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- PDB-1o1s: Structure of FPT bound to isoprenoid analog 3b -

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Basic information

Entry
Database: PDB / ID: 1o1s
TitleStructure of FPT bound to isoprenoid analog 3b
Components
  • Protein farnesyltransferase alpha subunit
  • Protein farnesyltransferase beta subunit
KeywordsTRANSFERASE / Prenyltransferase
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
Chem-1NH / Protein farnesyltransferase subunit beta / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsTurek-Etienne, T.C. / Strickland, C.L. / Distefano, M.D.
CitationJournal: Biochemistry / Year: 2003
Title: Biochemical and Structural Studies with Prenyl Diphosphate Analogues Provide Insights into Isoprenoid Recognition by Protein Farnesyl Transferase
Authors: Turek-Etienne, T.C. / Strickland, C.L. / Distefano, M.D.
History
DepositionJan 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein farnesyltransferase alpha subunit
B: Protein farnesyltransferase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7084
Polymers92,1182
Non-polymers5902
Water13,385743
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-48 kcal/mol
Surface area27700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.83, 171.83, 69.09
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protein farnesyltransferase alpha subunit / CAAX farnesyltransferase alpha subunit / RAS proteins prenyltransferase alpha / FTase-alpha


Mass: 44368.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET15b / Production host: Escherichia coli (E. coli)
References: UniProt: Q04631, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Protein Protein farnesyltransferase beta subunit / CAAX farnesyltransferase beta subunit / RAS proteins prenyltransferase beta / FTase-beta


Mass: 47749.340 Da / Num. of mol.: 1 / Fragment: residue 1-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET15b / Production host: Escherichia coli (E. coli)
References: UniProt: Q02293, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-1NH / (2E,6E)-8-[(3-BENZOYLBENZYL)OXY]-3,7-DIMETHYLOCTA-2,6-DIENYL TRIHYDROGEN DIPHOSPHATE


Mass: 524.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H30O9P2
Details: The isoprenoid analog 3b was synthesized as described in the publication
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 743 / 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: 3.19 Å3/Da / Density % sol: 61.5 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 5.7
Details: PEG 4000, Sodium Acetate, KCl, pH 5.7, hanging drop, temperature 298.0K
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 15, 2000 / Details: osmic mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 54254 / Num. obs: 54254 / % possible obs: 97.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 30.9
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.354 / Num. unique all: 5279 / % possible all: 95.6
Reflection
*PLUS
Highest resolution: 2.3 Å

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Processing

Software
NameClassification
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.3→8 Å / Rfactor Rwork: 0.19 / Rfactor all: 0.19 / Rfactor obs: 0.19
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5835 0 36 743 6614
Refinement
*PLUS
Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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