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Contents |
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77 a.a.
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155 a.a.
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143 a.a.
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191 a.a.
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* Residue conservation analysis
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PDB id:
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| Name: |
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Viral protein, replication
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Title:
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Crystal structure of sars-cov super complex of non-structural proteins: the hexadecamer
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Structure:
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Replicase polyprotein 1ab, light chain. Chain: a, b, c, d. Synonym: replicase nsp7. Engineered: yes. Replicase polyprotein 1ab, heavy chain. Chain: e, f, g, h. Synonym: replicase nsp8. Engineered: yes
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Source:
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Sars coronavirus. Organism_taxid: 227859. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
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Biol. unit:
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60mer (from PDB file)
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Resolution:
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2.40Å
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R-factor:
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0.213
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R-free:
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0.251
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Authors:
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Y.J.Zhai,F.Sun,M.Bartlam,Z.Rao
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Key ref:
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Y.Zhai
et al.
(2005).
Insights into SARS-CoV transcription and replication from the structure of the nsp7-nsp8 hexadecamer.
Nat Struct Biol,
12,
980-986.
PubMed id:
DOI:
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Date:
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28-Jul-05
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Release date:
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15-Nov-05
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PROCHECK
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Headers
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References
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P0C6X7
(R1AB_CVHSA) -
Replicase polyprotein 1ab from Severe acute respiratory syndrome coronavirus
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Seq:
Struc:
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7073 a.a.
77 a.a.*
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P0C6X7
(R1AB_CVHSA) -
Replicase polyprotein 1ab from Severe acute respiratory syndrome coronavirus
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Seq:
Struc:
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7073 a.a.
155 a.a.
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Enzyme class 2:
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Chains A, B, C, D, E, F, G, H:
E.C.2.1.1.-
- ?????
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Enzyme class 3:
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Chains A, B, C, D, E, F, G, H:
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 4:
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Chains A, B, C, D, E, F, G, H:
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 5:
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Chains A, B, C, D, E, F, G, H:
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 6:
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Chains A, B, C, D, E, F, G, H:
E.C.2.7.7.50
- mRNA guanylyltransferase.
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Reaction:
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a 5'-end diphospho-ribonucleoside in mRNA + GTP + H+ = a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + diphosphate
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5'-end diphospho-ribonucleoside in mRNA
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+
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GTP
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+
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H(+)
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=
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5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA
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+
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diphosphate
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Enzyme class 7:
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Chains A, B, C, D, E, F, G, H:
E.C.3.1.13.-
- ?????
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Enzyme class 8:
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Chains A, B, C, D, E, F, G, H:
E.C.3.4.19.12
- ubiquitinyl hydrolase 1.
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Reaction:
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Thiol-dependent hydrolysis of ester, thiolester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
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Enzyme class 9:
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Chains A, B, C, D, E, F, G, H:
E.C.3.4.22.-
- ?????
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Enzyme class 10:
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Chains A, B, C, D, E, F, G, H:
E.C.3.4.22.69
- Sars coronavirus main proteinase.
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Enzyme class 11:
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Chains A, B, C, D, E, F, G, H:
E.C.3.6.4.12
- Dna 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
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+
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phosphate
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+
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H(+)
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Enzyme class 12:
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Chains A, B, C, D, E, F, G, H:
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
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+
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phosphate
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+
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H(+)
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Enzyme class 13:
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Chains A, B, C, D, E, F, G, H:
E.C.4.6.1.-
- ?????
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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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DOI no:
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Nat Struct Biol
12:980-986
(2005)
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PubMed id:
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| |
|
Insights into SARS-CoV transcription and replication from the structure of the nsp7-nsp8 hexadecamer.
|
|
Y.Zhai,
F.Sun,
X.Li,
H.Pang,
X.Xu,
M.Bartlam,
Z.Rao.
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ABSTRACT
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Coronavirus replication and transcription machinery involves multiple
virus-encoded nonstructural proteins (nsp). We report the crystal structure of
the hexadecameric nsp7-nsp8 supercomplex from the severe acute respiratory
syndrome coronavirus at 2.4-angstroms resolution. nsp8 has a novel 'golf-club'
fold with two conformations. The supercomplex is a unique hollow, cylinder-like
structure assembled from eight copies of nsp8 and held tightly together by eight
copies of nsp7. With an internal diameter of approximately 30 angstroms, the
central channel has dimensions and positive electrostatic properties favorable
for nucleic acid binding, implying that its role is to confer processivity on
RNA-dependent RNA polymerase.
