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(-) Description

Title :  ATOMIC STRUCTURE OF A NON-ENVELOPED VIRUS REVEALS PH SENSORS FOR A COORDINATED PROCESS OF CELL ENTRY
 
Authors :  X. Zhang, A. Patel, C. Celma, P. Roy, Z. H. Zhou
Date :  10 Jan 15  (Deposition) - 09 Dec 15  (Release) - 20 Jan 16  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  3.50
Chains :  Asym./Biol. Unit :  D
Keywords :  Non-Enveloped Virus, Cell Entry, Ph Sensor, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Zhang, A. Patel, C. C. Celma, X. Yu, P. Roy, Z. H. Zhou
Atomic Model Of A Nonenveloped Virus Reveals Ph Sensors For A Coordinated Process Of Cell Entry.
Nat. Struct. Mol. Biol. V. 23 74 2016
PubMed-ID: 26641711  |  Reference-DOI: 10.1038/NSMB.3134

(-) Compounds

Molecule 1 - VP5
    Chains: D
    Organism Scientific: BLUETONGUE VIRUS 1
    Organism Taxid: 35327

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : D

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3J9E)

(-) Sites  (0, 0)

(no "Site" information available for 3J9E)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3J9E)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Val D:15 -Gly D:16
2Leu D:19 -Thr D:20
3Ser D:45 -Ala D:46
4Leu D:78 -Gly D:79
5Ala D:140 -Glu D:141
6Gly D:340 -Ile D:341
7Ala D:421 -Gly D:422
8His D:446 -Thr D:447

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3J9E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3J9E)

(-) Exons   (0, 0)

(no "Exon" information available for 3J9E)

(-) 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 D from PDB  Type:PROTEIN  Length:520
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.....eee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh......eee....hhhhhhhh...................hhhhhhhhhhhhhhhh............hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh..hhhhh..eeeee.......eeeeee..hhhhh..eeeeee....eeeeee.................hhhhhhhhhhhhhhhh.........hhhhh.....eeeeee....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.eee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j9e D   2 GKVIRSLNRFGKKVGNALTSNTAKKIYSTIGKAAERFAESEIGSAAIDGLVQGSVHSIITGESYGESVKQAVLLNVLGSGEEIPDPLSPGERGIQAKLKELEDEQRNELVRLKYNDKIKEKFGKELEEVYNFMNGEANAEIEDEKQFDILNKAVTSYNKILTEEDLQMRRLATALQKEIGERTHAETVMVKEYRDKIDALKNAIEVERDGMQEEAIQEIAGMTADVLEAASEEVPLIGAGMATAVATGRAIEGAYKLKKVINALSGIDLTHLRTPKIEPSVVSTILEYRAKEIPDNALAVSVLSKNRAIQENHKELMHIKNEILPRFKKAMDEEKEICGIEDKVIHPKVMMKFKIPRAQQPQIHVYSAPWDSDDVFFFHCISHHHANESFFLGFDLSIDLVHYEDLTAHWHALGAAQTAAGRTLTEAYREFLNLAISNAFGTQMHTRRLVRSKTVHPIYLGSLHYDISFSDLRGNAQRIVYDDELQMHILRGPIHFQRRAILGALKFGCKVLGDRLDVPL 521
                                    11        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       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521
   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 3J9E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3J9E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3J9E)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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  Sites
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  Cis Peptide Bonds
    Ala D:140 - Glu D:141   [ RasMol ]  
    Ala D:421 - Gly D:422   [ RasMol ]  
    Gly D:340 - Ile D:341   [ RasMol ]  
    His D:446 - Thr D:447   [ RasMol ]  
    Leu D:19 - Thr D:20   [ RasMol ]  
    Leu D:78 - Gly D:79   [ RasMol ]  
    Ser D:45 - Ala D:46   [ RasMol ]  
    Val D:15 - Gly D:16   [ RasMol ]  
 

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 Related Entries

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(-) Related Entries Specified in the PDB File

3j9d