4UJ4

Crystal structure of human Rab11-Rabin8-FIP3

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.2 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Structure of Rab11-FIP3-Rabin8 reveals simultaneous binding of FIP3 and Rabin8 effectors to Rab11.

Vetter, M., Stehle, R., Basquin, C., Lorentzen, E.

(2015) Nat. Struct. Mol. Biol. 22: 695-702

  • DOI: 10.1038/nsmb.3065
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The small GTPase Rab11 and its effectors FIP3 and Rabin8 are essential to membrane-trafficking pathways required for cytokinesis and ciliogenesis. Although effector binding is generally assumed to be sequential and mutually exclusive, we show that Ra ...

    The small GTPase Rab11 and its effectors FIP3 and Rabin8 are essential to membrane-trafficking pathways required for cytokinesis and ciliogenesis. Although effector binding is generally assumed to be sequential and mutually exclusive, we show that Rab11 can simultaneously bind FIP3 and Rabin8. We determined crystal structures of human Rab11-GMPPNP-Rabin8 and Rab11-GMPPNP-FIP3-Rabin8. The structures reveal that the C-terminal domain of Rabin8 adopts a previously undescribed fold that interacts with Rab11 at an unusual effector-binding site neighboring the canonical FIP3-binding site. We show that Rab11-GMPPNP-FIP3-Rabin8 is more stable than Rab11-GMPPNP-Rabin8, owing to direct interaction between Rabin8 and FIP3 within the dual effector-bound complex. The data allow us to propose a model for how membrane-targeting complexes assemble at the trans-Golgi network and recycling endosomes, through multiple weak interactions that create high-avidity complexes.

    Organizational Affiliation: 

    Department of Chemistry, Technical University Munich, Munich, Germany.,Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ras-related protein Rab-11A
A, D, G, J
185Homo sapiensMutation(s): 1 
Gene Names: RAB11A (RAB11)
Find proteins for P62491 (Homo sapiens)
Go to Gene View: RAB11A
Go to UniProtKB:  P62491
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Rab-3A-interacting protein
B, E, H, K
195Homo sapiensMutation(s): 0 
Gene Names: RAB3IP (RABIN8)
Find proteins for Q96QF0 (Homo sapiens)
Go to Gene View: RAB3IP
Go to UniProtKB:  Q96QF0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Rab11 family-interacting protein 3
C, F, I, L
66Homo sapiensMutation(s): 0 
Gene Names: RAB11FIP3 (ARFO1, KIAA0665)
Find proteins for O75154 (Homo sapiens)
Go to Gene View: RAB11FIP3
Go to UniProtKB:  O75154
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download SDF File 
Download CCD File 
A, D, G, J
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP
Download SDF File 
Download CCD File 
A, D, G, J
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.2 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.252 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.120α = 90.00
b = 161.701β = 90.00
c = 192.762γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-08-19
    Type: Database references
  • Version 1.2: 2015-09-16
    Type: Database references
  • Version 1.3: 2018-06-06
    Type: Data collection, Database references, Source and taxonomy, Structure summary