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Selected figure(s)
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Figure 3.
Figure 3. Architecture and assembly of the hexadecameric
nsp7–nsp8 complex. (a) The interaction sites between nsp7
and nsp8I/II. Green, nsp7; blue, nsp8. (b) T1 and T2
heterotetramer formation. The two dimers from one tetramer are
illustrated by the surface representation and ribbon diagram,
respectively. Residues: green, polar; yellow, hydrophobic; red,
acidic; blue, basic. Ribbons: green, nsp7; blue, nsp8I; orange,
nsp8II. (c) Possible pathway for assembly of the complex by
heterotetramers T1 and T2. (d) Hexadecameric supercomplex
construction with 'bricks' of nsp8 and 'mortar' of nsp7. The
angle between nsp8I and nsp8II is labeled in magenta. In c and
d, nsp7 molecules interacting with nsp8I and nsp8II are colored
yellow-green and blue-green, respectively.
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Figure 4.
Figure 4. Hypothetical interaction between RNA and the
hexadecameric nsp7–nsp8 complex. (a) The electrostatic
potential surface of the hexadecamer modeled with (right) and
without (left) duplex RNA in the positive channel. Blue,
positive charge (+10 k[B]T); red, negative charge (-10 k[B]T).
(b) Model of the hexadecameric nsp7–nsp8 supercomplex with
hypothetical duplex RNA. Left, top view, showing the channel's
proper dimensions to accommodate dsRNA. Right, side view,
showing a possible mode of interaction where the four nsp8II NH3
helices insert into the dsRNA grooves. (c,d) Results of EMSAs of
nsp7, nsp8 and their mutants. Each lane contains 75 pmol dsRNA
(c) or dsDNA (d). Lanes 1–7 contain 650 pmol of each protein;
lanes 8–13 contain 90 pmol of hexadecamer.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(2005,
12,
980-986)
copyright 2005.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
|
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| |
PubMed id
|
|
Reference
|
|
|
|
|
|
A.J.te Velthuis,
S.H.van den Worm,
A.C.Sims,
R.S.Baric,
E.J.Snijder,
and
M.J.van Hemert
(2010).
Zn(2+) inhibits coronavirus and arterivirus RNA polymerase activity in vitro and zinc ionophores block the replication of these viruses in cell culture.
|
| |
PLoS Pathog,
6,
e1001176.
|
|
|
|
|
|
|
M.C.Hagemeijer,
M.H.Verheije,
M.Ulasli,
I.A.Shaltiël,
L.A.de Vries,
F.Reggiori,
P.J.Rottier,
and
C.A.de Haan
(2010).
Dynamics of coronavirus replication-transcription complexes.
|
| |
J Virol,
84,
2134-2149.
|
|
|
|
|
|
|
S.Fang,
H.Shen,
J.Wang,
F.P.Tay,
and
D.X.Liu
(2010).
Functional and genetic studies of the substrate specificity of coronavirus infectious bronchitis virus 3C-like proteinase.
|
| |
J Virol,
84,
7325-7336.
|
|
|
|
|
|
|
Z.J.Miknis,
E.F.Donaldson,
T.C.Umland,
R.A.Rimmer,
R.S.Baric,
and
L.W.Schultz
(2009).
Severe acute respiratory syndrome coronavirus nsp9 dimerization is essential for efficient viral growth.
|
| |
J Virol,
83,
3007-3018.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
B.Canard,
J.S.Joseph,
and
P.Kuhn
(2008).
International research networks in viral structural proteomics: again, lessons from SARS.
|
| |
Antiviral Res,
78,
47-50.
|
|
|
|
|
|
|
J.Pan,
X.Peng,
Y.Gao,
Z.Li,
X.Lu,
Y.Chen,
M.Ishaq,
D.Liu,
M.L.Dediego,
L.Enjuanes,
and
D.Guo
(2008).
Genome-wide analysis of protein-protein interactions and involvement of viral proteins in SARS-CoV replication.
|
| |
PLoS ONE,
3,
e3299.
|
|
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|
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|
K.Knoops,
M.Kikkert,
S.H.Worm,
J.C.Zevenhoven-Dobbe,
Y.van der Meer,
A.J.Koster,
A.M.Mommaas,
and
E.J.Snijder
(2008).
