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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ENTEROVIRUS D68 IN COMPLEX WITH 3'SLN
 
Authors :  Y. Liu, J. Sheng, G. Meng, C. Xiao, M. G. Rossmann
Date :  26 May 15  (Deposition) - 18 Nov 15  (Release) - 25 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (60x)
Keywords :  Enterovirus, Capsid, Beta Jelly Roll, Virus, Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Liu, J. Sheng, J. Baggen, G. Meng, C. Xiao, H. J. Thibaut, F. J. Van Kuppeveld, M. G. Rossmann
Sialic Acid-Dependent Cell Entry Of Human Enterovirus D68.
Nat Commun V. 6 8865 2015
PubMed-ID: 26563423  |  Reference-DOI: 10.1038/NCOMMS9865

(-) Compounds

Molecule 1 - CAPSID PROTEIN VP1
    Cell Line: HUMAN RHABDOMYOSARCOMA CELLS
    Chains: A
    Fragment: UNP RESIDUES 565-861
    Organism Scientific: ENTEROVIRUS D68
    Organism Taxid: 42789
    Other Details: GROWN IN HUMAN RHABDOSARCOMA CELLS
 
Molecule 2 - CAPSID PROTEIN VP2
    Cell Line: HUMAN RHABDOMYOSARCOMA CELLS
    Chains: B
    Fragment: UNP RESIDUES 70-317
    Organism Scientific: ENTEROVIRUS D68
    Organism Taxid: 42789
    Other Details: GROWN IN HUMAN RHABDOSARCOMA CELLS
 
Molecule 3 - CAPSID PROTEIN VP3
    Cell Line: HUMAN RHABDOMYOSARCOMA CELLS
    Chains: C
    Fragment: UNP RESIDUES 318-564
    Organism Scientific: ENTEROVIRUS D68
    Organism Taxid: 42789
    Other Details: GROWN IN HUMAN RHABDOSARCOMA CELLS
 
Molecule 4 - CAPSID PROTEIN VP4
    Cell Line: HUMAN RHABDOMYOSARCOMA CELLS
    Chains: D
    Fragment: UNP RESIDUES 2-69
    Organism Scientific: ENTEROVIRUS D68
    Organism Taxid: 42789
    Other Details: GROWN IN HUMAN RHABDOSARCOMA CELLS

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (60x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
14U21Ligand/Ion(6R)-5-(ACETYLAMINO)-3,5-DIDEOXY-6-[(1R,2R)-1,2,3-TRIHYDROXYPROPYL]-BETA-L-THREO-HEX-2-ULOPYRANONOSYL-(2->3)-BETA-D-GALACTOPYRANOSYL-(1->4)-2-(ACETYLAMINO)-2-DEOXY-BETA-D-GLUCOPYRANOSE
Biological Unit 1 (1, 60)
No.NameCountTypeFull Name
14U260Ligand/Ion(6R)-5-(ACETYLAMINO)-3,5-DIDEOXY-6-[(1R,2R)-1,2,3-TRIHYDROXYPROPYL]-BETA-L-THREO-HEX-2-ULOPYRANONOSYL-(2->3)-BETA-D-GALACTOPYRANOSYL-(1->4)-2-(ACETYLAMINO)-2-DEOXY-BETA-D-GLUCOPYRANOSE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:270 , PRO A:274 , ASN A:275 , GLY A:282 , ASN A:283 , ASP C:91 , ARG C:95 , ARG C:104 , PRO C:231 , ASP C:232 , ILE C:233binding site for residue 4U2 A 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:273 -Pro A:274
2Leu B:82 -Pro B:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BNP)

(-) 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:287
                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....................eehhhhh.....hhhhhh..........hhhhhhhhhhh..eeeeeeeeee...........eeeee.....hhhhhhhhh.eeeeeeeeeeeeeeeeee........eeeeeee...........hhhhhh....eeeee.....eeeee........ee.................hhhhh..eeeeee........eeeeeeeeeeeeeeeeeee............................................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bnp A   1 VESIIKTATDTVKSEINAELGVVPSLNAVETGATSNTEPEEAIQTRTVINQHGVSETLVENFLGRAALVSKKSFEYKNHASSSTHKNFFKWTINTKSFVQLRRKLELFTYLRFDAEITILTTVAVNYMGLPDLTLQAMFVPTGALTPKEQDSFHWQSGSNASVFFKISDPPARMTIPFMCINSAYSVFYDGFAGFEKNGLYGINPADTIGNLCVRIVNEHQPVGFTVTVRVYMKPKHIKAWAPRPPRTMPYMSIANANYKGRDTAPNTLNAIIGNRASVTTMPHNIV 295
                                    10        20        30        40        50        60        70        80  ||    92       102       112       122     ||138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       
                                                                                                             83|                                       128|                                                                                                                                                                
                                                                                                              86                                        135                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..eeeee......ee.hhh..................hhhhh...ee...ee.......eeeeehhhhh.hhhhhhhhhheeeeeeeeeeeee.......eeeeeeeeee.............hhhhhhhhhhhee..hhhhh.......hhhhh.eeeee.....eeeeee................eeeeeeeeeeee........eeeeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bnp B  10 SDRVLQLKLGNSAIVTQEAANYCCAYGEWPNYLPDHEAVAIDKPTQPETSTDRFYTLRSVKWESNSTGWWWKLPDALNNIGMFGQNVQYHYLYRSGFLIHVQCNATKFHQGALLVVAIPEHQRGAHDTTTSPGFNDIMKGERGGTFNHPYVLDDGTSIACATIFPHQWINLRTNNSATIVLPWMNVAPMDFPLRHNQWTLAVIPVVPLGTRTMSSVVPITVSIAPMCCEFNGLRHAI 246
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       


Chain C from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................................ee.hhhhhhh..ee.........hhhhhhheeee.......eeeeee...........hhhhhhhh...eee..eeeeeee........eeeeeee........hhhhhh..eeeeee.....eeeeee........ee.............eeeeee............eeeeeeeeee....eee................hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bnp C   1 GVPTYLLPGSGQFLTTDDHSSAPVLPCFNPTPEMHIPGQIRNMLEMIQVESMMEINNTDGANGMERLRVDISVQADLDQLLFNIPLDIQLDGPLRNTLVGNISRYYTHWSGSLEMTFMFCGSFMATGKLILCYTPPGGSCPTTRETAMLGTHIVWDFGLQSSITLIIPWISGSHYRMFNSDAKSTNANVGYVTCFMQTNLIVPSESSDTCSLIGFIAAKDDFSLRLMRDSPDIGQSNHLHGAEAAYQ 247
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       


Chain D from PDB  Type:PROTEIN  Length:39
                                                                       
               SCOP domains --------------------------------------- SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.......ee.hhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
                 Transcript --------------------------------------- Transcript
                 5bnp D  30 NFYKDSYAASASKQDFSQDPSKFTEPVVEGLKAGAPVLK  68
                                    39        49        59
   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 5BNP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (36, 36)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        Q68T42_9ENTO | Q68T42: 4wm7 4wm8 5bnn 5bno

(-) Related Entries Specified in the PDB File

5bnn 5bno