1vcp: Difference between revisions

Revision as of 16:33, 21 February 2008

SEMLIKI FOREST VIRUS CAPSID PROTEIN (CRYSTAL FORM I)

OverviewOverview

Alphaviruses are enveloped, insect-borne viruses, which contains a positive-sense RNA genome. The protein capsid is surrounded by a lipid membrane, which is penetrated by glycoprotein spikes. The structure of the Sindbis virus (SINV) (the type virus) core protein (SCP) was previously determined and found to have a chymotrypsin-like structure. SCP is a serine proteinase which cleaves itself from a polyprotein. Semliki Forest virus (SFV) is among the most distantly related alphaviruses to SINV. Similar to SCP, autocatalysis is inhibited in SFCP after cleavage of the polyprotein by leaving the carboxy-terminal tryptophan in the specificity pocket. The structures of two different crystal forms (I and II) of SFV core protein (SFCP) have been determined to 3.0 A and 3.3 A resolution, respectively. The SFCP monomer backbone structure is very similar to that of SCP. The dimeric association between monomers, A and B, found in two different crystal forms of SCP is also present in both crystal forms of SFCP. However, a third monomer, C, occurs in SFCP crystal form I. While monomers A and B make a tail-to-tail dimer contact, monomers B and C make a head-to-head dimer contact. A hydrophobic pocket on the surface of the capsid protein, the proposed site of binding of the E2 glycoprotein, has large conformational differences with respect to SCP and, in contrast to SCP, is found devoid of bound peptide. In particular, Tyr184 is pointing out of the hydrophobic pocket in SFCP, whereas the equivalent tyrosine in SCP is pointing into the pocket. The conformation of Tyr184, found in SFCP, is consistent with its availability for iodination, as observed in the homologous SINV cores. This suggests, by comparison with SCP, that E2 binding to cores causes major conformational changes, including the burial of Tyr184, which would stabilize the intact virus on budding from an infected cell. The head-to-tail contacts found in the pentameric and hexameric associations within the virion utilize in the same monomer surface regions as found in the crystalline dimer interfaces.

About this StructureAbout this Structure

1VCP is a Single protein structure of sequence from Semliki forest virus with as ligand. Full crystallographic information is available from OCA.

ReferenceReference

Structure of Semliki Forest virus core protein., Choi HK, Lu G, Lee S, Wengler G, Rossmann MG, Proteins. 1997 Mar;27(3):345-59. PMID:9094737

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OCA

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-[[Image:1vcp.jpg|left|200px]]<br /><applet load="1vcp" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1vcp.jpg|left|200px]]<br /><applet load="1vcp" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1vcp, resolution 3.0&Aring;" />
 '''SEMLIKI FOREST VIRUS CAPSID PROTEIN (CRYSTAL FORM I)'''<br />
 ==Overview==
-Alphaviruses are enveloped, insect-borne viruses, which contains a, positive-sense RNA genome. The protein capsid is surrounded by a lipid, membrane, which is penetrated by glycoprotein spikes. The structure of the, Sindbis virus (SINV) (the type virus) core protein (SCP) was previously, determined and found to have a chymotrypsin-like structure. SCP is a, serine proteinase which cleaves itself from a polyprotein. Semliki Forest, virus (SFV) is among the most distantly related alphaviruses to SINV., Similar to SCP, autocatalysis is inhibited in SFCP after cleavage of the, polyprotein by leaving the carboxy-terminal tryptophan in the specificity, pocket. The structures of two different crystal forms (I and II) of SFV, core protein (SFCP) have been determined to 3.0 A and 3.3 A resolution, respectively. The SFCP monomer backbone structure is very similar to that, of SCP. The dimeric association between monomers, A and B, found in two, different crystal forms of SCP is also present in both crystal forms of, SFCP. However, a third monomer, C, occurs in SFCP crystal form I. While, monomers A and B make a tail-to-tail dimer contact, monomers B and C make, a head-to-head dimer contact. A hydrophobic pocket on the surface of the, capsid protein, the proposed site of binding of the E2 glycoprotein, has, large conformational differences with respect to SCP and, in contrast to, SCP, is found devoid of bound peptide. In particular, Tyr184 is pointing, out of the hydrophobic pocket in SFCP, whereas the equivalent tyrosine in, SCP is pointing into the pocket. The conformation of Tyr184, found in, SFCP, is consistent with its availability for iodination, as observed in, the homologous SINV cores. This suggests, by comparison with SCP, that E2, binding to cores causes major conformational changes, including the burial, of Tyr184, which would stabilize the intact virus on budding from an, infected cell. The head-to-tail contacts found in the pentameric and, hexameric associations within the virion utilize in the same monomer, surface regions as found in the crystalline dimer interfaces.
+Alphaviruses are enveloped, insect-borne viruses, which contains a positive-sense RNA genome. The protein capsid is surrounded by a lipid membrane, which is penetrated by glycoprotein spikes. The structure of the Sindbis virus (SINV) (the type virus) core protein (SCP) was previously determined and found to have a chymotrypsin-like structure. SCP is a serine proteinase which cleaves itself from a polyprotein. Semliki Forest virus (SFV) is among the most distantly related alphaviruses to SINV. Similar to SCP, autocatalysis is inhibited in SFCP after cleavage of the polyprotein by leaving the carboxy-terminal tryptophan in the specificity pocket. The structures of two different crystal forms (I and II) of SFV core protein (SFCP) have been determined to 3.0 A and 3.3 A resolution, respectively. The SFCP monomer backbone structure is very similar to that of SCP. The dimeric association between monomers, A and B, found in two different crystal forms of SCP is also present in both crystal forms of SFCP. However, a third monomer, C, occurs in SFCP crystal form I. While monomers A and B make a tail-to-tail dimer contact, monomers B and C make a head-to-head dimer contact. A hydrophobic pocket on the surface of the capsid protein, the proposed site of binding of the E2 glycoprotein, has large conformational differences with respect to SCP and, in contrast to SCP, is found devoid of bound peptide. In particular, Tyr184 is pointing out of the hydrophobic pocket in SFCP, whereas the equivalent tyrosine in SCP is pointing into the pocket. The conformation of Tyr184, found in SFCP, is consistent with its availability for iodination, as observed in the homologous SINV cores. This suggests, by comparison with SCP, that E2 binding to cores causes major conformational changes, including the burial of Tyr184, which would stabilize the intact virus on budding from an infected cell. The head-to-tail contacts found in the pentameric and hexameric associations within the virion utilize in the same monomer surface regions as found in the crystalline dimer interfaces.
 ==About this Structure==
-VCP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Semliki_forest_virus Semliki forest virus] with HG as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1VCP OCA].
+VCP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Semliki_forest_virus Semliki forest virus] with <scene name='pdbligand=HG:'>HG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCP OCA].
 ==Reference==
@@ Line 13: / Line 13: @@
 [[Category: Semliki forest virus]]
 [[Category: Single protein]]
-[[Category: Choi, H.K.]]
+[[Category: Choi, H K.]]
 [[Category: Lu, G.]]
-[[Category: Rossmann, M.G.]]
+[[Category: Rossmann, M G.]]
 [[Category: HG]]
 [[Category: glycoprotein]]
@@ Line 23: / Line 23: @@
 [[Category: virus coat protein]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 04:35:25 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:33:52 2008''