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PDBsum entry 1svb
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Viral protein
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PDB id
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1svb
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Contents |
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* Residue conservation analysis
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Enzyme class 1:
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E.C.2.1.1.56
- mRNA (guanine-N(7))-methyltransferase.
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Reaction:
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a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L- methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-homocysteine
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5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA
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+
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S-adenosyl-L- methionine
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=
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5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA
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+
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S-adenosyl-L-homocysteine
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Enzyme class 2:
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E.C.2.1.1.57
- methyltransferase cap1.
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Reaction:
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a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)- (2'-O-methyl-ribonucleoside) in mRNA + S-adenosyl-L-homocysteine + H+
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5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA
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+
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S-adenosyl-L-methionine
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=
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5'-end (N(7)-methyl 5'-triphosphoguanosine)- (2'-O-methyl-ribonucleoside) in mRNA
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+
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S-adenosyl-L-homocysteine
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+
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H(+)
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Enzyme class 3:
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E.C.2.7.7.48
- RNA-directed Rna polymerase.
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Reaction:
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RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
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RNA(n)
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+
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ribonucleoside 5'-triphosphate
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=
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RNA(n+1)
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+
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diphosphate
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Enzyme class 4:
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E.C.3.4.21.91
- flavivirin.
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Reaction:
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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.
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Enzyme class 5:
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E.C.3.6.1.15
- nucleoside-triphosphate phosphatase.
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Reaction:
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a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H+
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ribonucleoside 5'-triphosphate
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+
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H2O
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=
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ribonucleoside 5'-diphosphate
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+
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phosphate
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+
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H(+)
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Enzyme class 6:
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E.C.3.6.4.13
- Rna helicase.
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Reaction:
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ATP + H2O = ADP + phosphate + H+
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ATP
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+
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H2O
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=
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ADP
Bound ligand (Het Group name = )
matches with 41.38% similarity
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+
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phosphate
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+
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H(+)
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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.
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Nature
375:291-298
(1995)
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PubMed id:
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The envelope glycoprotein from tick-borne encephalitis virus at 2 A resolution.
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F.A.Rey,
F.X.Heinz,
C.Mandl,
C.Kunz,
S.C.Harrison.
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ABSTRACT
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The crystallographically determined structure of a soluble fragment from the
major envelope protein of a flavivirus reveals an unusual architecture. The
flat, elongated dimer extends in a direction that would be parallel to the viral
membrane. Residues that influence binding of monoclonal antibodies lie on the
outward-facing surface of the protein. The clustering of mutations that affect
virulence in various flaviviruses indicates a possible receptor binding site
and, together with other mutational and biochemical data, suggests a picture for
the fusion-activating, conformational change triggered by low pH.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
|
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R.M.DuBois,
M.C.Vaney,
M.A.Tortorici,
R.A.Kurdi,
G.Barba-Spaeth,
T.Krey,
and
F.A.Rey
(2013).
Functional and evolutionary insight from the crystal structure of rubella virus protein E1.
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| |
Nature,
493,
552-556.
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PDB codes:
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A.Ikawa-Yoshida,
K.Yoshii,
K.Kuwahara,
M.Obara,
H.Kariwa,
and
I.Takashima
(2011).
Development of an ELISA system for tick-borne encephalitis virus infection in rodents.
|
| |
Microbiol Immunol,
55,
100-107.
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|
|
|
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|
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A.Umamaheswari,
M.M.Kumar,
D.Pradhan,
and
H.Marisetty
(2011).
Docking studies towards exploring antiviral compounds against envelope protein of yellow fever virus.
|
| |
Interdiscip Sci,
3,
64-77.
|
|
|
|
|
|
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B.R.Murphy,
and
S.S.Whitehead
(2011).
Immune response to dengue virus and prospects for a vaccine.
|
| |
Annu Rev Immunol,
29,
587-619.
|
|
|
|
|
|
|
D.W.Beasley
(2011).
Vaccines and immunotherapeutics for the prevention and treatment of infections with West Nile virus.
|
| |
Immunotherapy,
3,
269-285.
|
|
|
|
|
|
|
N.Cifuentes-Muñoz,
G.P.Barriga,
P.D.Valenzuela,
and
N.D.Tischler
(2011).
Aromatic and polar residues spanning the candidate fusion peptide of the Andes virus Gc protein are essential for membrane fusion and infection.
|
| |
J Gen Virol,
92,
552-563.
|
|
|
|
|
|
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R.Gäumann,
D.Růžek,
K.Mühlemann,
M.Strasser,
and
C.M.Beuret
(2011).
