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- PDB-1jcq: CRYSTAL STRUCTURE OF HUMAN PROTEIN FARNESYLTRANSFERASE COMPLEXED ... -

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Basic information

Entry
Database: PDB / ID: 1jcq
TitleCRYSTAL STRUCTURE OF HUMAN PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH FARNESYL DIPHOSPHATE AND THE PEPTIDOMIMETIC INHIBITOR L-739,750
Components(PROTEIN FARNESYLTRANSFERASE, ...Farnesyltransferase) x 2
KeywordsTRANSFERASE / FTASE / PFT / PFTASE / FT / FPT / FARNESYLTRANSFERASE / FARNESYL TRANSFERASE / FARNESYL PROTEIN TRANSFERASE / CAAX / RAS / CANCER / TUMOR REGRESSION / L-739 / 750 / PEPTIDOMIMETIC / INHIBITOR
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 farnesylation / protein geranylgeranyltransferase type I / 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 farnesylation / protein geranylgeranyltransferase type I / 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 / Chem-739 / ACETIC ACID / FARNESYL DIPHOSPHATE / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha / Protein farnesyltransferase subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLong, S.B. / Casey, P.J. / Beese, L.S.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: The crystal structure of human protein farnesyltransferase reveals the basis for inhibition by CaaX tetrapeptides and their mimetics.
Authors: Long, S.B. / Hancock, P.J. / Kral, A.M. / Hellinga, H.W. / Beese, L.S.
#1: Journal: Structure / Year: 2000
Title: The Basis for K-Ras4B Binding Specificity to Protein Farnesyltransferase Revealed by 2A Resolution Ternary Complex Structures
Authors: Long, S.B. / Casey, P.J. / Beese, L.S.
#2: Journal: Science / Year: 1997
Title: Crystal Structure of Protein Farnesyltransferase at 2.25A Resolution
Authors: Park, H.-W. / Boduluri, S.R. / Moomaw, J.F. / Casey, P.J. / Beese, L.S.
History
DepositionJun 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_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.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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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, ALPHA SUBUNIT
B: PROTEIN FARNESYLTRANSFERASE, BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0557
Polymers93,6872
Non-polymers1,3685
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9610 Å2
ΔGint-70 kcal/mol
Surface area27820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.476, 178.476, 64.842
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Cell settinghexagonal
Space group name H-MP61
DetailsThe biological unit of protein farnesyltransferase (FTase) is a heterodimer of alpha and beta subunits. There is one FTase heterodimer per asymmetric unit.

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Components

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PROTEIN FARNESYLTRANSFERASE, ... , 2 types, 2 molecules AB

#1: Protein PROTEIN FARNESYLTRANSFERASE, ALPHA SUBUNIT / Farnesyltransferase / E.C.2.5.1.- / CAAX FARNESYLTRANSFERASE ALPHA SUBUNIT / RAS PROTEINS PRENYLTRANSFERASE ALPHA / FTASE-ALPHA / ...CAAX FARNESYLTRANSFERASE ALPHA SUBUNIT / RAS PROTEINS PRENYLTRANSFERASE ALPHA / FTASE-ALPHA / PRENYL-PROTEIN TRANSFERASE RAM2 HOMOLOG


Mass: 44864.840 Da / Num. of mol.: 1 / Fragment: ALPHA SUBUNIT / Mutation: GLU-GLU-PHE TAG ON THE C-TERMINUS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P49354, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Protein PROTEIN FARNESYLTRANSFERASE, BETA SUBUNIT / Farnesyltransferase / E.C.2.5.1.- / CAAX FARNESYLTRANSFERASE BETA SUBUNIT / RAS PROTEINS PRENYLTRANSFERASE BETA / FTASE-BETA / PRENYL- ...CAAX FARNESYLTRANSFERASE BETA SUBUNIT / RAS PROTEINS PRENYLTRANSFERASE BETA / FTASE-BETA / PRENYL-PROTEIN TRANSFERASE DPR1/RAM1 SUBUNIT


Mass: 48822.406 Da / Num. of mol.: 1 / Fragment: BETA SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P49356, Transferases; Transferring alkyl or aryl groups, other than methyl groups

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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, 338 molecules

#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE / Farnesyl pyrophosphate


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2
#7: Chemical ChemComp-739 / 2(S)-{2(S)-[2(R)-AMINO-3-MERCAPTO]PROPYLAMINO-3(S)-METHYL}PENTYLOXY-3-PHENYLPROPIONYLMETHIONINE SULFONE / L-739,750


Mass: 517.702 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H39N3O6S2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 61.32 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: PEG 8000, Ammonium Acetate, DTT, Tris-HCl, pH 5.7, VAPOR DIFFUSION, HANGING DROP at 290K
Crystal grow
*PLUS
Temperature: 17 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 %(w/v)PEG80001reservoir
2200-600 mMammonium acetate1reservoir
320 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 6, 1998 / Details: Mirrors
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→35 Å / Num. all: 52774 / Num. obs: 46302 / % possible obs: 87.5 % / Observed criterion σ(I): 0 / Redundancy: 5.59 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 21.3
Reflection shellResolution: 2.3→2.33 Å / Redundancy: 2.95 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 2.13 / Num. unique all: 1694 / % possible all: 96.3
Reflection
*PLUS
Lowest resolution: 35 Å / % possible obs: 99.7 % / Num. measured all: 294786 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
Lowest resolution: 2.4 Å / Rmerge(I) obs: 0.416

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D8D

1d8d


Resolution: 2.3→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: Bulk solvent model used
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2341 5 %RANDOM
Rwork0.179 ---
all0.1805 52774 --
obs0.179 46863 89 %-
Displacement parametersBiso mean: 42.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5898 0 82 338 6318
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d20.7
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_mcbond_it1.211.5
X-RAY DIFFRACTIONx_mcangle_it2.082
X-RAY DIFFRACTIONx_scbond_it2.032
X-RAY DIFFRACTIONx_scangle_it3.242.5
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.244 238 5.2 %
Rwork0.25 4305 -
obs-4543 69.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1parhcsdx.prtophcsdx.pr
X-RAY DIFFRACTION2param19.soltoph19.sol
X-RAY DIFFRACTION3aceace
X-RAY DIFFRACTION4fppfpp
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 42.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.244 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.25 / Rfactor obs: 0.25

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