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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN ASTROVIRUS 2 CAPSID PROTEIN SPIKE DOMAIN AT 1.87-A RESOLUTION
 
Authors :  W. A. Bogdanoff, R. M. Dubois
Date :  01 Jul 16  (Deposition) - 09 Nov 16  (Release) - 18 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Viral Protein, Capsid Protein, Icosahedral Virus. (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. A. Bogdanoff, J. Campos, E. I. Perez, L. Yin, D. L. Alexander, R. M. Dubois
Structure Of A Human Astrovirus Capsid-Antibody Complex And Mechanistic Insights Into Virus Neutralization.
J. Virol. V. 91 2017
PubMed-ID: 27807234  |  Reference-DOI: 10.1128/JVI.01859-16

(-) Compounds

Molecule 1 - CAPSID POLYPROTEIN VP25
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 429-644
    Gene: ORF2
    Organism Common: HASTV-2
    Organism Scientific: HUMAN ASTROVIRUS-2
    Organism Taxid: 12701

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5KOU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:442 -Pro A:443
2Ser B:442 -Pro B:443
3Ser C:442 -Pro C:443
4Ser D:442 -Pro D:443

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KOU)

(-) Sequences/Alignments

Asymmetric 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:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee..............ee........hhhhhh.eeee....eee..eeeeeeeeeee...............eeeee..eeeeeeeeeeeeeeee...eeeeeeeeeeee...eeeeeeee.ee............ee....eeeeeee....eeeeeeeeeee........................hhhhh........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5kou A 429 GELRVLLTVGSIMSPNSADRQVWLNKTLTAPGTNSNDNLVKIAHDLGHYLIMQGFMHIKTVEWYTPDFQPSRDPTPIAGMSVMVNITKKADVYFMKQFKNSYTNNRHQITSIFLIKPLADFKVQCYMSYFKRESHDNDGVANLTVRSMTSPETIRFQVGEWYLLTSTTLKENNLPEGWVWDRVELKSDTPYYADQALTYFITPPPVDSQILFEGNT 644
                                   438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638      


Chain B from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..............ee...............eeee....eee..eeeeeeeeeee...............eeeee..eeeeeeeeeeeeeeeee..eeeeeeeeeeee...eeeeeeee.ee............ee....eeeeeee....eeeeeeeeee.........................hhhhh........eeeeeee.hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kou B 429 GELRVLLTVGSIMSPNSADRQVWLNKTLTAPGTNSNDNLVKIAHDLGHYLIMQGFMHIKTVEWYTPDFQPSRDPTPIAGMSVMVNITKKADVYFMKQFKNSYTNNRHQITSIFLIKPLADFKVQCYMSYFKRESHDNDGVANLTVRSMTSPETIRFQVGEWYLLTSTTLKENNLPEGWVWDRVELKSDTPYYADQALTYFITPPPVDSQILFEGNTAAAELALVP 653
                                   438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648     


Chain C from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..............ee...............eeee....eee..eeeeeeeeeee...............eeeee..eeeeeeeeeeeeee......eeeeeeeeeee...eeeeeeee.ee............ee....eeeeeee....eeeeeeeeee.........................hhhhh........eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kou C 429 GELRVLLTVGSIMSPNSADRQVWLNKTLTAPGTNSNDNLVKIAHDLGHYLIMQGFMHIKTVEWYTPDFQPSRDPTPIAGMSVMVNITKKADVYFMKQFKNSYTNNRHQITSIFLIKPLADFKVQCYMSYFKRESHDNDGVANLTVRSMTSPETIRFQVGEWYLLTSTTLKENNLPEGWVWDRVELKSDTPYYADQALTYFITPPPVDSQILFEGNTAAA 647
                                   438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638         


Chain D from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..............ee...............eeee....eee..eeeeeeeeeee...............eeeee..eeeeeeeeeeeeee.....eeeeeeeeeeee...eeeeeeee.ee............ee....eeeeeee....eeeeeeeeeee........................hhhhh........eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kou D 429 GELRVLLTVGSIMSPNSADRQVWLNKTLTAPGTNSNDNLVKIAHDLGHYLIMQGFMHIKTVEWYTPDFQPSRDPTPIAGMSVMVNITKKADVYFMKQFKNSYTNNRHQITSIFLIKPLADFKVQCYMSYFKRESHDNDGVANLTVRSMTSPETIRFQVGEWYLLTSTTLKENNLPEGWVWDRVELKSDTPYYADQALTYFITPPPVDSQILFEGNTA 645
                                   438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638
   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 5KOU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

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  Cis Peptide Bonds
    Ser A:442 - Pro A:443   [ RasMol ]  
    Ser B:442 - Pro B:443   [ RasMol ]  
    Ser C:442 - Pro C:443   [ RasMol ]  
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  5kou
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  CAPSD_HASV2 | Q82446
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 Related Entries

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UniProtKB/Swiss-Prot
        CAPSD_HASV2 | Q82446: 5kov

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