3RWM | pdb_00003rwm

Crystal Structure of Ypt32 in Complex with GppNHp

• PDB DOI: https://doi.org/10.2210/pdb3RWM/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-05-09 Released: 2011-10-26 
• Deposition Author(s): Sultana, A., Dregger, C., Jin, Y., Franklin, E., Weisman, L.S., Khan, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.240 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

The activation cycle of Rab GTPase Ypt32 reveals structural determinants of effector recruitment and GDI binding.

Sultana, A., Jin, Y., Dregger, C., Franklin, E., Weisman, L.S., Khan, A.R.

(2011) FEBS Lett 585: 3520-3527

• PubMed: 22024479 
• DOI: https://doi.org/10.1016/j.febslet.2011.10.013
• Primary Citation Related Structures: 
  3RWM, 3RWO


• PubMed Abstract: 
  

  Rab GTPases localize to distinct sub-cellular compartments and regulate vesicle trafficking in eukaryotic cells. Yeast Rabs Ypt31/32 and Sec4 have 68% homology and bind to common interactors, yet play distinct roles in the transport of exocytic vesicles. The structures of Ypt31/32 have not previously been reported in the uncomplexed state. We describe the crystal structures of GTP and GDP forms of Ypt32 to understand the molecular basis for Rab function. The structure of Ypt32(GTP) reveals that the switch II conformation is distinct from Sec4(GTP) in spite of a highly conserved amino acid sequence. Also, Ypt32(GDP) reveals a remarkable change in conformation of the switch II helix induced by binding to GDI, which has not been described previously.

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Organizational Affiliation: 
• School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 21.67 kDa 
• Atom Count: 1,747 
• Modeled Residue Count: 179 
• Deposited Residue Count: 185 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein YPT32/YPT11	A [auth B]	185	Saccharomyces cerevisiae S288C	Mutation(s): 1  Gene Names: YGL210W, YPT11, YPT32
UniProt
Find proteins for P51996 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P51996  Go to UniProtKB:  P51996

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	B, D [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
MG	C [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.240 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.09	α = 90
b = 49.89	β = 90
c = 90.66	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-26 
Deposition Author(s): Sultana, A., Dregger, C., Jin, Y., Franklin, E., Weisman, L.S., Khan, A.R.

Revision History  

• Version 1.0: 2011-10-26
  Type: Initial release
  
• Version 1.1: 2011-11-09
  Changes: Database references
• Version 1.2: 2011-12-14
  Changes: Database references
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations