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- PDB-7t08: Cryptococcus neoformans protein farnesyltransferase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7t08
TitleCryptococcus neoformans protein farnesyltransferase in complex with FPP and inhibitor 2q
Components
  • Protein farnesyltransferase subunit beta
  • Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / Antifungal / TRANSFERASE / TRANSFERASE-Inhibitor complex / 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-XO1 / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha / Protein farnesyltransferase subunit beta
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.803 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)102,94765
Polymers97,7202
Non-polymers5,22763
Water12,124673
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19930 Å2
ΔGint122 kcal/mol
Surface area30150 Å2
MethodPISA
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-675-

HOH

21B-1082-

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 serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (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 serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (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 , 6 types, 736 molecules

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


Mass: 62.068 Da / Num. of mol.: 57 / 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-3FX / (2R)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid


Mass: 237.316 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H19NO4S
#6: Chemical ChemComp-XO1 / 4-{[5-({(2S)-2-butyl-5-oxo-4-[3-(trifluoromethoxy)phenyl]piperazin-1-yl}methyl)-1H-imidazol-1-yl]methyl}-2-fluorobenzonitrile


Mass: 529.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H27F4N5O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 673 / 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
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: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.803→50.17 Å / Num. obs: 120525 / % possible obs: 98.66 % / Redundancy: 6.4 % / CC1/2: 0.984 / CC star: 0.996 / Rmerge(I) obs: 0.1582 / Rpim(I) all: 0.06742 / Rrim(I) all: 0.1723 / Net I/σ(I): 6.79
Reflection shellResolution: 1.803→1.868 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.6034 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 10862 / CC1/2: 0.952 / CC star: 0.988 / Rpim(I) all: 0.2535 / Rrim(I) all: 0.6559 / % possible all: 90.05

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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: 1.803→50.17 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1936 6069 5.05 %
Rwork0.1751 219084 -
obs0.1761 120482 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.32 Å2 / Biso mean: 37.8604 Å2 / Biso min: 20.46 Å2
Refinement stepCycle: final / Resolution: 1.803→50.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6354 0 336 673 7363
Biso mean--45.64 45.63 -
Num. residues----801
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8031-1.82360.32282790.2958514469
1.8236-1.84510.31783700.29397411100
1.8451-1.86760.27953980.27797385100
1.8676-1.89120.27583850.26087399100
1.8912-1.91610.23633840.2357385100
1.9161-1.94230.21294190.21937350100
1.9423-1.97010.23394080.2187422100
1.9701-1.99950.20513640.20787369100
1.9995-2.03070.22213990.20727427100
2.0307-2.0640.20894270.20567302100
2.064-2.09960.18983680.1904725298
2.0996-2.13780.19563790.19067425100
2.1378-2.17890.21673880.18537449100
2.1789-2.22340.18833880.18087381100
2.2234-2.27180.19733720.18787432100
2.2718-2.32460.20764050.18277435100
2.3246-2.38280.21863970.18097398100
2.3828-2.44720.18924190.17797396100
2.4472-2.51920.21943700.18017434100
2.5192-2.60050.18263940.17937417100
2.6005-2.69350.20593980.18147360100
2.6935-2.80130.2234190.18177370100
2.8013-2.92880.16534140.17747419100
2.9288-3.08320.18993410.1753723397
3.0832-3.27640.20464240.17247360100
3.2764-3.52930.18973690.17027436100
3.5293-3.88450.17583730.15287391100
3.8845-4.44650.17334120.14697427100
4.4465-5.60180.16654480.1509726599
5.6018-50.170.18463450.1675721097

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