3TW8

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 

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 U S A 108: 18672-18677

  • DOI: 10.1073/pnas.1110415108
  • Primary Citation of Related Structures:  
    3TW8

  • 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. In higher eukaryotes, proteins containing DENN-domains comprise a major GEF family ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DENN domain-containing protein 1B A, C391Homo sapiensMutation(s): 0 
Gene Names: DENND1B, C1orf218, FAM31B
Find proteins for Q6P3S1 (Homo sapiens)
Explore Q6P3S1 
Go to UniProtKB:  Q6P3S1
NIH Common Fund Data Resources
PHAROS:  Q6P3S1
GTEx:  ENSG00000213047
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ras-related protein Rab-35 B, D181Homo sapiensMutation(s): 0 
Gene Names: RAB35, RAB1C, RAY
Find proteins for Q15286 (Homo sapiens)
Explore Q15286 
Go to UniProtKB:  Q15286
NIH Common Fund Data Resources
PHAROS:  Q15286
GTEx:  ENSG00000111737
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.588α = 90
b = 56.563β = 95.63
c = 175.305γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
SHARPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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