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- PDB-2zis: Crystal Structure of rat protein farnesyltransferase complexed wi... -

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Basic information

Entry
Database: PDB / ID: 2zis
TitleCrystal Structure of rat protein farnesyltransferase complexed with a bezoruran inhibitor and FPP
Components(Protein farnesyltransferase subunit ...) x 2
KeywordsTRANSFERASE / Prenyltransferase / Metal-binding / Phosphoprotein
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / protein geranylgeranyltransferase type I / positive regulation of tubulin deacetylation / protein farnesyltransferase ...Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / protein geranylgeranyltransferase type I / positive regulation of tubulin deacetylation / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / Rab geranylgeranyltransferase activity / regulation of fibroblast proliferation / protein geranylgeranylation / positive regulation of skeletal muscle acetylcholine-gated channel clustering / negative regulation of nitric-oxide synthase biosynthetic process / farnesyltranstransferase activity / microtubule associated complex / enzyme-linked receptor protein signaling pathway / positive regulation of nitric-oxide synthase biosynthetic process / positive regulation of Rac protein signal transduction / alpha-tubulin binding / positive regulation of cell cycle / response to cytokine / wound healing / lipid metabolic process / response to organic cyclic compound / receptor tyrosine kinase binding / positive regulation of fibroblast proliferation / fibroblast proliferation / microtubule binding / cell population proliferation / molecular adaptor activity / negative regulation of cell population proliferation / positive regulation of cell population proliferation / negative regulation of apoptotic process / zinc ion binding / cytoplasm
Similarity search - Function
Protein farnesyltransferase subunit beta / Protein prenylyltransferase / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase and squalene oxidase repeat / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid ...Protein farnesyltransferase subunit beta / Protein prenylyltransferase / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase and squalene oxidase repeat / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
ACETIC ACID / FARNESYL DIPHOSPHATE / Chem-NH8 / Protein farnesyltransferase subunit beta / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.6 Å
AuthorsFukami, T.A. / Sogabe, S. / Nagata, Y. / Kondoh, O. / Ishii, N.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Synthesis and structure-activity relationships of novel benzofuran farnesyltransferase inhibitors
Authors: Asoh, K. / Kohchi, M. / Hyoudoh, I. / Ohtsuka, T. / Masubuchi, M. / Kawasaki, K. / Ebiike, H. / Shiratori, Y. / Fukami, T.A. / Kondoh, O. / Tsukaguchi, T. / Ishii, N. / Aoki, Y. / Shimma, N. / Sakaitani, M.
History
DepositionFeb 22, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 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 subunit alpha
B: Protein farnesyltransferase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,41010
Polymers93,0912
Non-polymers1,3208
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-23.2 kcal/mol
Surface area27750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.826, 171.826, 69.063
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein farnesyltransferase subunit ... , 2 types, 2 molecules AB

#1: Protein Protein farnesyltransferase subunit alpha / CAAX farnesyltransferase subunit alpha / Ras proteins prenyltransferase alpha / FTase-alpha / Type ...CAAX farnesyltransferase subunit alpha / Ras proteins prenyltransferase alpha / FTase-alpha / Type I protein geranyl-geranyltransferase subunit alpha / GGTase-I-alpha


Mass: 44086.090 Da / Num. of mol.: 1 / Mutation: I156T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fnta / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CP / References: UniProt: Q04631, protein farnesyltransferase
#2: Protein Protein farnesyltransferase subunit beta / CAAX farnesyltransferase subunit beta / RAS proteins prenyltransferase beta / FTase-beta


Mass: 49004.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fntb / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CP / References: UniProt: Q02293, protein farnesyltransferase

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Non-polymers , 6 types, 411 molecules

#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2
#6: Chemical ChemComp-NH8 / 3-{2-[(S)-(4-cyanophenyl)(hydroxy)(1-methyl-1H-imidazol-5-yl)methyl]-5-nitro-1-benzofuran-7-yl}benzonitrile


Mass: 475.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H17N5O4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O

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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: 3.2 Å3/Da / Density % sol: 60.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20mg/ml protein, 0.5mM FPP, 1mM inhibitor, 10% PEG6000, 0.2M Mg acetate, 0.1M Na acetate buffer, pH4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jun 5, 2001 / Details: mirrors
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. obs: 35232 / % possible obs: 97.6 % / Rmerge(I) obs: 0.069 / Χ2: 1.048 / Net I/σ(I): 16.1
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.690.42333231.009193
2.69-2.80.33934021.031195
2.8-2.930.2534581.078196.7
2.93-3.080.17935331.117198.7
3.08-3.280.12135641.121199.1
3.28-3.530.08235481.172199.3
3.53-3.880.05635851.106199.3
3.88-4.450.03935871.014199.2
4.45-5.60.03236050.935198.9
5.6-1000.02336270.89197.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.316 / Cor.coef. Fo:Fc: 0.769
Highest resolutionLowest resolution
Rotation3 Å42.96 Å
Translation3 Å42.96 Å

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Processing

Software
NameVersionClassificationNB
DENZO1.9.0data reduction
SCALEPACK1.9.0data scaling
MOLREP6.2.5phasing
CNX2000refinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 1FPP

1fpp


Resolution: 2.6→42.96 Å / FOM work R set: 0.855 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.222 1761 4.9 %
Rwork0.184 --
obs-35232 97.7 %
Displacement parametersBiso mean: 37.178 Å2
Baniso -1Baniso -2Baniso -3
1--3.295 Å2-7.025 Å20 Å2
2---3.295 Å20 Å2
3---6.589 Å2
Refinement stepCycle: LAST / Resolution: 2.6→42.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5825 0 87 403 6315
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.358
X-RAY DIFFRACTIONc_mcbond_it1.0961.5
X-RAY DIFFRACTIONc_scbond_it1.6952
X-RAY DIFFRACTIONc_mcangle_it1.8632
X-RAY DIFFRACTIONc_scangle_it2.6462.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 35

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6-2.630.285400.25905945
2.63-2.650.248420.256907949
2.65-2.680.271350.241910945
2.68-2.710.331460.245903949
2.71-2.740.289460.255920966
2.74-2.770.287430.228947990
2.77-2.80.256490.238926975
2.8-2.830.245540.234918972
2.83-2.870.351400.254946986
2.87-2.910.261540.2279471001
2.91-2.950.266710.2339321003
2.95-2.990.244460.2239711017
2.99-3.040.27450.2229591004
3.04-3.080.28510.239591010
3.08-3.130.277620.2059611023
3.13-3.190.264550.2079761031
3.19-3.250.2440.1919851029
3.25-3.310.301510.2219541005
3.31-3.380.267500.2069581008
3.38-3.450.229600.1929661026
3.45-3.530.198560.184938994
3.53-3.620.244470.18110081055
3.62-3.710.227600.184939999
3.71-3.820.201420.1559981040
3.82-3.950.18430.1659711014
3.95-4.090.18480.1589861034
4.09-4.250.265500.1699641014
4.25-4.450.161410.1359751016
4.45-4.680.225440.1629911035
4.68-4.970.139550.149581013
4.97-5.360.205510.1659901041
5.36-5.90.226630.1839581021
5.9-6.750.233480.1729921040
6.75-8.50.162660.1399761042
8.5-1000.156630.1389771040
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4fpp.paramfpp.top
X-RAY DIFFRACTION55056.param5056.top

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