PDBsum entry 2qtv

Protein transport

PDB id: 2qtv

Contents

Protein chains

733 a.a. *

164 a.a. *

36 a.a. *

Ligands

GNP

Metals

_ZN

_MG

Waters ×231

* Residue conservation analysis

PDB id:

2qtv

Name:

Protein transport

Title:

Structure of sec23-sar1 complexed with the active fragment of sec31

Structure:

Protein transport protein sec23. Chain: a. Engineered: yes. Small copii coat gtpase sar1. Chain: b. Fragment: residues 23-189. Synonym: gtp-binding protein sar1, secretion-associated ras-related protein 1. Engineered: yes.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: sec23. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Gene: sar1. Gene: sec31, web1. Expression_system_taxid: 7108

Resolution:

2.50Å R-factor: 0.205 R-free: 0.262

Authors:

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

Key ref:

X.Bi et al. (2007). Insights into COPII coat nucleation from the structure of Sec23.Sar1 complexed with the active fragment of Sec31. Dev Cell, 13, 635-645. PubMed id: 17981133 DOI: 10.1016/j.devcel.2007.10.006

Date:

02-Aug-07 Release date: 15-Jan-08

Protein chain

P15303  (SEC23_YEAST) -  Protein transport protein SEC23 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 768 a.a.

Struc: 733 a.a.

Protein chain

P20606  (SAR1_YEAST) -  Small COPII coat GTPase SAR1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 190 a.a.

Struc: 164 a.a.

Protein chain

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

Seq: 1273 a.a.

Struc: 36 a.a.

Enzyme reactions

• Enzyme class: Chain B: E.C.3.6.5.- - ?????

DOI no: 10.1016/j.devcel.2007.10.006

Dev Cell 13:635-645 (2007)

PubMed id: 17981133

Insights into COPII coat nucleation from the structure of Sec23.Sar1 complexed with the active fragment of Sec31.

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

ABSTRACT

The COPII vesicular coat forms on the endoplasmic reticulum from Sar1-GTP, Sec23/24 and Sec13/31 protein subunits. Here, we define the interaction between Sec23/24.Sar1 and Sec13/31, involving a 40 residue Sec31 fragment. In the crystal structure of the ternary complex, Sec31 binds as an extended polypeptide across a composite surface of the Sec23 and Sar1-GTP molecules, explaining the stepwise character of Sec23/24.Sar1 and Sec13/31 recruitment to the membrane. The Sec31 fragment stimulates GAP activity of Sec23/24, and a convergence of Sec31 and Sec23 residues at the Sar1 GTPase active site explains how GTP hydrolysis is triggered leading to COPII coat disassembly. The Sec31 active fragment is accommodated in a binding groove supported in part by Sec23 residue Phe380. Substitution of the corresponding residue F382L in human Sec23A causes cranio-lenticulo-sutural dysplasia, and we suggest that this mutation disrupts the nucleation of COPII coat proteins at endoplasmic reticulum exit sites.

Selected figure(s)

Figure 3.
Figure 3. Crystal Structure of Sec23•Sar1 Complexed with the Active Fragment of Sec31
The ribbon representation is shown with the membrane-distal surface of the complex facing forward. Sec23 is orange and Sar1 is red. The Sec31 active fragment is in five colors: the N-terminal element that interacts solely with Sar1 (purple, residues 907–920); a short element that interacts with both Sec23 and Sar1 residues at the interface (white, residues 920–922); two elements that interact with Sec23 (blue, residues 923–927; green, residues 935–942); and the intervening stretch that interacts loosely with Sec23 (yellow, residues 928–934). The blue contour lines show difference electron density calculated prior to the inclusion of the Sec31 active fragment (at 2.5 Å resolution, contoured at 2.9 σ). Domains of the Sec23 protein are labeled, and the interface with Sec24 is indicated at the bottom of the picture. The switch 2 (labeled Sw2) and helix α3 elements of Sar1 to which Sec31 binds are indicated.

Figure 4.
Figure 4. Layered Appearance of COPII Coat Proteins in a Model of Sec23/24•Sar1 Bound to Sec31
The ribbon representation on the left is a side view of Sec23/24•Sar1 complexed with the Sec31 active fragment. Sec23 is orange, Sar1 is red, GppNHp is blue, the Sec31 fragment is blue, and Sec24 is green. This is a composite model that includes Sec24 taken from a Sec23/24 crystal structure determined previously (Bi et al., 2002). The gray line indicates the curvature of membrane vesicle, and the dotted red line suggests the attachment of Sar1 to membrane via its N-terminal sequence. The view on the right is rotated 90° to show the membrane-distal surface in space-filling representation (same orientation as in Figure 3).

The above figures are reprinted from an Open Access publication published by Cell Press: Dev Cell (2007, 13, 635-645) copyright 2007.

Figures were selected by an automated process.