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- PDB-1fpp: PROTEIN FARNESYLTRANSFERASE COMPLEX WITH FARNESYL DIPHOSPHATE -

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Basic information

Entry
Database: PDB / ID: 1fpp
TitlePROTEIN FARNESYLTRANSFERASE COMPLEX WITH FARNESYL DIPHOSPHATE
Components(PROTEIN FARNESYLTRANSFERASE) x 2
KeywordsPRENYLTRANSFERASE / MEMBRANE LOCALIZATION / HETERODIMER / 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 / peptide pheromone maturation / protein farnesylation / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesyltransferase ...Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / peptide pheromone maturation / protein farnesylation / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / Rab geranylgeranyltransferase activity / protein geranylgeranylation / regulation of fibroblast proliferation / regulation of microtubule-based movement / geranylgeranyl diphosphate synthase activity / positive regulation of skeletal muscle acetylcholine-gated channel clustering / acetyltransferase activator activity / microtubule associated complex / enzyme-linked receptor protein signaling pathway / positive regulation of Rac protein signal transduction / alpha-tubulin binding / positive regulation of cell cycle / wound healing / receptor tyrosine kinase binding / lipid metabolic process / positive regulation of fibroblast proliferation / fibroblast proliferation / microtubule binding / molecular adaptor activity / cell population proliferation / negative regulation of cell population proliferation / positive regulation of cell population proliferation / negative regulation of apoptotic process / enzyme binding / 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 alpha-alpha toroid domain / 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 alpha-alpha toroid domain / 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
FARNESYL DIPHOSPHATE / PHOSPHATE ION / Protein farnesyltransferase subunit beta / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.75 Å
AuthorsDunten, P. / Kammlott, U. / Crowther, R. / Weber, D. / Palermo, R. / Birktoft, J.
CitationJournal: Biochemistry / Year: 1998
Title: Protein farnesyltransferase: structure and implications for substrate binding.
Authors: Dunten, P. / Kammlott, U. / Crowther, R. / Weber, D. / Palermo, R. / Birktoft, J.
History
DepositionJul 10, 1998Processing site: BNL
Revision 1.0Jun 8, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
B: PROTEIN FARNESYLTRANSFERASE
A: PROTEIN FARNESYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3635
Polymers92,8202
Non-polymers5433
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-60 kcal/mol
Surface area28240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.000, 170.000, 68.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 2 types, 2 molecules BA

#1: Protein PROTEIN FARNESYLTRANSFERASE / FTASE


Mass: 48722.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PURIFIED RECOMBINANT FTASE WAS TREATED WITH PROTEASE GLUC PRIOR TO CRYSTALLIZATION
Source: (gene. exp.) Rattus norvegicus (Norway rat)
Description: VIRAL EXPRESSION CONSTRUCTS WERE PROVIDED BY M. S. BROWN AND J. L. GOLDSTEIN (SOUTHWESTERN MEDICAL CENTER, DALLAS, TX)
Gene: FNTA, FNTB / Cell line (production host): HIGH FIVE (INVITROGEN) / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q02293, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Protein PROTEIN FARNESYLTRANSFERASE / FTASE


Mass: 44098.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PURIFIED RECOMBINANT FTASE WAS TREATED WITH PROTEASE GLUC PRIOR TO CRYSTALLIZATION
Source: (gene. exp.) Rattus norvegicus (Norway rat)
Description: VIRAL EXPRESSION CONSTRUCTS WERE PROVIDED BY M. S. BROWN AND J. L. GOLDSTEIN (SOUTHWESTERN MEDICAL CENTER, DALLAS, TX)
Gene: FNTA, FNTB / Cell line (production host): HIGH FIVE (INVITROGEN) / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q04631, Transferases; Transferring alkyl or aryl groups, other than methyl groups

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Non-polymers , 4 types, 20 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 17 / 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 Å3/Da / Density % sol: 59 %
Description: X12B DATA WERE MERGED WITH HOME DATA TO OBTAIN A DATA SET WITH OVERALL COMPLETENESS OF 96%
Crystal growpH: 4.5 / Details: pH 4.5
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Details: protein solution was mixed with an equal volume of precipitant
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mg/mlenzyme1drop
21 mMcompound1drop
320 mMTris-HCl1drop
410 mM1dropNaCl
50.02 mM1dropZnCl2
610 mMdithiothreitol1drop
70.4 M1reservoirNH4H2PO4precipitant
810 mMdithiothreitol1reservoirprecipitant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1997
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.75→35 Å / Num. obs: 24856 / % possible obs: 84 % / Redundancy: 1.9 % / Rsym value: 0.049 / Net I/σ(I): 15
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 8 / Rsym value: 0.134 / % possible all: 85
Reflection
*PLUS
Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 85 % / Rmerge(I) obs: 0.134

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Processing

Software
NameClassification
ESSENSmodel building
SHARPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
ESSENSphasing
RefinementMethod to determine structure: MIR / Resolution: 2.75→12 Å
RfactorNum. reflection% reflection
Rfree0.3 2889 10 %
Rwork0.23 --
obs0.24 28142 96 %
Refinement stepCycle: LAST / Resolution: 2.75→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5843 0 30 17 5890

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