RSS

PDB:2GZD

Protein Name

Rab11/FIP2(RBD domain) complex

Species

Human

Biological Context

Since many of substances necessary for the cell are big molecules with polarity, they cannot pass through the cell membrane which consisted of hydrophobic lipid double membrane. Then, it is transported into the cell by the mechanism termed the endocytosis. It involves the invagination of the plasma membrane and its subsequent pinching off to form endocytic vesicles (endosome). Some of the endocytosed components are recycled back to the plasma membrane while the rest are transported to the lysosomes where they are degraded. The Rab family of small GTPases contains nearly 70 proteins, and many of them contribute to endocytosis. Many of Rab express the function in the state of bound with effector protein, not isolated form. The five crystal structures of Rab3-rabphillin, Rab4-rabenosyn5, Rab5-rabaptin5(PDB:1TU3), Rab7-RILP, Rab22-rabenosyn5 have been determined. Each structure have highly conserved regions termed switch 1 and switch 2. Switch 1 and/or switch 2 contribute to interactions with the Rab binding domain (RBD) of effectors. The structure newly determined is a complex of Rab11 and its effector protein FIP2. This complex regulate the endosomal recycling transport. FIP2 is a 512 residue protein that contains a C2 domain at the N-terminus(residues 1-129), a myosin Vb binding region(130-290), and an RBD(Rab binding domain) at the C terminus(477-496). A complex of Rab11-FIP2-myosin VD may provide the link between endosomes and the cytoskeleton to regulate the delivery of vesicular cargo to the plasma membrane. Moreover, it was suggested that Rab11 have multiple effector binding sites which bind to other effector proteins(Rabphilin-11,Sec15), not only FIP2.

Structure Description

2gzd2gzd_x2gzd_y

The structure showed here is a complex of GTP-bound Rab11a(1-173) and the RBD region(468-502) of the FIP2 (Fig.1). Two molecules of Rab11 join together through FIP2 dimer, and form the symmetrical tetramer. This tetramer is anchored to lipid bilayers of cell membrane via C-terminal prenylation sites at cysteine residues. The structures of Rab11 have central six-strand β sheet flanked by α helices on both sides, and this structural feature is similar to other Rabs. RBD region of FIP2 compose of an long α helix followed by a 3-10 helix and a short β strand. In the region of Site-A of Fig.1, the switch 1 and switch 2 of Rab11 form interactions to FIP2, respectively. First, Switch1 is buried between two FIP2 alpha helices. Tyr480(Chain-D) and Ile481(Chain-C) of FIP2 construct a hydrogen bond and a van der waals bingind to the backbone of switch 1 respectively (Fig.3). Tyr480 and Ile481 are very important. When this two residues are replaced by another residues with mutation experiment, Rab11 abolishs to bind to FIP2. Next, switch 2 is a very flexible structure. In the complex, switch2 has moved away from original position and toward α3. It is thought that this flexibility contributes to the substrate specificity of Rab11. Moreover, salt bridge formed between Asp482 of FIP2 and Arg74 of the switch2 is also specific to Rab11. The conformations of switch2 in most other Rabs place the guanidino group of this residue in steric conflict with the effector protein. In the region of site-B of Fig.1, Leu496, Arg497, and Val498 of FIP2 construct the hydrogen bond to beta 2 of Rab11 respectively. These interactions are also important for binding of Rab11-FIP2. On the other hand, it is thought that the role of GTP bonded with Rab11 is adjusting the structure of a switch 1 and a switch 2 so that Rab11 can bind to FIP2. The experimental data proved that GDP-Rab11 does not bind to FIP2 than GTP-Rab11 obiously.

2GZD1 2GZD3
(Fig.1) Rab11-(FIP2)2-Rab11 (Fig.3) Zoom up of Site A
2GZD2
(Fig.2) The model of Rab11-(FIP2)2-Rab11 binding to membrane

Protein Data Bank (PDB)

References

Source

Jagoe, W.N. Lindsay, A.J. Read, R.J. McCoy, A.J. McCaffrey, M.W. Khan, A.R.; "Crystal structure of rab11 in complex with rab11 family interacting protein 2."; Structure; (2006) 14:1273-1283 PubMed:16905101.

Others

author: Jun-ichi Ito


Japanese version:PDB:2GZD