PDBsum entry 2ddu

Signaling protein

PDB id: 2ddu

Contents

Protein chain

301 a.a. *

Metals

_MG

_CA

_CL

Waters ×100

* Residue conservation analysis

PDB id:

2ddu

Name:

Signaling protein

Title:

Crystal structure of the third repeat domain of reelin

Structure:

Reelin. Chain: a. Fragment: residues 1222-1597. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: cricetulus griseus. Expression_system_taxid: 10029. Expression_system_cell_line: cho-lec 3.2.8.1. Expression_system_cell: mammalian cell

Resolution:

2.05Å R-factor: 0.236 R-free: 0.265

Authors:

T.Nogi,N.Yasui,J.Takagi

Key ref:

T.Nogi et al. (2006). Structure of a signaling-competent reelin fragment revealed by X-ray crystallography and electron tomography. EMBO J, 25, 3675-3683. PubMed id: 16858396 DOI: 10.1038/sj.emboj.7601240

Date:

03-Feb-06 Release date: 26-Sep-06

Protein chain

Q60841  (RELN_MOUSE) -  Reelin from Mus musculus

Seq: 3461 a.a.

Struc: 301 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.4.21.- - ?????

DOI no: 10.1038/sj.emboj.7601240

EMBO J 25:3675-3683 (2006)

PubMed id: 16858396

Structure of a signaling-competent reelin fragment revealed by X-ray crystallography and electron tomography.

T.Nogi, N.Yasui, M.Hattori, K.Iwasaki, J.Takagi.

ABSTRACT

The large extracellular glycoprotein reelin directs neuronal migration during brain development and plays a fundamental role in layer formation. It is composed of eight tandem repeats of an approximately 380-residue unit, termed the reelin repeat, which has a central epidermal growth factor (EGF) module flanked by two homologous subrepeats with no obvious sequence similarity to proteins of known structure. The 2.05 A crystal structure of the mouse reelin repeat 3 reveals that the subrepeat assumes a beta-jelly-roll fold with unexpected structural similarity to carbohydrate-binding domains. Despite the interruption by the EGF module, the two subdomains make direct contact, resulting in a compact overall structure. Electron micrographs of a four-domain fragment encompassing repeats 3-6, which is capable of inducing Disabled-1 phosphorylation in neurons, show a rod-like shape. Furthermore, a three-dimensional molecular envelope of the fragment obtained by single-particle tomography can be fitted with four concatenated repeat 3 atomic structures, providing the first glimpse of the structural unit for this important signaling molecule.

Selected figure(s)

Figure 2.
Figure 2 Structure of reelin repeat 3. (A) Stereo presentation of repeat 3. Subdomains are differently colored: subrepeat A (cyan), EGF (green), and subrepeat B (magenta). Bound calcium ion and disulfide bridges are shown as a gold sphere and yellow stick model, respectively. In subrepeat A, segments missing in the final model owing to poor electron density are indicated by dotted lines. (B) Stereo diagram of weighted 2|F[0]|-|F[C]| electron density map in the region corresponding to the Asp-box motif. Figures were prepared with MOLSCRIPT (Kraulis, 1991), CONSCRIPT (Lawrence and Bourke, 2000), and RASTER3D (Merritt and Bacon, 1997).

Figure 4.
Figure 4 Similarity between the reelin subrepeat and the CBM. (A) Reelin subrepeat B (R3B) and the ligand-binding domain of bacterial cellulase (1GWL), in surface presentation, viewed from the same orientation. Their surfaces are color-coded by the type of residue: red for acidic, blue for basic, and yellow for aromatic residues. In 1GWL, its bound ligand oligomannose is shown in a stick model, whereas in R3B the 'ligand-like' inserted loop from the subrepeat A, with important residues making direct side-chain contacts, is shown. (B) Stereo presentation of the close-up view at the subrepeat A–B interface. R3B residues involved in the recognition of R3A loop are shown in stick models inside the half-transparent molecular surface and labeled. Both hydrophobic and hydrogen bonding interactions are evident. The figure was made using PyMol (DeLano, 2002).

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2006, 25, 3675-3683) copyright 2006.

Figures were selected by the author.