PDBsum entry 1oz4

Transport protein

PDB id: 1oz4

Contents

Protein chains

698 a.a. *

Ligands

ADP ×6

AF3 ×3

Metals

_ZN ×2

* Residue conservation analysis

Superseded by:

3cf1

PDB id:

1oz4

Name:

Transport protein

Title:

Vcp/p97

Structure:

Transitional endoplasmic reticulum atpase. Chain: a, b, c. Synonym: ter atpase, 15s mg2+, - atpase p97 subunit, valosin containing protein, vcp, cdc48. Engineered: yes

Source:

Mus musculus. Mouse. Expressed in: escherichia coli

Biol. unit:

Hexamer (from PDB file)

Resolution:

4.70Å R-factor: 0.289 R-free: 0.307

Authors:

B.Delabarre,A.T.Brunger

Key ref:

B.DeLaBarre and A.T.Brunger (2003). Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains. Nat Struct Biol, 10, 856-863. PubMed id: 12949490 DOI: 10.1038/nsb972

Date:

07-Apr-03 Release date: 09-Sep-03

Protein chains

Q01853  (TERA_MOUSE) -  Transitional endoplasmic reticulum ATPase from Mus musculus

Seq: 806 a.a.

Struc: 698 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1038/nsb972

Nat Struct Biol 10:856-863 (2003)

PubMed id: 12949490

Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains.

B.DeLaBarre, A.T.Brunger.

ABSTRACT

The ATPase p97/VCP affects multiple events within the cell. These events include the alteration of both nuclear and mitotic Golgi membranes, the dislocation of ubiquitylated proteins from the endoplasmic reticulum and regulation of the NF-kappa b pathway. Here we present the crystal structure of full-length Mus musculus p97/VCP in complex with a mixture of ADP and ADP-AlF(x) at a resolution of 4.7 A. This is the first complete hexameric structure of a protein containing tandem AAA (ATPases associated with a variety of cellular activities) domains. Comparison of the crystal structure and cryo-electron microscopy (EM) reconstructions reveals large conformational changes in the helical subdomains during the hydrolysis cycle. Structural and functional data imply a communication mechanism between the AAA domains. A Zn(2+) occludes the central pore of the hexamer, suggesting that substrate does not thread through the pore of the molecule.

Selected figure(s)

Figure 2.
Figure 2. p97/VCP protomer and pore schematic. (a,b) Two orthogonal views of molecular surfaces of the p97/VCP hexamer, with the subdomains of alternate protomers colored red or as in Figure 1a. The Zn2+ and the putative His317 ligands are shown in the central pore. Molecular dimensions are based on C -C distances, with radii shown for the top view and diameters given for the side view at the narrowest region in the middle and as well as between opposing helices 12'. (c) Schematic view of the pore with dimensions as indicated. The protrusions shown within the D2 region of the pore indicate the presence of a disordered section of the protein (residues 586 -597) that may point into the central pore. (d) Protomer-protomer interactions. The 'A-facing' elements are colored and labeled in red, the 'B-facing' elements are colored according to subdomain. The view has been selected to highlight the 'wrap-around' interaction involving helix 5/ 5'.

Figure 3.
Figure 3. Protomer views and schematic. (a,b) Orthogonal views of the p97/VCP protomer with subdomains colored as in Figure 1a. The disordered connection between 12' and 13' is indicated as a dashed green line. Selected helices are labeled. (c) Schematic models of the p97/VCP protomer in the ADP -AlF[x] and ADP states colored according to subdomain. The model of the ADP state is derived from the comparison of the p97/VCP crystal structure with the cryo-EM map of the ADP state^27; in the ADP state the N-terminal domain is highly mobile and the protrusion following helix 12' of the D2 helical domain becomes ordered.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2003, 10, 856-863) copyright 2003.

Figures were selected by the author.