PDBsum entry 2d7c

Protein transport

PDB id: 2d7c

Contents

Protein chains

167 a.a. *

42 a.a. *

Ligands

GTP ×2

MES

Metals

_MG ×2

Waters ×410

* Residue conservation analysis

PDB id:

2d7c

Name:

Protein transport

Title:

Crystal structure of human rab11 in complex with fip3 rab-binding domain

Structure:

Ras-related protein rab-11a. Chain: a, b. Fragment: residues 7-173. Synonym: rab-11. Engineered: yes. Mutation: yes. Rab11 family-interacting protein 3. Chain: c, d. Fragment: rab-binding domain.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Tetramer (from PQS)

Resolution:

1.75Å R-factor: 0.202 R-free: 0.224

Authors:

T.Shiba,H.Koga,H.W.Shin,M.Kawasaki,R.Kato,K.Nakayama,S.Wakatsuki

Key ref:

T.Shiba et al. (2006). Structural basis for Rab11-dependent membrane recruitment of a family of Rab11-interacting protein 3 (FIP3)/Arfophilin-1. Proc Natl Acad Sci U S A, 103, 15416-15421. PubMed id: 17030804 DOI: 10.1073/pnas.0605357103

Date:

16-Nov-05 Release date: 26-Sep-06

Protein chains

P62491  (RB11A_HUMAN) -  Ras-related protein Rab-11A from Homo sapiens

Seq: 216 a.a.

Struc: 167 a.a.*

Protein chains

O75154  (RFIP3_HUMAN) -  Rab11 family-interacting protein 3 from Homo sapiens

Seq: 756 a.a.

Struc: 42 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.3.6.5.2 - small monomeric GTPase.
• Reaction: GTP + H2O = GDP + phosphate + H⁺

GTP (Bound ligand (Het Group name = GTP) corresponds exactly) + H2O = GDP + phosphate + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.0605357103

Proc Natl Acad Sci U S A 103:15416-15421 (2006)

PubMed id: 17030804

Structural basis for Rab11-dependent membrane recruitment of a family of Rab11-interacting protein 3 (FIP3)/Arfophilin-1.

T.Shiba, H.Koga, H.W.Shin, M.Kawasaki, R.Kato, K.Nakayama, S.Wakatsuki.

ABSTRACT

Family of Rab11-interacting protein (FIP)3/Arfophlin-1 and FIP4/Arfophilin-2 are dual effectors for Rab11 and ADP ribosylation factor (ARF)5/ARF6, which are involved in membrane delivery from recycling endosomes to the plasma membrane during cytokinesis. Here, we define the distinct C-terminal binding regions of FIP3 and FIP4 for Rab11 and ARF5/ARF6. Furthermore, we determined the crystal structure of Rab11 in complex with the Rab11-binding domain (RBD) of FIP3. The long amphiphilic alpha-helix of FIP3-RBD forms a parallel coiled-coil homodimer, with two symmetric interfaces with two Rab11 molecules. The hydrophobic side of the RBD helix is involved in homodimerization and mediates the interaction with the Rab11 switch 1 region, whereas the opposite hydrophilic side interacts with the Rab11 switch 2 and is the major factor contributing to the binding specificity. The bivalent interaction of FIP3 with Rab11 at the C terminus allows FIP3 to coordinately function with other binding partners, including ARFs.

Selected figure(s)

Figure 4.
Fig. 4. Superposition of Rab11 in different forms. The switch 1 and switch 2 regions are shown. The side chains of Arg-72 and Arg-74 in the switch 2 region are indicated by ball-and-stick models. GTP/GDP molecules also are presented as ball-and-stick models. The GDP-bound form (PDB ID code 1OIV) is blue, the GTP-bound free form (PDB ID code 1OIW) is green, and molecule A GTP-bound Rab11 in complex with FIP3-RBD is red, whereas molecule B is orange.

Figure 6.
Fig. 6. Interaction between Rab11 and FIP3-RBD. Shown are close-up views of the switch 1 (a), switch 2 (b), and interswitch (c) regions of Rab11 in complex with FIP3-RBD. The color scheme is the same as that of Fig. 3b. Residues involved in the interaction are labeled and indicated by ball-and-stick models. The cyan dashed lines indicate hydrogen bonds or electrostatic interactions.

Figures were selected by an automated process.