SARS-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum.
|
| |
PLoS Biol,
6,
e226.
|
|
|
|
|
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|
M.J.van Hemert,
S.H.van den Worm,
K.Knoops,
A.M.Mommaas,
A.E.Gorbalenya,
and
E.J.Snijder
(2008).
SARS-coronavirus replication/transcription complexes are membrane-protected and need a host factor for activity in vitro.
|
| |
PLoS Pathog,
4,
e1000054.
|
|
|
|
|
|
|
M.Oostra,
M.C.Hagemeijer,
M.van Gent,
C.P.Bekker,
E.G.te Lintelo,
P.J.Rottier,
and
C.A.de Haan
(2008).
Topology and membrane anchoring of the coronavirus replication complex: not all hydrophobic domains of nsp3 and nsp6 are membrane spanning.
|
| |
J Virol,
82,
12392-12405.
|
|
|
|
|
|
|
R.L.Graham,
J.S.Sparks,
L.D.Eckerle,
A.C.Sims,
and
M.R.Denison
(2008).
SARS coronavirus replicase proteins in pathogenesis.
|
| |
Virus Res,
133,
88.
|
|
|
|
|
|
|
R.Züst,
T.B.Miller,
S.J.Goebel,
V.Thiel,
and
P.S.Masters
(2008).
Genetic interactions between an essential 3' cis-acting RNA pseudoknot, replicase gene products, and the extreme 3' end of the mouse coronavirus genome.
|
| |
J Virol,
82,
1214-1228.
|
|
|
|
|
|
|
A.von Brunn,
C.Teepe,
J.C.Simpson,
R.Pepperkok,
C.C.Friedel,
R.Zimmer,
R.Roberts,
R.Baric,
and
J.Haas
(2007).
Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome.
|
| |
PLoS ONE,
2,
e459.
|
|
|
|
|
|
|
D.J.Deming,
R.L.Graham,
M.R.Denison,
and
R.S.Baric
(2007).
Processing of open reading frame 1a replicase proteins nsp7 to nsp10 in murine hepatitis virus strain A59 replication.
|
| |
J Virol,
81,
10280-10291.
|
|
|
|
|
|
|
E.F.Donaldson,
A.C.Sims,
R.L.Graham,
M.R.Denison,
and
R.S.Baric
(2007).
Murine hepatitis virus replicase protein nsp10 is a critical regulator of viral RNA synthesis.
|
| |
J Virol,
81,
6356-6368.
|
|
|
|
|
|
|
G.S.Briggs,
P.A.McEwan,
J.Yu,
T.Moore,
J.Emsley,
and
R.G.Lloyd
(2007).
Ring structure of the Escherichia coli DNA-binding protein RdgC associated with recombination and replication fork repair.
|
| |
J Biol Chem,
282,
12353-12357.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.Ziebuhr,
B.Schelle,
N.Karl,
E.Minskaia,
S.Bayer,
S.G.Siddell,
A.E.Gorbalenya,
and
V.Thiel
(2007).
Human coronavirus 229E papain-like proteases have overlapping specificities but distinct functions in viral replication.
|
| |
J Virol,
81,
3922-3932.
|
|
|
|
|
|
|
M.Bartlam,
Y.Xu,
and
Z.Rao
(2007).
Structural proteomics of the SARS coronavirus: a model response to emerging infectious diseases.
|
| |
J Struct Funct Genomics,
8,
85-97.
|
|
|
|
|
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|
M.Oostra,
E.G.te Lintelo,
M.Deijs,
M.H.Verheije,
P.J.Rottier,
and
C.A.de Haan
(2007).
Localization and membrane topology of coronavirus nonstructural protein 4: involvement of the early secretory pathway in replication.
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| |
J Virol,
81,
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|
|
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|
|
|
|
M.S.Almeida,
M.A.Johnson,
T.Herrmann,
M.Geralt,
and
K.Wüthrich
(2007).
Novel beta-barrel fold in the nuclear magnetic resonance structure of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus.
|
| |
J Virol,
81,
3151-3161.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
P.Serrano,
M.A.Johnson,
M.S.Almeida,
R.Horst,
T.Herrmann,
J.S.Joseph,
B.W.Neuman,
V.Subramanian,
K.S.Saikatendu,
M.J.Buchmeier,
R.C.Stevens,
P.Kuhn,
and
K.Wüthrich
(2007).
Nuclear magnetic resonance structure of the N-terminal domain of nonstructural protein 3 from the severe acute respiratory syndrome coronavirus.
|
| |
J Virol,
81,
12049-12060.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
S.G.Sawicki,
D.L.Sawicki,
and
S.G.Siddell
(2007).
