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- PDB-7t0c: Cryptococcus neoformans protein farnesyltransferase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7t0c
TitleCryptococcus neoformans protein farnesyltransferase in complex with FPP and inhibitor 2e
Components
  • Protein farnesyltransferase subunit beta
  • Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
KeywordsTransferase/Inhibitor / Inhibitor / Protein prenylyltransferase / Antifungal / TRANSFERASE / TRANSFERASE-Inhibitor complex
Function / homology
Function and homology information


prenylation / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / zinc ion binding
Similarity search - Function
Protein farnesyltransferase subunit beta / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase alpha-alpha toroid domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid
Similarity search - Domain/homology
Chem-3FX / FARNESYL DIPHOSPHATE / Chem-XN4 / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha / Protein farnesyltransferase subunit beta
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii H99 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 Å
AuthorsWang, Y. / Shi, Y. / Beese, L.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5P01AI104533 United States
CitationJournal: J.Med.Chem. / Year: 2022
Title: Structure-Guided Discovery of Potent Antifungals that Prevent Ras Signaling by Inhibiting Protein Farnesyltransferase.
Authors: Wang, Y. / Xu, F. / Nichols, C.B. / Shi, Y. / Hellinga, H.W. / Alspaugh, J.A. / Distefano, M.D. / Beese, L.S.
History
DepositionNov 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
B: Protein farnesyltransferase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,84963
Polymers97,7202
Non-polymers5,12861
Water9,980554
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.915, 141.915, 130.226
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-650-

HOH

21B-1018-

HOH

31B-1048-

HOH

41B-1052-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha / variant


Mass: 40913.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii H99 (fungus)
Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_02229 / Production host: Escherichia coli (E. coli) / References: UniProt: J9VSJ6
#2: Protein Protein farnesyltransferase subunit beta / FTase-beta


Mass: 56806.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii H99 (fungus)
Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_05740 / Production host: Escherichia coli (E. coli) / References: UniProt: T2BPA1, protein farnesyltransferase

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Non-polymers , 7 types, 615 molecules

#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-XN4 / (5S)-5-butyl-4-({1-[(4-chlorophenyl)methyl]-1H-imidazol-5-yl}methyl)-1-[3-(trifluoromethoxy)phenyl]piperazin-2-one


Mass: 520.974 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H28ClF3N4O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-3FX / (2R)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid


Mass: 237.316 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H19NO4S
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.34 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 100mM CAPSO pH9.5, 50-75mM Li2SO4, 200mM NaCl, 16%-21% PEG4000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.903→70.96 Å / Num. obs: 103150 / % possible obs: 98.96 % / Redundancy: 6.1 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.07054 / Rpim(I) all: 0.03105 / Rrim(I) all: 0.07723 / Net I/σ(I): 13.74
Reflection shellResolution: 1.903→1.971 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.6938 / Mean I/σ(I) obs: 2.57 / Num. unique obs: 9408 / CC1/2: 0.927 / CC star: 0.981 / Rpim(I) all: 0.3002 / Rrim(I) all: 0.7573 / % possible all: 91.11

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SFX

3sfx


Resolution: 1.903→70.96 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2013 5185 5.03 %
Rwork0.1786 187071 -
obs0.1798 103047 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.27 Å2 / Biso mean: 41.992 Å2 / Biso min: 21.4 Å2
Refinement stepCycle: final / Resolution: 1.903→70.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6366 0 363 554 7283
Biso mean--49.25 48.54 -
Num. residues----803
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.903-1.92430.28222580.303454772
1.9243-1.9470.35873030.32156345100
1.947-1.97070.33253620.29956250100
1.9707-1.99570.29132880.26986297100
1.9957-2.02190.27192970.2612629899
2.0219-2.04960.28343550.2537627299
2.0496-2.07890.26943100.24586299100
2.0789-2.10990.24473820.2268624799
2.1099-2.14290.23653120.2224625699
2.1429-2.17810.23923280.21996288100
2.1781-2.21560.23433340.21256323100
2.2156-2.25590.2473150.20816316100
2.2559-2.29930.2563290.20746273100
2.2993-2.34620.233300.19816334100
2.3462-2.39730.21313520.18946229100
2.3973-2.4530.21843610.18896303100
2.453-2.51440.2343130.18926317100
2.5144-2.58240.20093280.18956321100
2.5824-2.65830.20533420.1908622399
2.6583-2.74420.21113400.18616327100
2.7442-2.84220.19623670.18336264100
2.8422-2.9560.17673140.17656351100
2.956-3.09060.20443190.17856312100
3.0906-3.25350.2093590.18336279100
3.2535-3.45740.22373160.17646309100
3.4574-3.72430.19443230.1616323100
3.7243-4.09910.16423410.14826312100
4.0991-4.69220.14263460.13626288100
4.6922-5.91140.1953910.15316227100
5.9114-70.960.16822910.15796341100

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