Phylogenetic and virulence analysis of tick-borne encephalitis virus field isolates from Switzerland.
|
| |
J Med Virol,
83,
853-863.
|
|
|
|
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|
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S.Butrapet,
T.Childers,
K.J.Moss,
S.M.Erb,
B.E.Luy,
A.E.Calvert,
C.D.Blair,
J.T.Roehrig,
and
C.Y.Huang
(2011).
Amino acid changes within the E protein hinge region that affect dengue virus type 2 infectivity and fusion.
|
| |
Virology,
413,
118-127.
|
|
|
|
|
|
|
S.Indu,
V.Kochat,
S.Thakurela,
C.Ramakrishnan,
and
R.Varadarajan
(2011).
Conformational analysis and design of cross-strand disulfides in antiparallel β-sheets.
|
| |
Proteins,
79,
244-260.
|
|
|
|
|
|
|
A.G.Schmidt,
P.L.Yang,
and
S.C.Harrison
(2010).
Peptide inhibitors of dengue-virus entry target a late-stage fusion intermediate.
|
| |
PLoS Pathog,
6,
e1000851.
|
|
|
|
|
|
|
A.J.Schuh,
L.Li,
R.B.Tesh,
B.L.Innis,
and
A.D.Barrett
(2010).
Genetic characterization of early isolates of Japanese encephalitis virus: genotype II has been circulating since at least 1951.
|
| |
J Gen Virol,
91,
95.
|
|
|
|
|
|
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A.Ko,
E.W.Lee,
J.Y.Yeh,
M.R.Yang,
W.Oh,
J.S.Moon,
and
J.Song
(2010).
MKRN1 induces degradation of West Nile virus capsid protein by functioning as an E3 ligase.
|
| |
J Virol,
84,
426-436.
|
|
|
|
|
|
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A.Zheng,
M.Umashankar,
and
M.Kielian
(2010).
In vitro and in vivo studies identify important features of dengue virus pr-E protein interactions.
|
| |
PLoS Pathog,
6,
e1001157.
|
|
|
|
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|
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B.Kaufmann,
M.R.Vogt,
J.Goudsmit,
H.A.Holdaway,
A.A.Aksyuk,
P.R.Chipman,
R.J.Kuhn,
M.S.Diamond,
and
M.G.Rossmann
(2010).
Neutralization of West Nile virus by cross-linking of its surface proteins with Fab fragments of the human monoclonal antibody CR4354.
|
| |
Proc Natl Acad Sci U S A,
107,
18950-18955.
|
|
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PDB codes:
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B.Shrestha,
J.D.Brien,
S.Sukupolvi-Petty,
S.K.Austin,
M.A.Edeling,
T.Kim,
K.M.O'Brien,
C.A.Nelson,
S.Johnson,
D.H.Fremont,
and
M.S.Diamond
(2010).
The development of therapeutic antibodies that neutralize homologous and heterologous genotypes of dengue virus type 1.
|
| |
PLoS Pathog,
6,
e1000823.
|
|
|
|
|
|
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C.J.Baldick,
M.J.Wichroski,
A.Pendri,
A.W.Walsh,
J.Fang,
C.E.Mazzucco,
K.A.Pokornowski,
R.E.Rose,
B.J.Eggers,
M.Hsu,
W.Zhai,
G.Zhai,
S.W.Gerritz,
M.A.Poss,
N.A.Meanwell,
M.I.Cockett,
and
D.J.Tenney
(2010).
A novel small molecule inhibitor of hepatitis C virus entry.
|
| |
PLoS Pathog,
6,
0.
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E.Lee,
S.K.Leang,
A.Davidson,
and
M.Lobigs
(2010).
Both E protein glycans adversely affect dengue virus infectivity but are beneficial for virion release.
|
| |
J Virol,
84,
5171-5180.
|
|
|
|
|
|
|
G.D.Ebel
(2010).
Update on Powassan virus: emergence of a North American tick-borne flavivirus.
|
| |
Annu Rev Entomol,
55,
95.
|
|
|
|
|
|
|
H.L.Chen,
S.Y.Her,
K.C.Huang,
H.T.Cheng,
C.W.Wu,
S.C.Wu,
and
J.W.Cheng
(2010).
Identification of a heparin binding peptide from the Japanese encephalitis virus envelope protein.
|
| |
Biopolymers,
94,
331-338.
|
|
|
|
|
|
|
I.A.Rodenhuis-Zybert,
J.Wilschut,
and
J.M.Smit
(2010).
