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(-) Description

Title :  PROTRUDING DOMAIN OF GII.4 HUMAN NOROVIRUS CHDC2094 IN COMPLEX WITH HBGA TYPE B (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 :  1.41
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Viral Capsid Protein, Protruding Domain, Viral Protein, Norovirus, Hbga (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 - PROTRUDING DOMAIN OF GII.4 NOROVIRUS CHDC2094 CAPSID
    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  (4, 19)

Asymmetric/Biological Unit (4, 19)
No.NameCountTypeFull Name
1EDO12Ligand/Ion1,2-ETHANEDIOL
2FLC1Ligand/IonCITRATE ANION
3FUC2Ligand/IonALPHA-L-FUCOSE
4GLA4Ligand/IonALPHA D-GALACTOSE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:278 , LEU A:321 , HOH A:949 , HOH A:950 , GLU B:236binding 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:706binding site for residue EDO A 602
03AC3SOFTWARESER A:279 , ALA A:280 , GLN A:454 , HOH A:752 , SER B:279 , ALA B:280 , GLN B:454 , HOH B:809binding site for residue EDO A 603
04AC4SOFTWARETYR A:504 , MET A:529 , ASN B:309 , ASN B:310binding site for residue EDO A 604
05AC5SOFTWARELEU A:272 , LEU A:273 , GLY A:274 , THR A:276 , LEU A:321 , HOH A:739 , HOH A:865binding site for residue EDO A 605
06AC6SOFTWARELYS A:348 , THR A:350 , THR A:368 , HOH A:862 , HOH A:863binding site for residue EDO A 606
07AC7SOFTWARETHR A:335 , GLN A:336 , THR A:337 , ASN A:380 , LYS A:382 , HOH A:704 , HOH A:737 , HOH A:738 , HOH A:996binding site for residue EDO A 607
08AC8SOFTWARELEU B:272 , LEU B:273 , GLY B:274 , THR B:276 , LEU B:321 , HOH B:723 , HOH B:752binding site for residue EDO B 601
09AC9SOFTWAREGLY A:412 , HIS A:413 , PRO B:426 , ASN B:521 , HOH B:772 , HOH B:791 , HOH B:825binding site for residue EDO B 602
10AD1SOFTWAREGLY B:252 , PRO B:253 , GLN B:401 , TRP B:402 , PHE B:432 , ASP B:449 , HOH B:707binding site for residue EDO B 603
11AD2SOFTWARETHR B:350 , THR B:368binding site for residue EDO B 604
12AD3SOFTWAREVAL B:356 , HIS B:357 , HOH B:797binding site for residue EDO B 605
13AD4SOFTWARESER B:355 , VAL B:356 , HIS B:357 , HIS B:394 , ASN B:397 , HOH B:908binding site for residue FLC B 606
14AD5SOFTWARESER A:343 , THR A:344 , ARG A:345 , HIS A:347 , ASP A:374 , HOH A:712 , HOH A:733 , HOH A:745 , HOH A:755 , HOH A:756 , HOH A:757 , HOH A:926 , HOH A:977 , LYS B:348 , SER B:441 , GLY B:442binding site for Poly-Saccharide residues FUC A 608 through GLA A 610
15AD6SOFTWARETHR A:335 , GLN A:336 , THR A:337 , SER A:343 , THR A:344 , ARG A:345 , HIS A:347 , LYS A:348 , ASP A:374 , ASN A:380 , LYS A:382 , SER A:441 , GLY A:442 , HOH A:704 , HOH A:712 , HOH A:733 , HOH A:737 , HOH A:738 , HOH A:745 , HOH A:755 , HOH A:756 , HOH A:757 , HOH A:862 , HOH A:926 , HOH A:977 , HOH A:996 , SER B:343 , THR B:344 , ARG B:345 , HIS B:347 , LYS B:348 , ASP B:374 , SER B:441 , GLY B:442 , HOH B:712 , HOH B:719 , HOH B:776 , HOH B:826 , HOH B:835 , HOH B:839 , HOH B:948 , HOH B:952binding site for Poly-Saccharide residues FUC B 607 through GLA B 609

(-) SS Bonds  (0, 0)

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

(-) 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 5IYQ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IYQ)

(-) 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
                 5iyq 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:305
                                                                                                                                                                                                                                                                                                                                                 
               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.......eeeeeee......eeeeeeee...eeeee.............eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iyq B 225 KPFTVPILTVEEMSNSRFPIPLEKLYTGPSSAFVVQPQNGRCTTDGVLLGTTQLSAVNICNFRGDVTRVGISHDYTMNLVSQNWNNYDPTEEIPAPLGTPDFVGKIQGLLTQTTRADGSTRAHKATVSTGSVHFTPKLGSVQFTTDTNNDFQTGQNTKFTPVGVIQDGDHHQNEPQQWVLPNYSGTSGHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMNLDCLLPQEWVSHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYITVAHTGPYDLVIPPNGYFRFDSWVNQFYTLAPM 529
                                   234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524
   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 5IYQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  Cis Peptide Bonds
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

5iyn PROTRUDING DOMAIN OF GII.4 HUMAN NOROVIRUS CHDC2094
5iyp PROTRUDING DOMAIN OF GII.4 HUMAN NOROVIRUS CHDC2094 IN COMPLEX WITH HBGA TYPE A (TRIGLYCAN)