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

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Basic information

Entry
Database: PDB / ID: 2zir
TitleCrystal Structure of rat protein farnesyltransferase complexed with a benzofuran inhibitor and FPP
Components(Protein farnesyltransferase subunit ...Farnesyltransferase) 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 / 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 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 / receptor tyrosine kinase binding / response to organic cyclic compound / 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 / Chem-NH7 / 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: 2.4 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 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 / pdbx_struct_conn_angle / 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_asym_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_asym_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_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_ref_seq_dif.details / _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 subunit alpha
B: Protein farnesyltransferase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,54210
Polymers93,0912
Non-polymers1,4518
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10230 Å2
ΔGint-68.6 kcal/mol
Surface area27630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.996, 171.996, 69.179
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 / Farnesyltransferase / 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 / Farnesyltransferase / 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 , 5 types, 405 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#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 / Farnesyl pyrophosphate


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2
#6: Chemical ChemComp-NH7 / 2-[(S)-(4-chlorophenyl)(hydroxy)(1-methyl-1H-imidazol-5-yl)methyl]-N-morpholin-4-yl-7-phenyl-1-benzofuran-5-carboxamide


Mass: 543.013 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H27ClN4O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 61 %
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: 2.4→100 Å / Num. obs: 44027 / % possible obs: 95.9 % / Rmerge(I) obs: 0.045 / Χ2: 0.999 / Net I/σ(I): 21.8
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.490.39639260.926186.2
2.49-2.590.30540800.968189.8
2.59-2.70.24142271.004192.8
2.7-2.850.17243041.046194.4
2.85-3.020.11445121.069198.4
3.02-3.260.07345621.106199.7
3.26-3.590.04345601.069199.7
3.59-4.10.02845850.997199.7
4.1-5.170.0246030.878199.8
5.17-1000.01746680.906198.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.333 / Cor.coef. Fo:Fc: 0.752
Highest resolutionLowest resolution
Rotation3 Å43 Å
Translation3 Å43 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: 2.4→43 Å / FOM work R set: 0.837 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.23 2187 4.8 %
Rwork0.195 --
obs-44020 95.9 %
Displacement parametersBiso mean: 43.942 Å2
Baniso -1Baniso -2Baniso -3
1--0.556 Å2-3.961 Å20 Å2
2---0.556 Å20 Å2
3---1.112 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5834 0 94 397 6325
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.329
X-RAY DIFFRACTIONc_mcbond_it0.721.5
X-RAY DIFFRACTIONc_scbond_it0.922
X-RAY DIFFRACTIONc_mcangle_it1.2912
X-RAY DIFFRACTIONc_scangle_it1.4932.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 43

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.420.266440.249797841
2.42-2.440.326380.254881919
2.44-2.460.339590.268840899
2.46-2.480.237470.235896943
2.48-2.50.367520.263885937
2.5-2.520.311330.257904937
2.52-2.550.294460.258915961
2.55-2.570.303370.253939976
2.57-2.60.324480.259923971
2.6-2.620.322440.258909953
2.62-2.650.294480.2759521000
2.65-2.680.327620.246908970
2.68-2.710.268570.251923980
2.71-2.740.288560.2469551011
2.74-2.770.315520.215930982
2.77-2.80.192410.2059671008
2.8-2.840.294450.2279711016
2.84-2.880.276450.2349941039
2.88-2.910.236580.2189861044
2.91-2.960.286480.23410081056
2.96-30.277530.2319941047
3-3.050.236530.21410051058
3.05-3.10.341480.23110231071
3.1-3.150.268460.21610151061
3.15-3.210.264610.229801041
3.21-3.270.235480.22310191067
3.27-3.340.296420.21310051047
3.34-3.410.253560.20510171073
3.41-3.490.228540.20610181072
3.49-3.580.166520.17710101062
3.58-3.670.206390.17510261065
3.67-3.780.257560.19610131069
3.78-3.90.341440.16910261070
3.9-4.040.204460.17410131059
4.04-4.20.184510.16510341085
4.2-4.40.146590.14510081067
4.4-4.630.149600.15410141074
4.63-4.920.199690.1610121081
4.92-5.30.259550.19110231078
5.3-5.830.273530.19110211074
5.83-6.670.239630.19210241087
6.67-8.410.164480.14210451093
8.41-1000.163710.15210051076
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 DIFFRACTION55052.param5052.top

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