Dengue virus life cycle: viral and host factors modulating infectivity.
|
| |
Cell Mol Life Sci,
67,
2773-2786.
|
|
|
|
|
|
|
J.E.Voss,
M.C.Vaney,
S.Duquerroy,
C.Vonrhein,
C.Girard-Blanc,
E.Crublet,
A.Thompson,
G.Bricogne,
and
F.A.Rey
(2010).
Glycoprotein organization of Chikungunya virus particles revealed by X-ray crystallography.
|
| |
Nature,
468,
709-712.
|
|
|
PDB codes:
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|
|
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|
|
J.Hepojoki,
T.Strandin,
A.Vaheri,
and
H.Lankinen
(2010).
Interactions and oligomerization of hantavirus glycoproteins.
|
| |
J Virol,
84,
227-242.
|
|
|
|
|
|
|
J.M.Costin,
E.Jenwitheesuk,
S.M.Lok,
E.Hunsperger,
K.A.Conrads,
K.A.Fontaine,
C.R.Rees,
M.G.Rossmann,
S.Isern,
R.Samudrala,
and
S.F.Michael
(2010).
Structural optimization and de novo design of dengue virus entry inhibitory peptides.
|
| |
PLoS Negl Trop Dis,
4,
e721.
|
|
|
|
|
|
|
J.S.Schieffelin,
J.M.Costin,
C.O.Nicholson,
N.M.Orgeron,
K.A.Fontaine,
S.Isern,
S.F.Michael,
and
J.E.Robinson
(2010).
Neutralizing and non-neutralizing monoclonal antibodies against dengue virus E protein derived from a naturally infected patient.
|
| |
Virol J,
7,
28.
|
|
|
|
|
|
|
K.Matsui,
G.D.Gromowski,
L.Li,
and
A.D.Barrett
(2010).
Characterization of a dengue type-specific epitope on dengue 3 virus envelope protein domain III.
|
| |
J Gen Virol,
91,
2249-2253.
|
|
|
|
|
|
|
M.D.Dunn,
S.L.Rossi,
D.M.Carter,
M.R.Vogt,
E.Mehlhop,
M.S.Diamond,
and
T.M.Ross
(2010).
Enhancement of anti-DIII antibodies by the C3d derivative P28 results in lower viral titers and augments protection in mice.
|
| |
Virol J,
7,
95.
|
|
|
|
|
|
|
M.Kielian,
C.Chanel-Vos,
and
M.Liao
(2010).
Alphavirus Entry and Membrane Fusion.
|
| |
Viruses,
2,
796-825.
|
|
|
|
|
|
|
P.Danecek,
W.Lu,
and
C.H.Schein
(2010).
PCP consensus sequences of flaviviruses: correlating variance with vector competence and disease phenotype.
|
| |
J Mol Biol,
396,
550-563.
|
|
|
|
|
|
|
R.M.Markosyan,
and
F.S.Cohen
(2010).
Negative potentials across biological membranes promote fusion by class II and class III viral proteins.
|
| |
Mol Biol Cell,
21,
2001-2012.
|
|
|
|
|
|
|
S.C.Hsieh,
W.Y.Tsai,
and
W.K.Wang
(2010).
The length of and nonhydrophobic residues in the transmembrane domain of dengue virus envelope protein are critical for its retention and assembly in the endoplasmic reticulum.
|
| |
J Virol,
84,
4782-4797.
|
|
|
|
|
|
|
S.R.Kumar,
J.A.Patil,
D.Cecilia,
S.S.Cherian,
P.V.Barde,
A.M.Walimbe,
P.D.Yadav,
P.N.Yergolkar,
P.S.Shah,
V.S.Padbidri,
A.C.Mishra,
and
D.T.Mourya
(2010).
Evolution, dispersal and replacement of American genotype dengue type 2 viruses in India (1956-2005): selection pressure and molecular clock analyses.
|
| |
J Gen Virol,
91,
707-720.
|
|
|
|
|
|
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W.M.Wahala,
E.F.Donaldson,
R.de Alwis,
M.A.Accavitti-Loper,
R.S.Baric,
and
A.M.de Silva
(2010).
Natural strain variation and antibody neutralization of dengue serotype 3 viruses.
|
| |
PLoS Pathog,
6,
e1000821.
|
|
|
|
|
|
|
Y.T.Shih,
C.F.Yang,
and
W.J.Chen
(2010).
Upregulation of a novel eukaryotic translation initiation factor 5A (eIF5A) in dengue 2 virus-infected mosquito cells.
|
| |
Virol J,
7,
214.
|
|
|
|
|
|
|
A.A.Amarilla,
F.T.de Almeida,
D.M.Jorge,
H.L.Alfonso,
L.A.de Castro-Jorge,
N.A.Nogueira,
L.T.Figueiredo,
and
V.H.Aquino
(2009).
