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(-) Description

Title :  PROTRUDING DOMAIN OF GII.4 HUMAN NOROVIRUS CHDC2094
 
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 :  1.56
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Norovirus, Virus Capsid, Protruding Domain, 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  (1, 9)

Asymmetric/Biological Unit (1, 9)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:272 , LEU A:273 , GLY A:274 , THR A:276 , ILE A:317 , LEU A:321 , HOH A:710 , HOH A:734binding site for residue EDO A 601
2AC2SOFTWARETHR 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:715binding site for residue EDO A 602
3AC3SOFTWARETYR A:504 , MET A:529 , EDO A:605 , ASN B:309 , ASN B:310binding site for residue EDO A 603
4AC4SOFTWAREGLN A:401 , TRP A:402 , PHE A:432 , ASP A:449 , HOH A:747 , HOH A:846 , HOH A:927binding site for residue EDO A 604
5AC5SOFTWARETYR A:504 , LEU A:506 , VAL A:507 , MET A:529 , EDO A:603 , HOH A:723binding site for residue EDO A 605
6AC6SOFTWARELEU B:272 , LEU B:273 , GLY B:274 , THR B:276 , LEU B:321 , HOH B:708 , HOH B:712binding site for residue EDO B 601
7AC7SOFTWAREGLY B:252 , PRO B:253 , GLN B:401 , TRP B:402 , PHE B:432 , ASP B:449binding site for residue EDO B 602
8AC8SOFTWARETHR B:233 , VAL B:234 , GLU B:235 , PRO B:509 , PRO B:510 , GLY B:512 , HOH B:956binding site for residue EDO B 603
9AC9SOFTWAREGLY A:442 , SER B:343 , THR B:344 , ARG B:345 , HOH B:882binding site for residue EDO B 604

(-) SS Bonds  (0, 0)

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

(-) 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 5IYN)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IYN)

(-) 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...hhhhhhhhhh.......eeeeeee......eeeeeeee...eeeee.............eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iyn 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...........eeeee............eeeeeeeee......................................eeeeeeeee.eeee.....eeee...hhhhhhhhhh.......eeeeeee......eeeeeeee...eeeee.............eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5iyn 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)
  - → 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 5IYN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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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: 5iyp 5iyq 5iyr 5iyw

(-) Related Entries Specified in the PDB File

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