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- PDB-1ft2: CO-CRYSTAL STRUCTURE OF PROTEIN FARNESYLTRANSFERASE COMPLEXED WIT... -

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Basic information

Entry
Database: PDB / ID: 1ft2
TitleCO-CRYSTAL STRUCTURE OF PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH A FARNESYL DIPHOSPHATE SUBSTRATE
Components(PROTEIN FARNESYLTRANSFERASEFarnesyltransferase) x 2
KeywordsTRANSFERASE / PROTEIN FARNESYLTRANSFERASE / FARNESYL DIPHOSPHATE / CANCER THERAPEUTICS / PRENYLTRANSFERASE / ISOPRENOID
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 / 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 farnesylation / protein geranylgeranyltransferase type I / 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 Rac protein signal transduction / positive regulation of nitric-oxide synthase biosynthetic process / 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
FARNESYL DIPHOSPHATE / Protein farnesyltransferase subunit beta / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT USING 1FT1 COORDINATES / Resolution: 3.4 Å
AuthorsBeese, L.S. / Casey, P.J. / Long, S.B.
Citation
Journal: Biochemistry / Year: 1998
Title: Cocrystal structure of protein farnesyltransferase complexed with a farnesyl diphosphate substrate.
Authors: Long, S.B. / Casey, P.J. / Beese, L.S.
#1: Journal: Science / Year: 1997
Title: Crystal Structure of Protein Farnesyltransferase at 2.25 Angstrom Resolution
Authors: Park, H.W. / Boduluri, S.R. / Moomaw, J.F. / Casey, P.J. / Beese, L.S.
#2: Journal: Science / Year: 1997
Title: Erratum. Crystal Structure of Protein Farnesyltransferase at 2.25 Angstrom Resolution
Authors: Park, H.W. / Boduluri, S.R. / Moomaw, J.F. / Casey, P.J. / Beese, L.S.
#3: Journal: J.Biol.Chem. / Year: 1993
Title: High Level Expression of Mammalian Protein Farnesyltransferase in a Baculovirus System. The Purified Protein Contains Zinc
Authors: Chen, W.J. / Moomaw, J.F. / Overton, L. / Kost, T.A. / Casey, P.J.
History
DepositionJun 2, 1998Processing site: BNL
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,3064
Polymers82,8582
Non-polymers4482
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-55 kcal/mol
Surface area27880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.660, 166.660, 98.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein PROTEIN FARNESYLTRANSFERASE / Farnesyltransferase


Mass: 38028.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: CYTOPLASM / Gene: CDNA / Organ: BRAIN / Plasmid: BACULOVIRUS / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q04631, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Protein PROTEIN FARNESYLTRANSFERASE / Farnesyltransferase


Mass: 44829.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: CYTOPLASM / Gene: CDNA / Organ: BRAIN / Plasmid: BACULOVIRUS / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
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-FPP / FARNESYL DIPHOSPHATE / Farnesyl pyrophosphate


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2
Compound detailsTHIS PDB ENTRY CONTAINS THE COORDINATES OF A 3.4 ANGSTROM RESOLUTION CO-CRYSTAL STRUCTURE OF ...THIS PDB ENTRY CONTAINS THE COORDINATES OF A 3.4 ANGSTROM RESOLUTION CO-CRYSTAL STRUCTURE OF PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH ITS NATURAL SUBSTRATE FARNESYL DIPHOSPHATE.

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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: 3.79 Å3/Da / Density % sol: 68 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: HANGING DROP, PROTEIN CONCENTRATION OF 16MG/ML IN 20 MM KCL, 10UM ZNCL, 10MM DTT, 20MM TRIS PH 7.7, 0.12% OCTYL-BETA-D-GLUCOPYRANOSIDE, AND 1MM FARNESYL DIPHOSPHATE; RESERVOIR SOLUTION OF ...Details: HANGING DROP, PROTEIN CONCENTRATION OF 16MG/ML IN 20 MM KCL, 10UM ZNCL, 10MM DTT, 20MM TRIS PH 7.7, 0.12% OCTYL-BETA-D-GLUCOPYRANOSIDE, AND 1MM FARNESYL DIPHOSPHATE; RESERVOIR SOLUTION OF 15% PEG 8000, 200MM AMMONIUM ACETATE, PH 7.0, vapor diffusion - hanging drop
PH range: 7.0-7.7
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 7.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMTris-HCl1drop
20.6 %(w/v)octyl-beta-D-glucopyranoside1drop
31 mMFPP1drop
40.14 mMFTase1drop
515 %(w/v)PEG80001reservoir
6200 mMammonium acetate1reservoir
7100 mMimidazole-malic acid1reservoir
810 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 96 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 27, 1998 / Details: MSC DOUBLE-MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.4→35 Å / Num. obs: 17125 / % possible obs: 79.4 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 15
Reflection shellResolution: 3.4→3.44 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.199 / % possible all: 56.1
Reflection
*PLUS
Num. measured all: 42609
Reflection shell
*PLUS
% possible obs: 58.1 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT USING 1FT1 COORDINATES
Starting model: PDB ENTRY 1FT1

1ft1


Resolution: 3.4→35 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE CRYSTAL STRUCTURE OF PROTEIN FARNESYLTRANSFERASE WITHOUT SUBSTRATE BOUND WAS DETERMINED TO 2.25 ANGSTROM RESOLUTION (APO FTASE, PDB ID CODE: 1FT1). PHASES FOR THE CO-CRYSTAL STRUCTURE OF ...Details: THE CRYSTAL STRUCTURE OF PROTEIN FARNESYLTRANSFERASE WITHOUT SUBSTRATE BOUND WAS DETERMINED TO 2.25 ANGSTROM RESOLUTION (APO FTASE, PDB ID CODE: 1FT1). PHASES FOR THE CO-CRYSTAL STRUCTURE OF PROTEIN FARNESYLTRANSFERASE WITH FARNESYL DIPHOSPHATE BOUND WERE DERIVED FROM THIS HIGH RESOLUTION APO FTASE CRYSTAL STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 865 5.1 %SEE BELOW
Rwork0.219 ---
obs0.219 17125 79.3 %-
Displacement parametersBiso mean: 40.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 3.4→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5839 0 25 0 5864
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.36
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.141.5
X-RAY DIFFRACTIONx_mcangle_it3.622
X-RAY DIFFRACTIONx_scbond_it2.852
X-RAY DIFFRACTIONx_scangle_it4.492.5
LS refinement shellResolution: 3.4→3.55 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.32 78 5.1 %
Rwork0.274 1460 -
obs--58.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.ZNKTOP.ZNK
X-RAY DIFFRACTION3FPP_043198.XPRMFPP_043198.XPSF
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.36
LS refinement shell
*PLUS
Rfactor Rfree: 0.32

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