Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 21.62 kDa 
• Atom Count: 1631 
• Modelled Residue Count: 173 
• Deposited Residue Count: 186 
• Unique protein chains: 1

2BMD

high resolution structure of GDP-bound human Rab4a

• PDB DOI: 10.2210/pdb2BMD/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-03-13 Released: 2005-04-25 
• Deposition Author(s): Scheidig, A.J., Huber, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.205 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 

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

• PubMed: 15907487 
• 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 1.6 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAS-RELATED PROTEIN RAB4A	A	186	Homo sapiens	Mutation(s): 0  Gene Names: RAB4A, RAB4 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.205 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.14	α = 90
b = 63.75	β = 100.03
c = 38.28	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-03-13 
• Released Date: 2005-04-25 
Deposition Author(s): Scheidig, A.J., Huber, S.K.

Revision History  

• 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
• Version 1.4: 2019-05-22
  Changes: Data collection, Experimental preparation