1U8Y | pdb_00001u8y

CRystal structures of Ral-GppNHp and Ral-GDP reveal two novel binding sites that are also present in Ras and Rap

• PDB DOI: https://doi.org/10.2210/pdb1U8Y/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Saguinus oedipus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-08-09 Released: 2004-11-23 
• Deposition Author(s): Nicely, N.I., Kosak, J., de Serrano, V., Mattos, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.238 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.211 (DCC) 

Literature

Crystal Structures of Ral-GppNHp and Ral-GDP Reveal Two Binding Sites that Are Also Present in Ras and Rap

Nicely, N.I., Kosak, J., de Serrano, V., Mattos, C.

(2004) Structure 12: 2025-2036

• PubMed: 15530367 
• DOI: https://doi.org/10.1016/j.str.2004.08.011
• Primary Citation Related Structures: 
  1U8Y, 1U8Z, 1U90


• PubMed Abstract: 
  

  RalA is a GTPase with effectors such as Sec5 and Exo84 in the exocyst complex and RalBP1, a GAP for Rho proteins. We report the crystal structures of Ral-GppNHp and Ral-GDP. Disordered switch I and switch II, located away from crystal contacts, are observed in one of the molecules in the asymmetric unit of the Ral-GppNHp structure. In the other molecule in the asymmetric unit, a second Mg(2+) ion is bound to the GppNHp gamma-phosphate in an environment in which switch I is pulled away from the nucleotide and switch II is found in a tight beta turn. Clustering of conserved residues on the surface of Ral-GppNHp identifies two putative sites for protein-protein interaction. One site is adjacent to switch I. The other is modulated by switch II and is obstructed in Ral-GDP. The Ral structures are discussed in the context of the published structures of the Ral/Sec5 complex, Ras, and Rap.

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Organizational Affiliation: 
• Department of Molecular and Structural Biochemistry, 128 Polk Hall-CB 7622, North Carolina State University, Raleigh, NC 27695, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 39.49 kDa 
• Atom Count: 2,970 
• Modeled Residue Count: 322 
• Deposited Residue Count: 336 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Ral-A	A, B	168	Saguinus oedipus	Mutation(s): 0  Gene Names: Rala, Ral-a, Ral EC: 3.6.5.2
UniProt
Find proteins for P63320 (Saguinus oedipus) Explore P63320  Go to UniProtKB:  P63320

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.238 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.211 (DCC) 

Space Group: P 4₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.318	α = 90
b = 77.318	β = 90
c = 116.134	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-23 
Deposition Author(s): Nicely, N.I., Kosak, J., de Serrano, V., Mattos, C.

Revision History  

• Version 1.0: 2004-11-23
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations