PDBsum entry 1mqs

Endocytosis/exocytosis

PDB id: 1mqs

Contents

Protein chains

588 a.a. *

26 a.a. *

Waters ×20

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structural basis for the golgi membrane recruitment of sly1p by sed5p.

Authors

A.Bracher, W.Weissenhorn.

Ref.

EMBO J, 2002, 21, 6114-6124. [DOI no: 10.1093/emboj/cdf608]

PubMed id

12426383

Abstract

Cytosolic Sec1/munc18-like proteins (SM proteins) are recruited to membrane fusion sites by interaction with syntaxin-type SNARE proteins, constituting indispensable positive regulators of intracellular membrane fusion. Here we present the crystal structure of the yeast SM protein Sly1p in complex with a short N-terminal peptide derived from the Golgi-resident syntaxin Sed5p. Sly1p folds, similarly to neuronal Sec1, into a three-domain arch-shaped assembly, and Sed5p interacts in a helical conformation predominantly with domain I of Sly1p on the opposite site of the nSec1/syntaxin-1-binding site. Sequence conservation of the major interactions suggests that homologues of Sly1p as well as the paralogous Vps45p group bind their respective syntaxins in the same way. Furthermore, we present indirect evidence that nSec1 might be able to contact syntaxin 1 in a similar fashion. The observed Sly1p-Sed5p interaction mode therefore indicates how SM proteins can stay associated with the assembling fusion machinery in order to participate in late fusion steps.

Figure 1.
Figure 1 Close-ups of Sly1p−Sed5p interactions. (A) Stereo diagram of the experimental electron density map of the Sly1p−Sed5p complex. The region shows the conserved Sly1p hydrophobic pocket (residues Leu137, Leu140, Ala141, Ile153 and Val156) that accommodates the Sed5p key residue Phe10. The map is contoured at 0.8 . (B) Hydrogen bond network at the interface of Sly1p and Sed5p. Residues 1−9 of Sed5p are shown as a ball-and-stick model in yellow; residues 131−134, 138 and 156−160 of Sly1p are shown in grey. Oxygen and nitrogen atoms are shown in red and blue, respectively. Hydrogen bonds are indicated as dashed lines. Note that the region comprising residues 10−21 of Sed5p is involved in hydrophobic interactions only. (C) Superposition of domain I of Sly1p in complex with Sed5p with the corresponding region in s-Sec1 including a helical segment from a neighbouring molecule forming a crystal contact (pdb code 1FVH). The r.m.s.d. for the fragments shown is 1.34 Šwithin 127 residues (35 identical). The peptide backbones are shown as C[ ]-traces. The colouring scheme is as follows: Sly1p, yellow; Sed5p, red; s-Sec1 domain I, white; and s-Sec1 residues 321−332, mimicking the Sed5p helical interaction, blue. N- and C-termini are indicated.

Figure 5.
Figure 5 Surface conservation of Sly1p homologues. The homology score for an alignment of Sly1p homologue sequences was plotted on to the surface of Sly1p using a scale from green (identical) to white (no conservation). Coils denote the backbone of Sed5p (yellow) and of an insertion containing helices 20 and 21 (red). (A) The orientation is similar to Figure 2. (B) Orientation after an 150° rotation around the vertical axis. Some conserved residues are indicated for orientation.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2002, 21, 6114-6124) copyright 2002.

Secondary reference #1

Title

Three-Dimensional structure of the neuronal-Sec1-Syntaxin 1a complex.

Authors

K.M.Misura, R.H.Scheller, W.I.Weis.

Ref.

Nature, 2000, 404, 355-362. [DOI no: 10.1038/35006120]

PubMed id

10746715

Figure 1.
Figure 1: Structure of nSec1 and syntaxin 1a. a, Topology diagram of nSec1. Domain 1 is shown in blue, domain 2 in green and domain 3 in yellow. Helices are denoted by cylinders and strands by arrows. Breaks in the structure are indicated with asterisks. In domains 1 and 2, helices with dashed and solid lines lie on opposite sides of the parallel -sheet. Note the left-handed crossover between strands 8 and 9. Dashed outlines denote domains 3a and 3b. b, Ribbon representation of nSec1, coloured as in a. c, d, Topology (c) and ribbon diagrams (d) of syntaxin 1a. The Habc domain is shown in red, the Habc/H3 linker in orange and the H3 region in purple. The conformations of nSec1 and syntaxin 1a are as they appear in the protein complex, but have been separated and reorientated here for clarity. In b and d the approximate dimensions are shown; the dimensions perpendicular to the plane of the page are 45 Å for nSec1 and 35 Å for syntaxin 1a. Panels b and d were prepared with the program MOLSCRIPT47, as were Figs 2 and 5. Secondary structure was assigned by PROCHECK46.

