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PDBsum entry 3j2p

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protein ligands Protein-protein interface(s) links
Viral protein PDB id
3j2p
Jmol
Contents
Protein chains
495 a.a.
72 a.a.
Ligands
NAG ×2
NAG-NAG ×2
PDB id:
3j2p
Name: Viral protein
Title: Cryoem structure of dengue virus capsid protein heterotetram
Structure: Envelope protein e. Chain: a, c. Fragment: unp residues 281-775. Small envelope protein m. Chain: b, d. Fragment: unp residues 206-280. Synonym: matrix protein
Source: Dengue virus 2. Denv-2. Organism_taxid: 11060. Strain: new guinea. Cell_line: mosquito cells c6/36. Cell_line: mosquito cells c6/36
Authors: X.Zhang,P.Ge,X.Yu,J.M.Brannan,G.Bi,Q.Zhang,S.Schein,Z.H.Zhou
Key ref: X.Zhang et al. (2013). Cryo-EM structure of the mature dengue virus at 3.5-Å resolution. Nat Struct Mol Biol, 20, 105-110. PubMed id: 23241927
Date:
30-Nov-12     Release date:   19-Dec-12    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P14340  (POLG_DEN2N) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
3391 a.a.
495 a.a.
Protein chains
Pfam   ArchSchema ?
P14340  (POLG_DEN2N) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
3391 a.a.
72 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 1: Chains A, B, C, D: E.C.2.1.1.56  - mRNA (guanine-N(7)-)-methyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: S-adenosyl-L-methionine + G(5')pppR-RNA = S-adenosyl-L-homocysteine + m7G(5')pppR-RNA
S-adenosyl-L-methionine
+ G(5')pppR-RNA
= S-adenosyl-L-homocysteine
+ m(7)G(5')pppR-RNA
   Enzyme class 2: Chains A, B, C, D: E.C.2.1.1.57  - Methyltransferase cap1.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: S-adenosyl-L-methionine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)- (purine-ribonucleotide)-(mRNA) = S-adenosyl-L-homocysteine + a 5'-(N(7)- methyl 5'-triphosphoguanosine)-(2'-O-methyl-purine-ribonucleotide)- (mRNA)
S-adenosyl-L-methionine
+ 5'-(N(7)-methyl 5'-triphosphoguanosine)- (purine-ribonucleotide)-(mRNA)
= S-adenosyl-L-homocysteine
+ 5'-(N(7)- methyl 5'-triphosphoguanosine)-(2'-O-methyl-purine-ribonucleotide)- (mRNA)
   Enzyme class 3: Chains A, B, C, D: E.C.2.7.7.48  - RNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Nucleoside triphosphate
+ RNA(n)
= diphosphate
+ RNA(n+1)
   Enzyme class 4: Chains A, B, C, D: E.C.3.4.21.91  - Flavivirin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Selective hydrolysis of Xaa-Xaa-|-Xbb bonds in which each of the Xaa can be either Arg or Lys and Xbb can be either Ser or Ala.
   Enzyme class 5: Chains A, B, C, D: E.C.3.6.1.15  - Nucleoside-triphosphate phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NTP + H2O = NDP + phosphate
NTP
+ H(2)O
= NDP
+ phosphate
   Enzyme class 6: Chains A, B, C, D: E.C.3.6.4.13  - Rna helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate
ATP
+ H(2)O
=
ADP
Bound ligand (Het Group name = NAG)
matches with 41.38% similarity
+ phosphate
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     viral envelope   2 terms 
  Biological process     viral infectious cycle   1 term 
  Biochemical function     protein dimerization activity     1 term  

 

 
    reference    
 
 
Nat Struct Mol Biol 20:105-110 (2013)
PubMed id: 23241927  
 
 
Cryo-EM structure of the mature dengue virus at 3.5-Å resolution.
X.Zhang, P.Ge, X.Yu, J.M.Brannan, G.Bi, Q.Zhang, S.Schein, Z.H.Zhou.
 
  ABSTRACT  
 
Regulated by pH, membrane-anchored proteins E and M function during dengue virus maturation and membrane fusion. Our atomic model of the whole virion from cryo-electron microscopy at 3.5-Å resolution reveals that in the mature virus at neutral extracellular pH, the N-terminal 20-amino-acid segment of M (involving three pH-sensing histidines) latches and thereby prevents spring-loaded E fusion protein from prematurely exposing its fusion peptide. This M latch is fastened at an earlier stage, during maturation at acidic pH in the trans-Golgi network. At a later stage, to initiate infection in response to acidic pH in the late endosome, M releases the latch and exposes the fusion peptide. Thus, M serves as a multistep chaperone of E to control the conformational changes accompanying maturation and infection. These pH-sensitive interactions could serve as targets for drug discovery.