2BME

high resolution structure of GppNHp-bound human Rab4a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

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This is version 1.3 of the entry. See complete history


Literature

High Resolution Crystal Structures of Human Rab4A in its Active and Inactive Conformations.

Huber, S.K.Scheidig, A.J.

(2005) FEBS Lett 579: 2821

  • DOI: 10.1016/j.febslet.2005.04.020
  • Primary Citation of Related Structures:  
    2BMD, 2BME

  • PubMed Abstract: 
  • The Ras-related human GTPase Rab4a is involved in the regulation of endocytosis through the sorting and recycling of early endosomes. Towards further insight, we have determined the three-dimensional crystal structure of human Rab4a in its GppNHp-bound state to 1 ...

    The Ras-related human GTPase Rab4a is involved in the regulation of endocytosis through the sorting and recycling of early endosomes. Towards further insight, we have determined the three-dimensional crystal structure of human Rab4a in its GppNHp-bound state to 1.6 Angstroms resolution and in its GDP-bound state to 1.8 Angstroms resolution, respectively. Despite the similarity of the overall structure with other Rab proteins, Rab4a displays significant differences. The structures are discussed with respect to the recently determined structure of human Rab5a and its complex with the Rab5-binding domain of the bivalent effector Rabaptin-5. The Rab4 specific residue His39 modulates the nucleotide binding pocket giving rise to a reduced rate for nucleotide hydrolysis and exchange. In comparison to Rab5, Rab4a has a different GDP-bound conformation within switch 1 region and displays shifts in position and orientation of the hydrophobic triad. The observed differences at the S2-L3-S3 region represent a new example of structural plasticity among Rab proteins and may provide a structural basis to understand the differential binding of similar effector proteins.


    Organizational Affiliation

    Max-Planck Institut für Molekulare Physiologie, Abteilung für Physikalische Biochemie, Dortmund, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RAS-RELATED PROTEIN RAB4AA, B, C, D186Homo sapiensMutation(s): 0 
Gene Names: RAB4ARAB4
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P20338 (Homo sapiens)
Explore P20338 
Go to UniProtKB:  P20338
PHAROS:  P20338
GTEx:  ENSG00000168118 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20338
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
L [auth C],
Q [auth D]
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
M [auth C],
P [auth D]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
BME
Query on BME

Download Ideal Coordinates CCD File 
H [auth A],
N [auth C]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth A],
K [auth B],
O [auth C],
R [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.79α = 90
b = 99.79β = 90
c = 95.54γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-25
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation, Other