYP)

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  Cis Peptide Bonds
    Glu A:398 - Pro A:399   [ RasMol ]  
    Glu B:398 - Pro B:399   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        D0QJ68_9CALI | D0QJ68: 5iyn 5iyq 5iyr 5iyw

(-) Related Entries Specified in the PDB File

5iyn PROTRUDING DOMAIN OF GII.4 HUMAN NOROVIRUS CHDC2094