1YRG | pdb_00001yrg

THE CRYSTAL STRUCTURE OF RNA1P: A NEW FOLD FOR A GTPASE-ACTIVATING PROTEIN

• PDB DOI: https://doi.org/10.2210/pdb1YRG/pdb

• Classification: TRANSCRIPTION
• Organism(s): Schizosaccharomyces pombe
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 1999-03-29 Released: 2000-03-29 
• Deposition Author(s): Hillig, R.C., Renault, L., Vetter, I.R., Drell, T., Wittinghofer, A., Becker, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 
  0.277 (Depositor) 
• R-Value Work: 
  0.228 (Depositor), 0.237 (DCC) 

Literature

The crystal structure of rna1p: a new fold for a GTPase-activating protein.

Hillig, R.C., Renault, L., Vetter, I.R., Drell 4th, T., Wittinghofer, A., Becker, J.

(1999) Mol Cell 3: 781-791

• PubMed: 10394366 
• DOI: https://doi.org/10.1016/s1097-2765(01)80010-1
• Primary Citation Related Structures: 
  1YRG


• PubMed Abstract: 
  

  rna1p is the Schizosaccharomyces pombe ortholog of the mammalian GTPase-activating protein (GAP) of Ran. Both proteins are essential for nuclear transport. Here, we report the crystal structure of rna1p at 2.66 A resolution. It contains 11 leucine-rich repeats that adopt the nonglobular shape of a crescent, bearing no resemblance to RhoGAP or RasGAP. The invariant residues of RanGAP form a contiguous surface, strongly indicating the Ran-binding interface. Alanine mutations identify Arg-74 as a critical residue for GTP hydrolysis. In contrast to RasGAP and RhoGAP, Arg-74 could be substituted by lysine and contributed significantly to the binding of Ran. Therefore, we suggest a GAP mechanism for rna1p, which constitutes a variation of the arginine finger mechanism found for Ras GAP and RhoGAP.

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Organizational Affiliation: 
• Max-Planck-Institut für molekulare Physiologie, Abteilung Strukturelle Biologie, Dortmund, Germany.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 86.28 kDa 
• Atom Count: 5,399 
• Modeled Residue Count: 686 
• Deposited Residue Count: 770 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPASE-ACTIVATING PROTEIN RNA1_SCHPO	A, B	385	Schizosaccharomyces pombe	Mutation(s): 0
UniProt
Find proteins for P41391 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore P41391  Go to UniProtKB:  P41391

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free:  0.277 (Depositor) 
• R-Value Work:  0.228 (Depositor), 0.237 (DCC) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175.53	α = 90
b = 175.53	β = 90
c = 55.8	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
MLPHARE	phasing
SHARP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-03-29 
Deposition Author(s): Hillig, R.C., Renault, L., Vetter, I.R., Drell, T., Wittinghofer, A., Becker, J.

Revision History  

• Version 1.0: 2000-03-29
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-31
  Changes: Database references
• Version 1.4: 2019-11-20
  Changes: Database references
• Version 1.5: 2020-01-22
  Changes: Database references, Derived calculations
• Version 1.6: 2023-12-27
  Changes: Data collection, Database references