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(-) Description

Title :  BINDING SPECIFICITY OF P[8] VP8* PROTEINS OF ROTAVIRUS VACCINE STRAINS WITH HISTO-BLOOD GROUP ANTIGENS
 
Authors :  X. Sun, N. Guo, D. Li, Y. Zhou, M. Jin, G. Xie, L. Pang, Q. Zhang, Y. Cao, Z. D
Date :  16 Apr 16  (Deposition) - 13 Jul 16  (Release) - 13 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Rotavirus, Vp8, Vaccine, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Sun, N. Guo, D. Li, M. Jin, Y. Zhou, G. Xie, L. Pang, Q. Zhang, Y. Cao, Z. J. Duan
Binding Specificity Of P[8] Vp8* Proteins Of Rotavirus Vaccine Strains With Histo-Blood Group Antigens.
Virology V. 495 129 2016
PubMed-ID: 27209447  |  Reference-DOI: 10.1016/J.VIROL.2016.05.010

(-) Compounds

Molecule 1 - OUTER CAPSID PROTEIN VP4
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Fragment: UNP RESIDUES 64-223
    Organism Scientific: ROTAVIRUS A
    Organism Taxid: 28875

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5JDB)

(-) Sites  (0, 0)

(no "Site" information available for 5JDB)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Gly A:4 -Pro A:5
2Thr A:117 -Pro A:118
3Gly B:4 -Pro B:5
4Thr B:117 -Pro B:118
5Gly C:4 -Pro C:5
6Thr C:117 -Pro C:118
7Gly D:4 -Pro D:5
8Thr D:117 -Pro D:118
9Gly E:4 -Pro E:5
10Thr E:117 -Pro E:118
11Gly F:4 -Pro F:5
12Thr F:117 -Pro F:118

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JDB)

(-) 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:160
                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eee.....eeeeee.....eeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee....eeeeeeee.......eeeeeeee...eeeeeee..eeeeeeee....eeeee........eeee...eeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jdb A   1 ILDGPYQPTTFTPPIDYWILINSNTNGVVYESTNNSDFWTAVVAIEPHVNPVDRQYTVFGENKQFNVRNDSDKWKFLEMFRSSSQNEFYNRRTLTSDTKLVGILKYGGRIWTFHGETPRATTDSSNTANLNDISIIIHSEFYIIPRSQESKCNEYINNGL 160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160


Chain B from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eee.....eeeeee.....eeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee....eeeeeeee.......eeeeeeee...eeeeeee..eeeeeeee....eeeeee.......eeee...eeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jdb B   1 ILDGPYQPTTFTPPIDYWILINSNTNGVVYESTNNSDFWTAVVAIEPHVNPVDRQYTVFGENKQFNVRNDSDKWKFLEMFRSSSQNEFYNRRTLTSDTKLVGILKYGGRIWTFHGETPRATTDSSNTANLNDISIIIHSEFYIIPRSQESKCNEYINNGL 160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160


Chain C from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eee.....eeeeee.....eeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee....eeeeeeee.......eeeeeeee...eeeeeee..eeeeeeee....eeeeee.......eeee...eeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jdb C   1 ILDGPYQPTTFTPPIDYWILINSNTNGVVYESTNNSDFWTAVVAIEPHVNPVDRQYTVFGENKQFNVRNDSDKWKFLEMFRSSSQNEFYNRRTLTSDTKLVGILKYGGRIWTFHGETPRATTDSSNTANLNDISIIIHSEFYIIPRSQESKCNEYINNGL 160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160


Chain D from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eee.....eeeeee.....eeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee....eeeeeeee.......eeeeeeee...eeeeeee..eeeeeeee....eeeeee.......eeee...eeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jdb D   1 ILDGPYQPTTFTPPIDYWILINSNTNGVVYESTNNSDFWTAVVAIEPHVNPVDRQYTVFGENKQFNVRNDSDKWKFLEMFRSSSQNEFYNRRTLTSDTKLVGILKYGGRIWTFHGETPRATTDSSNTANLNDISIIIHSEFYIIPRSQESKCNEYINNGL 160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160


Chain E from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eee.....eeeeee.....eeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee....eeeeeeee.......eeeeeeee...eeeeeee..eeeeeeee....eeeeee.......eeee...eeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jdb E   1 ILDGPYQPTTFTPPIDYWILINSNTNGVVYESTNNSDFWTAVVAIEPHVNPVDRQYTVFGENKQFNVRNDSDKWKFLEMFRSSSQNEFYNRRTLTSDTKLVGILKYGGRIWTFHGETPRATTDSSNTANLNDISIIIHSEFYIIPRSQESKCNEYINNGL 160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160


Chain F from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eee.....eeeeee.....eeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee....eeeeeeee.......eeeeeeee...eeeeeee..eeeeeeee....eeeeee.......eeee...eeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jdb F   1 ILDGPYQPTTFTPPIDYWILINSNTNGVVYESTNNSDFWTAVVAIEPHVNPVDRQYTVFGENKQFNVRNDSDKWKFLEMFRSSSQNEFYNRRTLTSDTKLVGILKYGGRIWTFHGETPRATTDSSNTANLNDISIIIHSEFYIIPRSQESKCNEYINNGL 160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   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 5JDB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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Asymmetric/Biological Unit
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  Cis Peptide Bonds
    Gly A:4 - Pro A:5   [ RasMol ]  
    Gly B:4 - Pro B:5   [ RasMol ]  
    Gly C:4 - Pro C:5   [ RasMol ]  
    Gly D:4 - Pro D:5   [ RasMol ]  
    Gly E:4 - Pro E:5   [ RasMol ]  
    Gly F:4 - Pro F:5   [ RasMol ]  
    Thr A:117 - Pro A:118   [ RasMol ]  
    Thr B:117 - Pro B:118   [ RasMol ]  
    Thr C:117 - Pro C:118   [ RasMol ]  
    Thr D:117 - Pro D:118   [ RasMol ]  
    Thr E:117 - Pro E:118   [ RasMol ]  
    Thr F:117 - Pro F:118   [ RasMol ]  
 

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