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(-) Description

Title :  CRYSTALLOGRAPHIC STRUCTURE OF APO HUMAN ROTAVIRUS K8 VP8*
 
Authors :  X. Yu, H. Blanchard
Date :  30 Jun 15  (Deposition) - 08 Jun 16  (Release) - 08 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Carbohydrate-Recognizing Protein, Lectin, Rotavirus, Vp8*, Viral Protein, Sugard Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Yu, R. Mishra, G. Holloway, M. Von Itzstein, B. S. Coulson, H. Blanchard
Substantial Receptor-Induced Structural Rearrangement Of Rotavirus Vp8*: Potential Implications For Cross-Species Infection.
Chembiochem V. 16 2176 2015
PubMed-ID: 26250751  |  Reference-DOI: 10.1002/CBIC.201500360

(-) Compounds

Molecule 1 - OUTER CAPSID PROTEIN VP4
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 64-224
    Mutation: YES
    Organism Common: RV-A
    Organism Scientific: ROTAVIRUS A (STRAIN HUMAN/JAPAN/K8/1977 G1- P3A[9]-IX-RX-CX-MX-A1-NX-TX-EX-H3)
    Organism Taxid: 39012
    Strain: HUMAN/JAPAN/K8/1977 G1-P3A[9]-IX-RX-CX-MX-A1-NX-TX-EX-H3
    Synonym: HEMAGGLUTININ

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2IPA7Ligand/IonISOPROPYL ALCOHOL
3SO41Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:86 , THR A:87 , ARG A:88 , GLN A:118 , HOH A:494 , HOH A:511 , HOH A:571binding site for residue IPA A 301
2AC2SOFTWAREGLN A:124 , TRP A:138 , LYS A:163 , HOH A:410 , HOH A:412 , HOH A:472 , HOH A:500binding site for residue IPA A 302
3AC3SOFTWAREASN A:132 , ASP A:133 , SER A:134 , LYS A:139binding site for residue IPA A 303
4AC4SOFTWARESER A:156 , THR A:157 , GLN A:178 , HOH A:521binding site for residue IPA A 304
5AC5SOFTWAREASN A:114 , THR A:115 , GLN A:116 , HIS A:129 , GLN A:210 , SER A:211binding site for residue IPA A 305
6AC6SOFTWARELEU A:146 , THR A:147 , GLY A:150 , THR A:151 , GLN A:218 , HOH A:446binding site for residue IPA A 306
7AC7SOFTWAREARG A:117 , GLN A:118 , HOH A:535binding site for residue IPA A 307
8AC8SOFTWARETHR A:115 , ARG A:117 , HOH A:429 , HOH A:499 , HOH A:502binding site for residue SO4 A 308
9AC9SOFTWARECYS A:105 , PHE A:140 , SER A:156 , THR A:157 , LEU A:158 , TRP A:176 , TYR A:177 , HOH A:405binding site for residue GOL A 309

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:67 -Pro A:68
2Thr A:181 -Pro A:182

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CAZ)

(-) 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:161
                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eee.....eeeee.....eeeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee.....eeeeeeee.......eeeeeeee....eeeeee..eeeeeeee....eeeeee.......eeee...eeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5caz A  64 TLDGPYQPTSLNLPVDYWMLIAPTREGKVAEGTNTTDRWFACVLVEPNVQNTQRQYVLDGQNVQLHVSNDSSTSWKFILFIKLTPDGTYTQYSTLSTPHKLCAWMKRDNRVYWYQGATPNASESYYLTINNDNSNVSSDAEFYLIPQSQTAMCTQYINNGL 224
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223
   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 5CAZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  5caz
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  VP4_ROTHJ | Q01641
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 Related Entries

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

UniProtKB/Swiss-Prot
        VP4_ROTHJ | Q01641: 5cb7

(-) Related Entries Specified in the PDB File

5cb7