4UJ3

Crystal structure of human Rab11-Rabin8-FIP3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.2 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

  • DOI: 10.1038/nsmb.3065
  • Primary Citation of Related Structures:  
    4UJ3, 4UJ4, 4UJ5

  • 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 Rab11 can simultaneously bind FIP3 and Rabin8 ...

    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 Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RAS-RELATED PROTEIN RAB-11A ADGJMPSV187Homo sapiensMutation(s): 1 
Gene Names: RAB11ARAB11
Find proteins for P62491 (Homo sapiens)
Explore P62491 
Go to UniProtKB:  P62491
NIH Common Fund Data Resources
PHAROS:  P62491
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RAB-3A-INTERACTING PROTEIN BEHKNQTW195Homo sapiensMutation(s): 0 
Gene Names: RAB3IPRABIN8
Find proteins for Q96QF0 (Homo sapiens)
Explore Q96QF0 
Go to UniProtKB:  Q96QF0
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PHAROS:  Q96QF0
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RAB11 FAMILY-INTERACTING PROTEIN 3 CFILORUX66Homo sapiensMutation(s): 0 
Gene Names: RAB11FIP3ARFO1KIAA0665
Find proteins for O75154 (Homo sapiens)
Explore O75154 
Go to UniProtKB:  O75154
NIH Common Fund Data Resources
PHAROS:  O75154
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
A, D, G, J, M, P, S, V
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
V
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
M
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A, D, G, J, M, P, S, V
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.498α = 90
b = 165.374β = 95.93
c = 218.687γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-08-19
    Changes: Database references
  • Version 1.2: 2015-09-16
    Changes: Database references