5HZH | pdb_00005hzh

Crystal structure of photoinhibitable Rac1 containing C450A mutant LOV2 domain

• PDB DOI: https://doi.org/10.2210/pdb5HZH/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Avena sativa
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-02-02 Released: 2016-12-21 
• Deposition Author(s): Tarnawski, M., Dagliyan, O., Chu, P.H., Shirvanyants, D., Dokholyan, N.V., Hahn, K.M., Schlichting, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Engineering extrinsic disorder to control protein activity in living cells.

Dagliyan, O., Tarnawski, M., Chu, P.H., Shirvanyants, D., Schlichting, I., Dokholyan, N.V., Hahn, K.M.

(2016) Science 354: 1441-1444

• PubMed: 27980211 
• DOI: https://doi.org/10.1126/science.aah3404
• Primary Citation Related Structures: 
  5HZH, 5HZI, 5HZJ, 5HZK


• PubMed Abstract: 
  

  Optogenetic and chemogenetic control of proteins has revealed otherwise inaccessible facets of signaling dynamics. Here, we use light- or ligand-sensitive domains to modulate the structural disorder of diverse proteins, thereby generating robust allosteric switches. Sensory domains were inserted into nonconserved, surface-exposed loops that were tight and identified computationally as allosterically coupled to active sites. Allosteric switches introduced into motility signaling proteins (kinases, guanosine triphosphatases, and guanine exchange factors) controlled conversion between conformations closely resembling natural active and inactive states, as well as modulated the morphodynamics of living cells. Our results illustrate a broadly applicable approach to design physiological protein switches.

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Organizational Affiliation: 
• Program in Molecular and Cellular Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
Program in Molecular and Cellular Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. [e-mail] [e-mail].
Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. [e-mail] [e-mail].

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.15 kDa 
• Atom Count: 2,622 
• Modeled Residue Count: 320 
• Deposited Residue Count: 332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related C3 botulinum toxin substrate 1,NPH1-1,Ras-related C3 botulinum toxin substrate 1	A	332	Homo sapiens, Avena sativa	Mutation(s): 2  Gene Names: RAC1, TC25, MIG5, NPH1-1 EC: 2.7.11.1 (UniProt), 3.6.5.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O49003 (Avena sativa) Explore O49003  Go to UniProtKB:  O49003
Find proteins for P63000 (Homo sapiens) Explore P63000  Go to UniProtKB:  P63000
PHAROS:  P63000 GTEx:  ENSG00000136238
UniProt Groups	P63000O49003

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	B [auth A]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
FMN	C [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
CA	E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.05	α = 90
b = 74.27	β = 94.62
c = 58.4	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-21 
Deposition Author(s): Tarnawski, M., Dagliyan, O., Chu, P.H., Shirvanyants, D., Dokholyan, N.V., Hahn, K.M., Schlichting, I.

Revision History  

• Version 1.0: 2016-12-21
  Type: Initial release
  
• Version 1.1: 2016-12-28
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description