A contemporary view of coronavirus transcription.
|
| |
J Virol,
81,
20-29.
|
|
|
|
|
|
|
V.C.Cheng,
S.K.Lau,
P.C.Woo,
and
K.Y.Yuen
(2007).
Severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection.
|
| |
Clin Microbiol Rev,
20,
660-694.
|
|
|
|
|
|
|
Z.Rao
(2007).
History of protein crystallography in China.
|
| |
Philos Trans R Soc Lond B Biol Sci,
362,
1035-1042.
|
|
|
|
|
|
|
A.E.Gorbalenya,
L.Enjuanes,
J.Ziebuhr,
and
E.J.Snijder
(2006).
Nidovirales: evolving the largest RNA virus genome.
|
| |
Virus Res,
117,
17-37.
|
|
|
|
|
|
|
D.Su,
Z.Lou,
F.Sun,
Y.Zhai,
H.Yang,
R.Zhang,
A.Joachimiak,
X.C.Zhang,
M.Bartlam,
and
Z.Rao
(2006).
Dodecamer structure of severe acute respiratory syndrome coronavirus nonstructural protein nsp10.
|
| |
J Virol,
80,
7902-7908.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
E.J.Snijder,
Y.van der Meer,
J.Zevenhoven-Dobbe,
J.J.Onderwater,
J.van der Meulen,
H.K.Koerten,
and
A.M.Mommaas
(2006).
Ultrastructure and origin of membrane vesicles associated with the severe acute respiratory syndrome coronavirus replication complex.
|
| |
J Virol,
80,
5927-5940.
|
|
|
|
|
|
|
H.Schütze,
R.Ulferts,
B.Schelle,
S.Bayer,
H.Granzow,
B.Hoffmann,
T.C.Mettenleiter,
and
J.Ziebuhr
(2006).
Characterization of White bream virus reveals a novel genetic cluster of nidoviruses.
|
| |
J Virol,
80,
11598-11609.
|
|
|
|
|
|
|
I.Imbert,
J.C.Guillemot,
J.M.Bourhis,
C.Bussetta,
B.Coutard,
M.P.Egloff,
F.Ferron,
A.E.Gorbalenya,
and
B.Canard
(2006).
A second, non-canonical RNA-dependent RNA polymerase in SARS coronavirus.
|
| |
EMBO J,
25,
4933-4942.
|
|
|
|
|
|
|
J.R.Mesters,
J.Tan,
and
R.Hilgenfeld
(2006).
Viral enzymes.
|
| |
Curr Opin Struct Biol,
16,
776-786.
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J.S.Joseph,
K.S.Saikatendu,
V.Subramanian,
B.W.Neuman,
A.Brooun,
M.Griffith,
K.Moy,
M.K.Yadav,
J.Velasquez,
M.J.Buchmeier,
R.C.Stevens,
and
P.Kuhn
(2006).
Crystal structure of nonstructural protein 10 from the severe acute respiratory syndrome coronavirus reveals a novel fold with two zinc-binding motifs.
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J Virol,
80,
7894-7901.
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PDB code:
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M.D.Sørensen,
B.Sørensen,
R.Gonzalez-Dosal,
C.J.Melchjorsen,
J.Weibel,
J.Wang,
C.W.Jun,
Y.Huanming,
and
P.Kristensen
(2006).
Severe acute respiratory syndrome (SARS): development of diagnostics and antivirals.
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| |
Ann N Y Acad Sci,
1067,
500-505.
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S.Ricagno,
M.P.Egloff,
R.Ulferts,
B.Coutard,
D.Nurizzo,
V.Campanacci,
C.Cambillau,
J.Ziebuhr,
and
B.Canard
(2006).
Crystal structure and mechanistic determinants of SARS coronavirus nonstructural protein 15 define an endoribonuclease family.
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| |
Proc Natl Acad Sci U S A,
103,
11892-11897.
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PDB code:
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X.Xu,
Y.Zhai,
F.Sun,
Z.Lou,
D.Su,
Y.Xu,
R.Zhang,
A.Joachimiak,
X.C.Zhang,
M.Bartlam,
and
Z.Rao
(2006).
New antiviral target revealed by the hexameric structure of mouse hepatitis virus nonstructural protein nsp15.
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| |
J Virol,
80,
7909-7917.
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PDB codes:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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