PDBsum entry 2p2l

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Unknown function PDB id
Protein chains
176 a.a. *
GDP ×3
_ZN ×8
Waters ×804
* Residue conservation analysis
PDB id:
Name: Unknown function
Title: Rac1-gdp-zinc complex
Structure: Ras-related c3 botulinum toxin substrate 1. Chain: a, b, c. Synonym: p21-rac1, ras- like protein tc25, cell migration-i gene 5 protein. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: rac1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
1.90Å     R-factor:   0.177     R-free:   0.208
Authors: G.Prehna,C.E.Stebbins
Key ref:
G.Prehna and C.E.Stebbins (2007). A Rac1-GDP trimer complex binds zinc with tetrahedral and octahedral coordination, displacing magnesium. Acta Crystallogr D Biol Crystallogr, 63, 628-635. PubMed id: 17452788 DOI: 10.1107/S0907444907010888
07-Mar-07     Release date:   01-May-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P63000  (RAC1_HUMAN) -  Ras-related C3 botulinum toxin substrate 1
192 a.a.
176 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   19 terms 
  Biological process     epithelial cell morphogenesis   72 terms 
  Biochemical function     nucleotide binding     10 terms  


DOI no: 10.1107/S0907444907010888 Acta Crystallogr D Biol Crystallogr 63:628-635 (2007)
PubMed id: 17452788  
A Rac1-GDP trimer complex binds zinc with tetrahedral and octahedral coordination, displacing magnesium.
G.Prehna, C.E.Stebbins.
The Rho family of small GTPases represent well characterized signaling molecules that regulate many cellular functions such as actin cytoskeletal arrangement and the cell cycle by acting as molecular switches. A Rac1-GDP-Zn complex has been crystallized in space group P3(2)21 and its crystal structure has been solved at 1.9 A resolution. These trigonal crystals reveal the unexpected ability of Rac1 to coordinate Zn atoms in a tetrahedral fashion by use of its biologically relevant switch I and switch II regions. Upon coordination of zinc, the switch I region is stabilized in the GDP-bound conformation and contributes to a Rac1 trimer in the asymmetric unit. Zinc coordination causes switch II to adopt a novel conformation with a symmetry-related molecule. Additionally, zinc was found to displace magnesium from its octahedral coordination at switch I, although GDP binding remained stable. This structure represents the first reported Rac1-GDP-Zn complex, which further underscores the conformational flexibility and versatility of the small GTPase switch regions.
  Selected figure(s)  
Figure 2.
Figure 2 Overall crystal structure of the Rac1-GDP-zinc complex. (a) The trimeric Rac1 complex is shown with chain A in violet, chain B in yellow and chain C in green. Switch I is indicated in red, switch II in blue and zinc in dark orange. The three GDP molecules are labeled. (b) The trimeric Rac1 complex after a 180° rotation from (a).
Figure 4.
Figure 4 The intermolecular interactions at switch I as viewed between chain A (violet) and chain C (green). All residues from chain A are labeled in violet and all residues from chain C are labeled in green. Water molecules are labeled in dark green and Zn atoms in orange. All non-C atoms in the protein chains are colored with red indicating oxygen and blue indicating nitrogen. Hydrogen-bonding interactions are indicated by dotted red lines.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 628-635) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19806182 S.Meyer, S.Böhme, A.Krüger, H.J.Steinhoff, J.P.Klare, and A.Wittinghofer (2009).
Kissing G domains of MnmE monitored by X-ray crystallography and pulse electron paramagnetic resonance spectroscopy.
  PLoS Biol, 7, e1000212.
PDB codes: 3gee 3geh 3gei
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.