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(-) Description

Title :  THE NOVEL ASYMMETRIC ENTRY INTERMEDIATE OF A PICORNAVIRUS CAPTURED WITH NANODISCS
 
Authors :  H. Lee, K. L. Shingler, L. J. Organtini, R. E. Ashley, A. M. Makhov, J. F. C S. Hafenstein
Date :  29 Apr 16  (Deposition) - 14 Sep 16  (Release) - 14 Sep 16  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  3.90
Chains :  Asym. Unit :  1,2,3,4
Biol. Unit 1:  1,2,3,4  (60x)
Keywords :  Picornavirus, Entry Intermediate, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Lee, K. L. Shingler, L. J. Organtini, R. E. Ashley, A. M. Makhov, J. F. Conway, S. Hafenstein
The Novel Asymmetric Entry Intermediate Of A Picornavirus Captured With Nanodiscs.
Sci Adv V. 2 01929 2016
PubMed-ID: 27574701  |  Reference-DOI: 10.1126/SCIADV.1501929

(-) Compounds

Molecule 1 - CAPSID PROTEIN VP1
    Chains: 1
    Fragment: UNP RESIDUES 571-851
    Organism Scientific: COXSACKIEVIRUS B3
    Organism Taxid: 12072
    Synonym: P1D, VIRION PROTEIN 1
 
Molecule 2 - CAPSID PROTEIN VP2
    Chains: 2
    Fragment: UNP RESIDUES 70-332
    Organism Scientific: COXSACKIEVIRUS B3
    Organism Taxid: 12072
    Synonym: P1B, VIRION PROTEIN 2
 
Molecule 3 - CAPSID PROTEIN VP3
    Chains: 3
    Fragment: UNP RESIDUES 333-570
    Organism Scientific: COXSACKIEVIRUS B3
    Organism Taxid: 12072
    Synonym: P1C, VIRION PROTEIN 3
 
Molecule 4 - CAPSID PROTEIN VP4
    Chains: 4
    Fragment: UNP RESIDUES 2-69
    Organism Scientific: COXSACKIEVIRUS B3
    Organism Taxid: 12072
    Synonym: P1A, VIRION PROTEIN 4

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PLM1Ligand/IonPALMITIC ACID
Biological Unit 1 (1, 60)
No.NameCountTypeFull Name
1PLM60Ligand/IonPALMITIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE 1:92 , PRO 1:94 , ARG 1:95 , LEU 1:114 , LEU 1:116 , TYR 1:143 , MET 1:178 , ASN 1:211 , MET 1:213BINDING SITE FOR RESIDUE PLM 1 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JD7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3JD7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JD7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JD7)

(-) Exons   (0, 0)

(no "Exon" information available for 3JD7)

(-) 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 1 from PDB  Type:PROTEIN  Length:270
                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....................hhhhh.....................hhhhhhhhhhh..eeeeeeeee......eeeee.hhhhhhhhhhhh..eeeee...eeeeeeeeee.............eeeeeee...........hhhhhh....eeeee......eee.........ee........................eeeeee........eeeeeeeee.....eeeee.................................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3jd7 1  12 GRVADTVGTGPTNSEAIPALTAAETGHTSQVVPSDTMQTRHVKNYHSRSESTIENFLCRSACVYFTEYENSGAKRYAEWVITPRQAAQLRRKLEFFTYVRFDLELTFVITSTQQPSTTQNQDAQILTHQIMYVPPGGPVPDKVDSYVWQTSTNPSVFWTEGNAPPRMSVPFLSIGNAYSNFYDGWSEFSRNGVYGINTLNNMGTLYARHVNAGSTGPIKSTIRIYFKPKHVKAWIPRPPRLCQYEKAKNVNFQPSGVTTTRQSITTMTNT 281
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281


Chain 2 from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee..eeeee......ee......................hhhhh...ee...eee......eeee...hhhhhhhhhhhhhheeeeeeeeeeeee.......eee..eeeee.............hhhhhh.....ee.........................hhhhhhhh.ee........eeeeee................eeeee...eeee........eeeeeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jd7 2   8 GYSDRVRSITLGNSTITTQECANVVVGYGVWPDYLKDSEATAEDQPTQPDVATCRFYTLDSVQWQKTSPGWWWKLPDALSNLGLFGQNMQYHYLGRTGYTIHVQCNASKFHQGCLLVVCVPEAEMGCATLNNTPSSAELLGGDTAKEFADKPVASGSNKLVQRVVYNAGMGVGVGNLTIFPHQWINLRTNNSATIVMPYTNSVPMDNMFRHNNVTLMVIPFVPLDYCPGSTTYVPITVTIAPMCAEYNGLRLAGHQ 263
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257      


Chain 3 from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................................ee..hhhhhh..ee.......hhhhhhhhhheee........eeeeee.....hhhhhhhhhhhhhhheeeee..eeeeeee......eeeeeeeee........hhhhhhh.eeeeee......eeee.........ee..........eeeeeeeeeee........eeeeeeeee....eeeee............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jd7 3   1 GLPTMNTPGSCQFLTSDDFQSPSAMPQYDVTPEMRIPGEVKNLMEIAEVDSVVPVQNVGEKVNSMEAYQIPVRSNEGSGTQVFGFPLQPGYSSVFSRTLLGEILNYYTHWSGSIKLTFMFCGSAMATGKFLLAYSPPGAGAPTKRVDAMLGTHVVWDVGLQSSCVLCIPWISQTHYRYVASDEYTAGGFITCWYQTNIVVPADAQSSCYIMCFVSACNDFSVRLLKDTPFISQENFFQ 238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        


Chain 4 from PDB  Type:PROTEIN  Length:56
                                                                                        
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee........eee.....hhhhh.........hhhhh................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 3jd7 4   2 GAQVSTQKTGAIHYTNINYYKDAASNSANRQDFTQDPSKFTEPVKDIMIKSLPALN  69
                                    11||      33        43        53        63      
                                     12|                                            
                                      25
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  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 3JD7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3JD7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3JD7)

(-) Gene Ontology  (50, 86)

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 Related Entries

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