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- PDB-3eu5: Crystal structure of FTase(ALPHA-subunit; BETA-subunit DELTA C10)... -

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Basic information

Entry
Database: PDB / ID: 3eu5
TitleCrystal structure of FTase(ALPHA-subunit; BETA-subunit DELTA C10) in complex with BiotinGPP
Components
  • Protein farnesyltransferase subunit betaFarnesyltransferase
  • Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
KeywordsTRANSFERASE / protein prenylation / prenylome analysis / Prenyltransferase / Metal-binding / Phosphoprotein / Zinc
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 geranylgeranyltransferase type I / protein farnesylation / regulation of fibroblast proliferation / positive regulation of tubulin deacetylation ...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 geranylgeranyltransferase type I / protein farnesylation / regulation of fibroblast proliferation / positive regulation of tubulin deacetylation / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / Rab geranylgeranyltransferase activity / protein geranylgeranylation / positive regulation of skeletal muscle acetylcholine-gated channel clustering / farnesyltranstransferase activity / negative regulation of nitric-oxide synthase biosynthetic process / 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 / response to inorganic substance / 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
Chem-GBO / 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: 2.8 Å
AuthorsGuo, Z. / Nguyen, U.T.T. / Delon, C. / Bon, R.S. / Blankenfeldt, W. / Goody, R.S. / Waldmann, H. / Wolters, D. / Alexandrov, K.
CitationJournal: Nat.Chem.Biol. / Year: 2009
Title: Analysis of the eukaryotic prenylome by isoprenoid affinity tagging
Authors: Nguyen, U.T.T. / Guo, Z. / Delon, C. / Wu, Y. / Deraeve, C. / Franzel, B. / Bon, R.S. / Blankenfeldt, W. / Goody, R.S. / Waldmann, H. / Wolters, D. / Alexandrov, K.
History
DepositionOct 9, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)92,4684
Polymers91,8472
Non-polymers6212
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-54 kcal/mol
Surface area28670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.065, 175.065, 70.618
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protein farnesyltransferase/geranylgeranyltransferase type-1 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: 44098.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: coexpression of alpha-subunit from pGATEV and engineered beta-subunit from pET27b
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pGATEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON-PLUS RIL (DE3)
References: UniProt: Q04631, protein farnesyltransferase, protein geranylgeranyltransferase type I
#2: Protein Protein farnesyltransferase subunit beta / Farnesyltransferase / FTase-beta / CAAX farnesyltransferase subunit beta / RAS proteins prenyltransferase beta


Mass: 47749.340 Da / Num. of mol.: 1
Fragment: DELTA C-terminus 10 AA, RABGGTase BETA-subunit, UNP residues 1-427
Source method: isolated from a genetically manipulated source
Details: coexpression of alpha-subunit from pGATEV and engineered beta-subunit from pET27b
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET27b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON-PLUS RIL (DE3) / References: UniProt: Q02293, protein farnesyltransferase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GBO / (2E,6E)-3,7-dimethyl-8-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)octa-2,6-dien-1-yl trihydrogen diphosphate / Biotin-GPP


Mass: 555.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H35N3O9P2S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 3.4 Å3/Da / Density % sol: 63.84 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% (w/v) PEG 4000, 0.2M MgCl2, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0007 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 25, 2008
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0007 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 30693 / Num. obs: 30615 / % possible obs: 99.7 % / Observed criterion σ(I): 5 / Redundancy: 7.6 % / Biso Wilson estimate: 53 Å2 / Rsym value: 0.069 / Net I/σ(I): 20.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 5.9 / Num. unique all: 30615 / Rsym value: 0.335 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FT1

1ft1


Resolution: 2.8→29.96 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.931 / SU B: 21.465 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20692 1544 5 %RANDOM
Rwork0.15258 ---
obs0.1553 29048 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.562 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.37 Å20 Å2
2--0.75 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5842 0 36 132 6010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226030
X-RAY DIFFRACTIONr_bond_other_d00.025350
X-RAY DIFFRACTIONr_angle_refined_deg1.7841.9538189
X-RAY DIFFRACTIONr_angle_other_deg3.6233.00112404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7975717
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42424.019311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.569151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5511542
X-RAY DIFFRACTIONr_chiral_restr0.0890.2871
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026714
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021251
X-RAY DIFFRACTIONr_nbd_refined0.2360.21556
X-RAY DIFFRACTIONr_nbd_other0.2390.25362
X-RAY DIFFRACTIONr_nbtor_refined0.20.22997
X-RAY DIFFRACTIONr_nbtor_other0.1120.23059
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2202
X-RAY DIFFRACTIONr_metal_ion_refined0.0090.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3120.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5220.216
X-RAY DIFFRACTIONr_mcbond_it1.5151.53577
X-RAY DIFFRACTIONr_mcbond_other3.611.51445
X-RAY DIFFRACTIONr_mcangle_it2.60225767
X-RAY DIFFRACTIONr_scbond_it3.17132453
X-RAY DIFFRACTIONr_scangle_it4.9994.52420
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 109 -
Rwork0.234 2108 -
obs--99.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.00050.0001-0.00030-0.00010.0002-0.0002-0.0002-0.0001-0.00030.0002-0.0003000.00010.0150-0.00020.01500.023755.9636-39.3233-2.0586
20.0001-0.0001-0.00010.00030.00010.00010.00010.00010.00040.0003-0.00020.00050-0.00020.00010.0152000.01510.00010.023664.5605-52.46349.1702
30000000000000000.0213-0.0002-0.00190.0214-0.00070.019554.8184-48.695210.0232
40.1549-0.59670.09917.31411.15330.533-0.00720.02530.0152-0.0561-0.05590.02450.0147-0.05130.063200.00020.0001-0.0001-0.0001056.8966-49.40072.4113
50.00010.0002-0.00040.0004-0.00070.001200.0004-0.00010.00050.0005-0.0002-0.0001-0.0001-0.00050.0143-0.00040.00010.0147-0.00010.023257.2259-48.43923.6657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 369
2X-RAY DIFFRACTION2B22 - 425
3X-RAY DIFFRACTION3B428
4X-RAY DIFFRACTION4B429
5X-RAY DIFFRACTION5B430 - 561

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