PDBsum entry 2pm9

Protein transport

PDB id: 2pm9

Contents

Protein chains

384 a.a. *

280 a.a. *

Waters ×28

* Residue conservation analysis

PDB id:

2pm9

Name:

Protein transport

Title:

Crystal structure of yeast sec13/31 vertex element of the copii vesicular coat

Structure:

Protein transport protein sec31. Chain: a. Fragment: residues 1-411. Synonym: protein web1. Engineered: yes. Protein transport protein sec13. Chain: b. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: web1, sec31. Expressed in: hi5 insect cells. Gene: sec13, anu3. Expressed in: hi5 insect cells

Resolution:

3.30Å R-factor: 0.251 R-free: 0.305

Authors:

J.Goldberg,S.Fath,J.D.Mancias,X.Bi

Key ref:

S.Fath et al. (2007). Structure and organization of coat proteins in the COPII cage. Cell, 129, 1325-1336. PubMed id: 17604721 DOI: 10.1016/j.cell.2007.05.036

Date:

20-Apr-07 Release date: 03-Jul-07

Protein chain

P38968  (SEC31_YEAST) -  Protein transport protein SEC31 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1273 a.a.

Struc: 384 a.a.*

Protein chain

Q04491  (SEC13_YEAST) -  Protein transport protein SEC13 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 297 a.a.

Struc: 280 a.a.*

* PDB and UniProt seqs differ at 7 residue positions (black crosses)

DOI no: 10.1016/j.cell.2007.05.036

Cell 129:1325-1336 (2007)

PubMed id: 17604721

Structure and organization of coat proteins in the COPII cage.

S.Fath, J.D.Mancias, X.Bi, J.Goldberg.

ABSTRACT

COPII-coated vesicles export newly synthesized proteins from the endoplasmic reticulum. The COPII coat consists of the Sec23/24-Sar1 complex that selects cargo and the Sec13/31 assembly unit that can polymerize into an octahedral cage and deform the membrane into a bud. Crystallographic analysis of the assembly unit reveals a 28 nm long rod comprising a central alpha-solenoid dimer capped by two beta-propeller domains at each end. We construct a molecular model of the COPII cage by fitting Sec13/31 crystal structures into a recently determined electron microscopy density map. The vertex geometry involves four copies of the Sec31 beta-propeller that converge through their axial ends; there is no interdigitation of assembly units of the kind seen in clathrin cages. We also propose that the assembly unit has a central hinge-an arrangement of interlocked alpha-solenoids-about which it can bend to adapt to cages of variable curvature.

Selected figure(s)

Figure 2.
Figure 2. Organization of the Assembly Unit in the COPII Cage
(A) Comparison of the molecular model of the Sec13/31 assembly unit with the asymmetric unit of the cryo-EM map of the mammalian COPII cage (Stagg et al., 2006). The objects are viewed along the local 2-fold rotation axis. The model, shown in space-filling representation, is a composite of the two crystal structures (oriented and colored as in Figures 1B and 1C). The arrows indicate the vert, similar 15 Å displacement of the Sec13 β-propellers from the axis of the α-solenoid rod and the corresponding features in the cryo-EM map.
(B) Orthogonal view shows the difference in the angle at the center of the assembly unit. Here, the arrows show the 15–20 Å displacement of the Sec31 β-propellers from the α-solenoid axis.
(C) The molecular model of the heterotetrameric assembly unit was separated into two Sec13/31 heterodimers, and these were fitted independently as rigid bodies into the cryo-EM map (see Experimental Procedures). The picture shows a complete vertex (two asymmetric units of the cage) and is viewed along the 2-fold symmetry axis that runs through the vertex. One symmetry-related pair (colored dark green and orange) converges at the vertex and is labeled proximal; the other symmetry-related pair (light green and red) is labeled distal.
(D) The molecular model of the cage comprises 24 copies of the assembly unit with octahedral or 432 symmetry. Superimposed is the 30 Å cryo-EM density map from Stagg et al. (2006).

Figure 4.
Figure 4. β-Propeller Folds and Vertex Geometry
(A) Schematic diagram of the vertex which forms from the convergence of four Sec31 β-propeller domains at the dyad symmetry axis. The diagram is based on the orientation shown in Figure 2C. Five contact interfaces are indicated with thick lines and are labeled: cI (involving proximal-proximal contacts), and cII and cIII (symmetry-related pairs involving proximal-distal contacts). The Sec13 β-propeller domains appear not to be involved in vertex contacts according to our model of the cage. The 50° angle between the axes of the Sec13 and Sec31 β-propellers is indicated (derived from the crystal structure of the vertex element).
(B) Ribbon diagram of the six-bladed Sec13 β-propeller (colored orange) emphasizing the seventh blade contributed by Sec31 (green). For clarity, the Sec31 β-propeller is omitted and only four helices of the α-solenoid are drawn in the background.
(C) Orthogonal view with the Sec31 β-propeller included. The 50° angle between the axes of the Sec13 and Sec31 β-propellers is indicated.

The above figures are reprinted by permission from Cell Press: Cell (2007, 129, 1325-1336) copyright 2007.

Figures were selected by an automated process.