Figure 2.
Figure 2: Ribbon representation of the nSec1-syntaxin 1a complex. a, View looking down the long syntaxin 1a helices; nSec1 is shown in the same orientation as in Fig. 1b. b, As in a, but rotated about the vertical axis by 90°. N- and C-termini are indicated, and the colour coding is as in Fig. 1.

The above figures are reproduced from the cited reference with permission from Macmillan Publishers Ltd

Secondary reference #2

Title

The X-Ray crystal structure of neuronal sec1 from squid sheds new light on the role of this protein in exocytosis.

Authors

A.Bracher, A.Perrakis, T.Dresbach, H.Betz, W.Weissenhorn.

Ref.

Structure, 2000, 8, 685-694. [DOI no: 10.1016/S0969-2126(00)00156-8]

PubMed id

10903948

Figure 3.
Figure 3. The charge distribution of s-Sec1. Surface potential representations of s-Sec1 colored according to electrostatic potential: < -10 k[B]T, red; > + 10 k[B]T, blue (k[B], Boltzmann constant; T, absolute temperature). Exposed residues are labeled with the sequence number. (a) s-Sec1 rotated by approximately 90° (with respect to the orientation in (b)) to indicate the negatively charged interface of domains I and II. (b) The orientation of the molecule corresponds approximately to the one shown in Figure 2a; it shows a prominent negatively charged groove within the central part of the molecule. The figures were generated using the program GRASP [77].

The above figure is reproduced from the cited reference with permission from Cell Press

Secondary reference #3

Title

Crystal structures of neuronal squid sec1 implicate inter-Domain hinge movement in the release of t-Snares.

Authors

A.Bracher, W.Weissenhorn.

Ref.

J Mol Biol, 2001, 306, 7. [DOI no: 10.1006/jmbi.2000.4347]

PubMed id

11178889

Figure 2.
Figure 2. (a) A close-up of domain 1 (same orientation as in Figure 1) shows the rotational movement of domain 1 along the indicated axis (green cylinder) calculated with the program Dyndom. 30 The inter-domain region, which may be a potential hinge region is indicated. All four s- Sec structures are shown, crystal 1 (light blue), crystal 2 (monomer A, light red; monomer B, yellow), crystal 3 (white). (b) Same close-up view of domain 1 as in (a) from the bottom which shows again the rotational movement/ translation of the lateral helices. (c) Close-up of domain 3a (similar orientation as in Figure 1) with crystal 1 (light blue), crystal 2 (monomer A, light red; monomer B, yel- low); crystal 3 (white) and rat nSec1 (cyan) and syntaxin 1a binding residues (blue); considerable structural varia- bility is found close to the disordered loop connecting helices 13 and 14/15. However, domains 3b and the con- necting regions of 3a (helix 16) diverge only slightly indi- cating a conserved conformation for this region for the unliganded s-Sec1 and the complexed rat nSec1 struc- tures. Figures 1 to 3 were generated with the programs MOLSCRIPT 37 and Raster 3D. 38

Figure 4.
Figure 4. A prominent acidic potential binding pocket is made up by residues from all three domains. Surface potential representation of s-Sec1 generated with coordinates from crystal 1 (a) and from crystal 2 (monomer B) (b). Both structures are shown in the same orientation after superposition of domain 2 only. Regions where electrostatic potential <-10 kBT are shown in red, while those > + 10 kBT are shown in blue (kB, Boltzmann constant; T, absolute temperature). Exposed residues are labeled with the sequence number and domains are indicated. Syntaxin 1 binds into the cleft between domains 1 and 3a as indicated by a black bar. Domain-1-acidic residues lining the potential binding pocket (D31, E78, E79, E105, E1110) are shifted in the two crystal forms due to the rotational movement of domain 1. Note the conserved distance between C a atoms of E257 (domain 3a) and D148 (domain 2) which is 18.25 and 18.3 Å in both crystal forms. In contrast the distances between crystal 1 C a atoms of E257 and D31 is 20.3 Å (17.8 Å , crystal 2), and E79 is 27 Å (20.8 Å , crystal 2), and R61 is 27 Å (23.4 Å , crystal 2) in crystal 1. This Figure was generated with the program GRASP. 42

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