PDBsum entry 1h2d

Virus/viral protein

PDB id: 1h2d

Contents

Protein chains

123 a.a.

DNA/RNA

Metals

_CL ×2

Waters ×109

PDB id:

1h2d

Name:

Virus/viral protein

Title:

Ebola virus matrix protein vp40 n-terminal domain in complex with RNA (low-resolution vp40[31-212] variant).

Structure:

Matrix protein vp40. Chain: a, b. Fragment: n-terminal domain, residues 31-212. Engineered: yes. Other_details: vp40[31-212] variant. 5'-r( Up Gp Ap)-3'. Chain: r, s. Other_details: ribonucleotide

Source:

Ebola virus. Organism_taxid: 205488. Strain: zaire mayinga. Expressed in: escherichia coli. Expression_system_taxid: 562. Escherichia coli. Organism_taxid: 562. Other_details: mRNA stop-codon sequence, biochemical synthesis by the expression host and uptake by the protein during overexpression

Biol. unit:

60mer (from PDB file)

Resolution:

2.60Å R-factor: 0.306 R-free: 0.329

Authors:

F.X.Gomis-Ruth,A.Dessen,A.Bracher,H.D.Klenk,W.Weissenhorn

Key ref:

F.X.Gomis-Rüth et al. (2003). The matrix protein VP40 from Ebola virus octamerizes into pore-like structures with specific RNA binding properties. Structure, 11, 423-433. PubMed id: 12679020 DOI: 10.1016/S0969-2126(03)00050-9

Date:

06-Aug-02 Release date: 10-Apr-03

Protein chains

Q05128  (VP40_EBOZM) -  Matrix protein VP40 from Zaire ebolavirus (strain Mayinga-76)

Seq: 326 a.a.

Struc: 123 a.a.

DNA/RNA chains

U-G-A 3 bases

U-G-A 3 bases

DOI no: 10.1016/S0969-2126(03)00050-9

Structure 11:423-433 (2003)

PubMed id: 12679020

The matrix protein VP40 from Ebola virus octamerizes into pore-like structures with specific RNA binding properties.

F.X.Gomis-Rüth, A.Dessen, J.Timmins, A.Bracher, L.Kolesnikowa, S.Becker, H.D.Klenk, W.Weissenhorn.

ABSTRACT

The Ebola virus membrane-associated matrix protein VP40 is thought to be crucial for assembly and budding of virus particles. Here we present the crystal structure of a disk-shaped octameric form of VP40 formed by four antiparallel homodimers of the N-terminal domain. The octamer binds an RNA triribonucleotide containing the sequence 5'-U-G-A-3' through its inner pore surface, and its oligomerization and RNA binding properties are facilitated by two conformational changes when compared to monomeric VP40. The selective RNA interaction stabilizes the ring structure and confers in vitro SDS resistance to octameric VP40. SDS-resistant octameric VP40 is also found in Ebola virus-infected cells, which suggests that VP40 has an additional function in the life cycle of the virus besides promoting virus assembly and budding off the plasma membrane.

Selected figure(s)

Figure 4.
Figure 4. Comparison of the NTDs Derived from the Closed Monomeric Conformation and from the Ring Structure Unveils Major Conformational Changes(A) Superposition of Ca atoms 71 to 191 results in an rms deviation of 2.8 Å. Sites of major conformational movements are indicated with arrows. The NTD from the closed monomeric conformation is shown in red and the one from the octamer structure in yellow.(B) Schematic overview of the two major conformational changes in VP40. An N-terminal loop (gray) and the C-terminal domain (gray) from the closed VP40 conformation must change their conformation to achieve octamerization. This is indicated by the ribbon drawing of the three regions involved; the potential movement of the two domains with respect to the N-terminal domain is highlighted by arrows.

The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 423-433) copyright 2003.

Figure was selected by an automated process.