3TW8

GEF domain of DENND 1B in complex with Rab GTPase Rab35


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Insights regarding guanine nucleotide exchange from the structure of a DENN-domain protein complexed with its Rab GTPase substrate.

Wu, X.Bradley, M.J.Cai, Y.Kummel, D.De La Cruz, E.M.Barr, F.A.Reinisch, K.M.

(2011) Proc.Natl.Acad.Sci.USA 108: 18672-18677

  • DOI: 10.1073/pnas.1110415108

  • PubMed Abstract: 
  • Rab GTPases are key regulators of membrane traffic pathways within eukaryotic cells. They are specifically activated by guanine nucleotide exchange factors (GEFs), which convert them from their "inactive" GDP-bound form to the "active" GTP-bound form ...

    Rab GTPases are key regulators of membrane traffic pathways within eukaryotic cells. They are specifically activated by guanine nucleotide exchange factors (GEFs), which convert them from their "inactive" GDP-bound form to the "active" GTP-bound form. In higher eukaryotes, proteins containing DENN-domains comprise a major GEF family. Here we describe at 2.1-Å resolution the first structure of a DENN-domain protein, DENND1B-S, complexed with its substrate Rab35, providing novel insights as to how DENN-domain GEFs interact with and activate Rabs. DENND1B-S is bi-lobed, and interactions with Rab35 are through conserved surfaces in both lobes. Rab35 binds via switch regions I and II, around the nucleotide-binding pocket. Positional shifts in Rab residues required for nucleotide binding may lower its affinity for bound GDP, and a conformational change in switch I, which makes the nucleotide-binding pocket more solvent accessible, likely also facilitates exchange.


    Organizational Affiliation

    Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DENN domain-containing protein 1B
A, C
391Homo sapiensMutation(s): 0 
Gene Names: DENND1B (C1orf218, FAM31B)
Find proteins for Q6P3S1 (Homo sapiens)
Go to Gene View: DENND1B
Go to UniProtKB:  Q6P3S1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ras-related protein Rab-35
B, D
181Homo sapiensMutation(s): 0 
Gene Names: RAB35 (RAB1C, RAY)
Find proteins for Q15286 (Homo sapiens)
Go to Gene View: RAB35
Go to UniProtKB:  Q15286
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.227 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 122.588α = 90.00
b = 56.563β = 95.63
c = 175.305γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CBASSdata collection
SHARPphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-16
    Type: Initial release
  • Version 1.1: 2011-11-30
    Type: Database references