Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 100.41 kDa 
• Atom Count: 7245 
• Residue Count: 800 
• Unique protein chains: 2

3Q7A

Cryptococcus neoformans protein farnesyltransferase in complex with FPP and L-778,123

• DOI: 10.2210/pdb3Q7A/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Cryptococcus neoformans var. grubii H99
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-01-04 Released: 2011-08-03 
• Deposition Author(s): Hast, M.A., Beese, L.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.203 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 

Literature

Structures of Cryptococcus neoformans Protein Farnesyltransferase Reveal Strategies for Developing Inhibitors That Target Fungal Pathogens.

Hast, M.A., Nichols, C.B., Armstrong, S.M., Kelly, S.M., Hellinga, H.W., Alspaugh, J.A., Beese, L.S.

(2011) J Biol Chem 286: 35149-35162

• PubMed: 21816822 
• DOI: 10.1074/jbc.M111.250506
• Primary Citation of Related Structures:  
  3SFX, 3SFY, 3Q73, 3Q75, 3Q78, 3Q7A, 3Q7F, 3Q79


• PubMed Abstract: 
  

Cryptococcus neoformans is a fungal pathogen that causes life-threatening infections in immunocompromised individuals, including AIDS patients and transplant recipients. Few antifungals can treat C. neoformans infections, and drug resistance is increasing. Protein farnesyltransferase (FTase) catalyzes post-translational lipidation of key signal transduction proteins and is essential in C. neoformans. We present a multidisciplinary study validating C. neoformans FTase (CnFTase) as a drug target, showing that several anticancer FTase inhibitors with disparate scaffolds can inhibit C. neoformans and suggesting structure-based strategies for further optimization of these leads. Structural studies are an essential element for species-specific inhibitor development strategies by revealing similarities and differences between pathogen and host orthologs that can be exploited. We, therefore, present eight crystal structures of CnFTase that define the enzymatic reaction cycle, basis of ligand selection, and structurally divergent regions of the active site. Crystal structures of clinically important anticancer FTase inhibitors in complex with CnFTase reveal opportunities for optimization of selectivity for the fungal enzyme by modifying functional groups that interact with structurally diverse regions. A substrate-induced conformational change in CnFTase is observed as part of the reaction cycle, a feature that is mechanistically distinct from human FTase. Our combined structural and functional studies provide a framework for developing FTase inhibitors to treat invasive fungal infections.

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Organizational Affiliation: 

Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyltransferase alpha subunit	A	349	Cryptococcus neoformans var. grubii H99	Mutation(s): 0
Find proteins for Q55S71 (Cryptococcus neoformans var. neoformans serotype D (strain B-3501A)) Explore Q55S71  Go to UniProtKB:  Q55S71

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyltransferase beta subunit	B	520	Cryptococcus neoformans var. grubii H99	Mutation(s): 0  EC: 2.5.1.58
Find proteins for Q55QV6 (Cryptococcus neoformans var. neoformans serotype D (strain B-3501A)) Explore Q55QV6  Go to UniProtKB:  Q55QV6

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C, D, E	2		N/A

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
778	B	4-[(5-{[4-(3-CHLOROPHENYL)-3-OXOPIPERAZIN-1-YL]METHYL}-1H-IMIDAZOL-1-YL)METHYL]BENZONITRILE C22 H20 Cl N5 O JNUGFGAVPBYSHF-UHFFFAOYSA-N
FPP	B	FARNESYL DIPHOSPHATE C15 H28 O7 P2 VWFJDQUYCIWHTN-YFVJMOTDSA-N
3FX	B	(2R)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid C9 H19 N O4 S INEWUCPYEUEQTN-SECBINFHSA-N
SO4	B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	C, D, E	sucrose	Oligosaccharide /  Nutrient		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.203 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.713	α = 90
b = 142.713	β = 90
c = 130.439	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-01-04 
• Released Date: 2011-08-03 
Deposition Author(s): Hast, M.A., Beese, L.S.

Revision History 

• Version 1.0: 2011-08-03
  Type: Initial release
  
• Version 1.1: 2011-10-19
  Changes: Database references
• Version 1.2: 2012-12-05
  Changes: Non-polymer description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary