PDBsum entry 1pdm

Structural protein

PDB id: 1pdm

Contents

Protein chains

(+ 6 more) 328 a.a.*

* C-alpha coords only

References listed in PDB file

Key reference

Title

Three-Dimensional structure of bacteriophage t4 baseplate.

Authors

V.A.Kostyuchenko, P.G.Leiman, P.R.Chipman, S.Kanamaru, M.J.Van raaij, F.Arisaka, V.V.Mesyanzhinov, M.G.Rossmann.

Ref.

Nat Struct Biol, 2003, 10, 688-693. [DOI no: 10.1038/nsb970]

PubMed id

12923574

Abstract

The baseplate of bacteriophage T4 is a multiprotein molecular machine that controls host cell recognition, attachment, tail sheath contraction and viral DNA ejection. We report here the three-dimensional structure of the baseplate-tail tube complex determined to a resolution of 12 A by cryoelectron microscopy. The baseplate has a six-fold symmetric, dome-like structure approximately 520 A in diameter and approximately 270 A long, assembled around a central hub. A 940 A-long and 96 A-diameter tail tube, coaxial with the hub, is connected to the top of the baseplate. At the center of the dome is a needle-like structure that was previously identified as a cell puncturing device. We have identified the locations of six proteins with known atomic structures, and established the position and shape of several other baseplate proteins. The baseplate structure suggests a mechanism of baseplate triggering and structural transition during the initial stages of T4 infection.

Figure 2.
Figure 2. Fit of the crystal structures, shown as C traces, into the cryoEM density. (a) The short tail fiber gp12 (magenta) and a part of gp11 (cyan) are viewed as area A in Figure 1. (b) gp9 (green), viewed as area B in Figure 1. An intermediate and two extreme directions of the long tail fiber, as suggested by the orientations of the gp9 trimer, are shown as green, red and blue lines, respectively. The orientation of the tail axis is vertical and is situated behind the display.

Figure 3.
Figure 3. Details of the baseplate structure. Proteins are labeled with their respective gene numbers. (a) The garland of short tail fibers gp12 (magenta) with gp11 structures (cyan C -trace) at the kinks of the gp12 fibers. Black line, six-fold axis of the baseplate. (b) The baseplate 'pins,' composed of gp7 (red), gp8 (dark blue C -trace), gp10 (yellow) and gp11 (cyan C -trace). Shown also is gp9 (green C -trace), the long tail fiber attachment protein, with a green line along its three-fold axis representing the direction of the long tail fibers. (c) Unassigned density around the center of the baseplate representing gp6, gp25 and gp53.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2003, 10, 688-693) copyright 2003.

Secondary reference #1

Title

Structure and location of gene product 8 in the bacteriophage t4 baseplate.

Authors

P.G.Leiman, M.M.Shneider, V.A.Kostyuchenko, P.R.Chipman, V.V.Mesyanzhinov, M.G.Rossmann.

Ref.

J Mol Biol, 2003, 328, 821-833. [DOI no: 10.1016/S0022-2836(03)00366-8]

PubMed id

12729757

Figure 2.
Figure 2. A ribbon diagram of the gp8 dimer. Three orthogonal orientations are shown. The two monomers are colored red and blue. The blue monomer at the top has the same orientation as the monomer in Figure 1.

Figure 4.
Figure 4. The k = 1808 rotation functions calculated using the 10 -- 3 A š resolution data of crystal form I (left) and crystal form II (right). The maps are scaled so that the highest peak has a value of 1000.0 and contoured starting from a level of 50.0 with intervals of 50.0. The orthogonalization convention and the polar angles are as defined by the PDB. For crystal form I, the peaks are labeled as follows: A , 2-fold screw axis (height of 9.5s); B , 2-fold axis (8.0s); C , two parallel dimer 2-folds (7.9s). For crystal form II: A00, 2-fold screw (13.0s); B00 , 2-fold (7.8s); C00 , two parallel dimer 2-folds (8.2s).

The above figures are reproduced from the cited reference with permission from Elsevier