|
|
main |
|
search |
|
tutorial |
|
faq |
|
Pfam::Home |
|
 CASP7 Protein CorreLogo
Set your name in
UserPreferences
JSPWiki v2.2.33
|
October 11, 2006Using data from the HCV Los Alamos database Setting up a new page for results HCV-GENOME October 5, 2006To view larger images click on the links at the bottom of the page.To view 3D models install the X3D viewer Octaga from http://www.octaga.com The NS5A 3D logo model is so small that the default view is a white screen. Turn around 180 degrees to see the model. It helps to turn off collision and gravity the two buttons next to the headlight on the menu bar. This way you won't get stuck on objects when navigating. NS5BPF00998Viral RNA dependent RNA polymerase 4732 sequences 15 PDB
The (265,313) pair is 27 angstroms apart between two helixes that appear to be on the dimer side of the A-B tertiary structures. The sequence position 271-G is common for the next seven pairs so is probably of some interest.
NS5APF08300Hepatitis C virus non-structural 5a zinc finger domain
PF08301Hepatitis C virus non-structural 5a domain 1bThis functional family has a high number of sequences that to allow alignment for the entire family has a large block of inserts. Mutual Information is not calculated for this region so the absense of MI columns in the CorreLogo graph is because it was not calculated.
PF01506Hepatitis C virus non-structural 5a protein membrane anchorThe molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR, P19525 1,2. The N-terminal region of the NS5a protein has been used in the construction of the alignment for this family. The C-terminal region has not been included because it is too heterogeneous. 532 sequences 5 PDB
The (18,20) pair is not shown in the following ribbon model as they are sequence neighbors. The (4,20) pair is 19 angstroms apart and would be interesting to understand the role of these two amino acids. If NS5A and NS5B have a protein interaction it could be in the NS5B pair (265,313) which is 27 angstroms apart and the NS5A pair (4,20) which is 19 angstroms apart.
NS4BPF01001Hepatitis C virus non-structural protein NS4bNo precise function has been assigned to NS4b. However, it is known that NS4b interacts with NS4a and NS3 to form a large replicase complex to direct the viral RNA replication. 501 sequences 0 PDB NS4BPF01349Flavivirus non-structural protein NS4BFlaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. The NS4B protein is small and poorly conserved among the Flaviviruses. NS4B contains multiple hydrophobic potential membrane spanning regions. NS4B may form membrane components of the viral replication complex and could be involved in membrane localisation of NS3 and Flavi_NS5. 471 sequences 0 PDB NS4APF01006Hepatitis C virus non-structural protein NS4aNS4a forms an integral part of the NS3 serine protease, as it is required in a number of cases as a cofactor of cleavage 1,3. It has also been reported that NS4a interacts with NS4b and NS3 to form a multi-subunit replicase complex 411 sequences 3 PDB NS3PF02907Hepatitis C virus NS3 proteaseHepatitis C virus NS3 protein is a serine protease which has a trypsin-like fold. The non-structural (NS) protein NS3 is one of the NS proteins involved in replication of the HCV genome. NS2-3 proteinase, a zinc-dependent enzyme, performs a single proteolytic cut to release the N-terminus of NS3. The action of NS3 proteinase (NS3P), which resides in the N-terminal one-third of the NS3 protein, then yields all remaining non-structural proteins. The C-terminal two-thirds of the NS3 protein contain a helicase. The functional relationship between the proteinase and helicase domains is unknown. NS3 has a structural zinc-binding site and requires cofactor NS4A. 1003 sequences 8 PDB
This model has many identified MI pairs. The amino acid at sequence position 128 and a S in this particular model is a common node for many of the other MI pairs. Sequence position 128 looks to be in the region that is important to setting up the fold for protein-protein interaction between sequence positions 109,110,34, and 60. Sequence positions 172,176,177 and 178 are part of a helix on the end of the protein structure and share distant mutual information with other regions in the model. With the high number of MI pairs in this model the 3D representation should be viewed
NS2PF01538Hepatitis C virus non-structural protein NS2The viral genome is translated into a single polyprotein of about 3000 amino acids. Generation of the mature non-structural proteins relies on the activity of viral proteases. Cleavage at the NS2/NS3 junction is accomplished by a metal-dependent autoprotease encoded within NS2 and the N-terminus of NS3. 1081 sequenes 0 PDB E2PF01560Hepatitis C virus non-structural protein E2/NS1The hypervariable region of the E2/NS1 region of hepatitis C virus varies greatly between viral isolates. E2 is thought to encode a structurally unconstrained envelope protein. 12712 sequences 0 PDB E1PF01539Hepatitis C virus envelope glycoprotein E1 9787 sequences 1 pdbCPF01542Hepatitis C virus core proteinThe viral core protein forms the internal viral coat that encapsidates the genomic RNA and is enveloped in a host cell-derived lipid membrane. The core protein has been shown, by yeast two-hybrid assay to interact with cellular DEAD box helicases. The N terminus of the core protein is involved in transcriptional repression. 2075 sequences 0 PDB CPF01543Hepatitis C virus capsid protein The Hepatitis C virus has a ssRNA genome. The virion is a nucleocapsid covered by a lipoprotein envelope consisting of two proteins, protein M and glycoprotein E. The nucleocapsid is a complex of protein C and mRNA. 2844 sequences 2 PDBAttachments:
|
||||||||||||||||
|
| For questions or comments please contact willishf@ufl.edu |
to calculate Mutual Information across the genome. This data set is a 161 sequences so enough to look at potential results. Each genome sequence is from a different patient and from a diverse international group.