Genetic diversity of the E protein of dengue type 3 virus.
|
| |
Virol J,
6,
113.
|
|
|
|
|
|
|
B.Kaufmann,
P.R.Chipman,
H.A.Holdaway,
S.Johnson,
D.H.Fremont,
R.J.Kuhn,
M.S.Diamond,
and
M.G.Rossmann
(2009).
Capturing a flavivirus pre-fusion intermediate.
|
| |
PLoS Pathog,
5,
e1000672.
|
|
|
|
|
|
|
B.S.Thompson,
B.Moesker,
J.M.Smit,
J.Wilschut,
M.S.Diamond,
and
D.H.Fremont
(2009).
A therapeutic antibody against west nile virus neutralizes infection by blocking fusion within endosomes.
|
| |
PLoS Pathog,
5,
e1000453.
|
|
|
|
|
|
|
C.E.Garry,
and
R.F.Garry
(2009).
Proteomics computational analyses suggest that the bornavirus glycoprotein is a class III viral fusion protein (gamma penetrene).
|
| |
Virol J,
6,
145.
|
|
|
|
|
|
|
C.Sánchez-San Martín,
C.Y.Liu,
and
M.Kielian
(2009).
Dealing with low pH: entry and exit of alphaviruses and flaviviruses.
|
| |
Trends Microbiol,
17,
514-521.
|
|
|
|
|
|
|
D.E.Volk,
F.J.May,
S.H.Gandham,
A.Anderson,
J.J.Von Lindern,
D.W.Beasley,
A.D.Barrett,
and
D.G.Gorenstein
(2009).
Structure of yellow fever virus envelope protein domain III.
|
| |
Virology,
394,
12-18.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
D.Mudhakir,
and
H.Harashima
(2009).
Learning from the viral journey: how to enter cells and how to overcome intracellular barriers to reach the nucleus.
|
| |
AAPS J,
11,
65-77.
|
|
|
|
|
|
|
G.Añez,
R.Men,
K.H.Eckels,
and
C.J.Lai
(2009).
Passage of dengue virus type 4 vaccine candidates in fetal rhesus lung cells selects heparin-sensitive variants that result in loss of infectivity and immunogenicity in rhesus macaques.
|
| |
J Virol,
83,
10384-10394.
|
|
|
|
|
|
|
H.F.Li,
C.H.Huang,
L.S.Ai,
C.K.Chuang,
and
S.S.Chen
(2009).
Mutagenesis of the fusion peptide-like domain of hepatitis C virus E1 glycoprotein: involvement in cell fusion and virus entry.
|
| |
J Biomed Sci,
16,
89.
|
|
|
|
|
|
|
I.M.Yu,
H.A.Holdaway,
P.R.Chipman,
R.J.Kuhn,
M.G.Rossmann,
and
J.Chen
(2009).
Association of the pr peptides with dengue virus at acidic pH blocks membrane fusion.
|
| |
J Virol,
83,
12101-12107.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.E.Lee,
and
E.O.Saphire
(2009).
Neutralizing ebolavirus: structural insights into the envelope glycoprotein and antibodies targeted against it.
|
| |
Curr Opin Struct Biol,
19,
408-417.
|
|
|
|
|
|
|
J.E.Lee,
and
E.O.Saphire
(2009).
Ebolavirus glycoprotein structure and mechanism of entry.
|
| |
Future Virol,
4,
621-635.
|
|
|
|
|
|
|
J.Jose,
J.E.Snyder,
and
R.J.Kuhn
(2009).
A structural and functional perspective of alphavirus replication and assembly.
|
| |
Future Microbiol,
4,
837-856.
|
|
|
|
|
|
|
K.L.Mansfield,
N.Johnson,
L.P.Phipps,
J.R.Stephenson,
A.R.Fooks,
and
T.Solomon
(2009).
Tick-borne encephalitis virus - a review of an emerging zoonosis.
|
| |
J Gen Virol,
90,
1781-1794.
|
|
|
|
|
|
|
L.Bernardo,
O.Fleitas,
A.Pavón,
L.Hermida,
G.Guillén,
and
M.G.Guzman
(2009).
Antibodies induced by dengue virus type 1 and 2 envelope domain III recombinant proteins in monkeys neutralize strains with different genotypes.
|
| |
Clin Vaccine Immunol,
16,
1829-1831.
|
|
|
|
|
|
|
M.A.Khasnatinov,
K.Ustanikova,
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Where a reference describes a PDB structure, the PDB
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