PDBsum entry 1vcq

Viral protein

PDB id

1vcq

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Contents

			Protein chains

					149 a.a. *

* Residue conservation analysis

PDB id:

1vcq

Links

Name:

Viral protein

Title:

Semliki forest virus capsid protein (crystal form ii)

Structure:

Semliki forest virus capsid protein. Chain: a, b. Engineered: yes. Other_details: crystal form ii

Source:

Semliki forest virus. Organism_taxid: 11033. Organ: kidney. Expressed in: cricetinae gen. Sp.. Expression_system_taxid: 36483

Resolution:

3.10Å

R-factor:

0.157

Authors:

G.Lu,H.-K.Choi,M.G.Rossmann

Key ref:

H.K.Choi et al. (1997). Structure of Semliki Forest virus core protein. Proteins, 27, 345-359. PubMed id: 9094737

Date:

04-Mar-96

Release date:

07-Dec-96

PROCHECK

	Headers

	References

Protein chains

P03315 (POLS_SFV) - Structural polyprotein from Semliki forest virus

Seq: Struc:

Seq: Struc:

Seq: Struc:					1253 a.a. 149 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.3.4.21.90 - togavirin.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

Autocatalytic release of the core protein from the N-terminus of the togavirus structural protein by hydrolysis of a Trp-|-Ser bond.

	Proteins 27:345-359 (1997)
PubMed id: 9094737

Structure of Semliki Forest virus core protein.
H.K.Choi, G.Lu, S.Lee, G.Wengler, M.G.Rossmann.

ABSTRACT

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.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21087473

S.Thomas, J.Rai, L.John, S.Günther, C.Drosten, B.M.Pützer, and S.Schaefer (2010).
Functional dissection of the alphavirus capsid protease: sequence requirements for activity.

Virol J, 7, 327.

19843282

F.Thor, M.Gautschi, R.Geiger, and A.Helenius (2009).
Bulk flow revisited: transport of a soluble protein in the secretory pathway.

Traffic, 10, 1819-1830.

19722838

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.

17452783

A.Deshpande, S.Wang, M.A.Walsh, and T.Dokland (2007).
Structure of the equine arteritis virus nucleocapsid protein reveals a dimer-dimer arrangement.

Acta Crystallogr D Biol Crystallogr, 63, 581-586.

PDB code:

2i9f

17211889

F.Dulin, I.Callebaut, N.Colloc'h, and J.P.Mornon (2007).
Sequence-based modeling of Abeta42 soluble oligomers.

Biopolymers, 85, 422-437.

16789821

A.H.Elcock (2006).
Molecular simulations of cotranslational protein folding: fragment stabilities, folding cooperativity, and trapping in the ribosome.

PLoS Comput Biol, 2, e98.

16962975

A.T.Russo, M.A.White, and S.J.Watowich (2006).
The crystal structure of the Venezuelan equine encephalitis alphavirus nsP2 protease.

Structure, 14, 1449-1458.

PDB code:

2hwk

16775348

H.Jayaram, H.Fan, B.R.Bowman, A.Ooi, J.Jayaram, E.W.Collisson, J.Lescar, and B.V.Prasad (2006).
X-ray structures of the N- and C-terminal domains of a coronavirus nucleocapsid protein: implications for nucleocapsid formation.

J Virol, 80, 6612-6620.

PDB codes:

2c86 2ca1 2ge7 2ge8 2gec

16627473

I.M.Yu, M.L.Oldham, J.Zhang, and J.Chen (2006).
Crystal structure of the severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein dimerization domain reveals evolutionary linkage between corona- and arteriviridae.

J Biol Chem, 281, 17134-17139.

PDB code:

2gib

12163505

I.H.Barrette-Ng, K.K.Ng, B.L.Mark, D.Van Aken, M.M.Cherney, C.Garen, Y.Kolodenko, A.E.Gorbalenya, E.J.Snijder, and M.N.James (2002).
Structure of arterivirus nsp4. The smallest chymotrypsin-like proteinase with an alpha/beta C-terminal extension and alternate conformations of the oxyanion hole.

J Biol Chem, 277, 39960-39966.

PDB code:

1mbm

12419221

M.Kowarik, S.Küng, B.Martoglio, and A.Helenius (2002).
Protein folding during cotranslational translocation in the endoplasmic reticulum.

Mol Cell, 10, 769-778.

11884577

R.M.Kofler, F.X.Heinz, and C.W.Mandl (2002).
Capsid protein C of tick-borne encephalitis virus tolerates large internal deletions and is a favorable target for attenuation of virulence.

J Virol, 76, 3534-3543.

12454504

T.C.Terwilliger (2002).
Rapid automatic NCS identification using heavy-atom substructures.

Acta Crystallogr D Biol Crystallogr, 58, 2213-2215.

11301009

J.Lescar, A.Roussel, M.W.Wien, J.Navaza, S.D.Fuller, G.Wengler, G.Wengler, and F.A.Rey (2001).
The Fusion glycoprotein shell of Semliki Forest virus: an icosahedral assembly primed for fusogenic activation at endosomal pH.

Cell, 105, 137-148.

PDB code:

1i9w

11119567

R.Perera, K.E.Owen, T.L.Tellinghuisen, A.E.Gorbalenya, and R.J.Kuhn (2001).
Alphavirus nucleocapsid protein contains a putative coiled coil alpha-helix important for core assembly.

J Virol, 75, 1.

11301008

S.V.Pletnev, W.Zhang, S.Mukhopadhyay, B.R.Fisher, R.Hernandez, D.T.Brown, T.S.Baker, M.G.Rossmann, and R.J.Kuhn (2001).
Locations of carbohydrate sites on alphavirus glycoproteins show that E1 forms an icosahedral scaffold.

Cell, 105, 127-136.

11222705

T.L.Tellinghuisen, R.Perera, and R.J.Kuhn (2001).
In vitro assembly of Sindbis virus core-like particles from cross-linked dimers of truncated and mutant capsid proteins.

J Virol, 75, 2810-2817.

10882067

E.J.Mancini, M.Clarke, B.E.Gowen, T.Rutten, and S.D.Fuller (2000).
Cryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki Forest virus.

Mol Cell, 5, 255-266.

PDB code:

1dyl

10998624

E.J.Mancini, and S.D.Fuller (2000).
Supplanting crystallography or supplementing microscopy? A combined approach to the study of an enveloped virus.

Acta Crystallogr D Biol Crystallogr, 56, 1278-1287.

10716920

G.Barbato, D.O.Cicero, F.Cordier, F.Narjes, B.Gerlach, S.Sambucini, S.Grzesiek, V.G.Matassa, R.De Francesco, and R.Bazzo (2000).
Inhibitor binding induces active site stabilization of the HCV NS3 protein serine protease domain.

EMBO J, 19, 1195-1206.

PDB code:

1dxw

10756045

T.L.Tellinghuisen, and R.J.Kuhn (2000).
Nucleic acid-dependent cross-linking of the nucleocapsid protein of Sindbis virus.

J Virol, 74, 4302-4309.

10047583

L.Liljas (1999).
Virus assembly.

Curr Opin Struct Biol, 9, 129-134.

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.