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- PDB-2iej: Human Protein Farnesyltransferase Complexed with Inhibitor Compou... -

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Basic information

Entry
Database: PDB / ID: 2iej
TitleHuman Protein Farnesyltransferase Complexed with Inhibitor Compound STN-48 And FPP Analog at 1.8A Resolution
Components
  • Protein farnesyltransferase subunit betaFarnesyltransferase
  • Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit
KeywordsTRANSFERASE / FTASE / FARNESYLTRANSFERASE / FARNESYL TRANSFERASE / CAAX / RAS / CANCER / TUMOR REGRESSION / STN-48 / PROTEIN PRENYLATION / LIPID MODIFICATION / PLASMODIUM / FALCIPARUM / MALARIA
Function / homology
Function and homology information


positive regulation of deacetylase activity / skeletal muscle acetylcholine-gated channel clustering / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein geranylgeranyltransferase type I / protein farnesylation / positive regulation of tubulin deacetylation / protein farnesyltransferase / protein farnesyltransferase activity ...positive regulation of deacetylase activity / skeletal muscle acetylcholine-gated channel clustering / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein geranylgeranyltransferase type I / protein farnesylation / 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 / microtubule associated complex / Apoptotic cleavage of cellular proteins / positive regulation of Rac protein signal transduction / alpha-tubulin binding / transforming growth factor beta receptor signaling pathway / lipid metabolic process / receptor tyrosine kinase binding / RAS processing / Inactivation, recovery and regulation of the phototransduction cascade / microtubule binding / Potential therapeutics for SARS / molecular adaptor activity / zinc ion binding / plasma membrane / cytosol / 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
sucrose / ACETATE ION / Chem-FII / Chem-S48 / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha / Protein farnesyltransferase subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHast, M.A. / Beese, L.S.
CitationJournal: Mol.Biochem.Parasitol. / Year: 2007
Title: Resistance mutations at the lipid substrate binding site of Plasmodium falciparum protein farnesyltransferase.
Authors: Eastman, R.T. / White, J. / Hucke, O. / Yokoyama, K. / Verlinde, C.L. / Hast, M.A. / Beese, L.S. / Gelb, M.H. / Rathod, P.K. / Van Voorhis, W.C.
History
DepositionSep 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _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_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit
B: Protein farnesyltransferase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,28411
Polymers93,6872
Non-polymers1,5979
Water12,755708
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10550 Å2
ΔGint-65 kcal/mol
Surface area28430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.253, 178.253, 64.661
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsThe asymmetric unit contains one biological assembly.

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit / CAAX farnesyltransferase alpha subunit / Ras proteins prenyltransferase alpha / FTase-alpha / Type ...CAAX farnesyltransferase alpha subunit / Ras proteins prenyltransferase alpha / FTase-alpha / Type I protein geranyl-geranyltransferase alpha subunit / GGTase-I-alpha


Mass: 44864.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FNTA / Plasmid: pAK-41 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3
References: UniProt: P49354, protein farnesyltransferase, protein geranylgeranyltransferase type I
#2: Protein Protein farnesyltransferase subunit beta / Farnesyltransferase / CAAX farnesyltransferase subunit beta / RAS proteins prenyltransferase beta / FTase-beta


Mass: 48822.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FNTB / Plasmid: pAK-41 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P49356, protein farnesyltransferase

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Sugars , 1 types, 1 molecules

#3: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 716 molecules

#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-S48 / METHYL N-{(3S)-1-[(1-METHYL-1H-IMIDAZOL-5-YL)METHYL]-6-PHENYL-1,2,3,4-TETRAHYDROQUINOLIN-3-YL}-N-[(1-METHYL-1H-IMIDAZOL-4-YL)SULFONYL]GLYCINATE


Mass: 534.630 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H30N6O4S
#7: Chemical ChemComp-FII / [(3,7,11-TRIMETHYL-DODECA-2,6,10-TRIENYLOXYCARBAMOYL)-METHYL]-PHOSPHONIC ACID / FPP ANALOG


Mass: 359.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H30NO5P
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 708 / 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: 3.18 Å3/Da / Density % sol: 61.29 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.2
Details: crystallized via hanging drop against well solution containing 300 mM ammonium acetate pH 5.2, 12% PEG 8K , VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 8, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 107537 / % possible obs: 97.6 % / Biso Wilson estimate: 29.748 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 22.72
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.8-1.90.2713.7371601436088.7
1.9-2.10.1698.1973152337798.1
2.1-2.30.08915.9772611619699.5
2.3-2.50.05823.3549161145899.6
2.5-2.90.03931.7697241453199.6
2.9-3.50.02941536641122399.7
3.5-4.50.03340.837091788399.7
4.5-60.02354.819207407699.7
60.01859.69902212899.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→33.69 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.856 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.188 5376 5 %RANDOM
Rwork0.163 ---
obs0.165 107537 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.827 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5917 0 106 708 6731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226178
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.9658395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0955725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46524.108314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.237151020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.431540
X-RAY DIFFRACTIONr_chiral_restr0.0910.2890
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024791
X-RAY DIFFRACTIONr_nbd_refined0.1970.23114
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24253
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2594
X-RAY DIFFRACTIONr_metal_ion_refined0.0350.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.234
X-RAY DIFFRACTIONr_mcbond_it0.931.53738
X-RAY DIFFRACTIONr_mcangle_it1.45525859
X-RAY DIFFRACTIONr_scbond_it2.26932823
X-RAY DIFFRACTIONr_scangle_it3.6094.52535
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 357 -
Rwork0.23 6778 -
obs-7135 100 %

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