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- PDB-1kzp: PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH A FARNESYLATED K-RAS4B... -

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Basic information

Entry
Database: PDB / ID: 1kzp
TitlePROTEIN FARNESYLTRANSFERASE COMPLEXED WITH A FARNESYLATED K-RAS4B PEPTIDE PRODUCT
Components
  • (Protein Farnesyltransferase ...) x 2
  • Farnesylated K-Ras4B peptide product
KeywordsTRANSFERASE/TRANSFERASE SUBSTRATE / FTASE / PFT / PFTASE / FT / FPT / FARNESYLTRANSFERASE / FARNESYL TRANSFERASE / FARNESYL PROTEIN TRANSFERASE / CAAX / RAS CANCER / TRANSFERASE-TRANSFERASE SUBSTRATE COMPLEX
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / peptide pheromone maturation / protein farnesylation / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesyltransferase ...Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / peptide pheromone maturation / protein farnesylation / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / Rab geranylgeranyltransferase activity / protein geranylgeranylation / regulation of fibroblast proliferation / regulation of microtubule-based movement / geranylgeranyl diphosphate synthase activity / positive regulation of skeletal muscle acetylcholine-gated channel clustering / acetyltransferase activator activity / microtubule associated complex / response to mineralocorticoid / GMP binding / forebrain astrocyte development / LRR domain binding / enzyme-linked receptor protein signaling pathway / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / response to isolation stress / response to gravity / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / myoblast proliferation / RAS signaling downstream of NF1 loss-of-function variants / skeletal muscle cell differentiation / RUNX3 regulates p14-ARF / positive regulation of glial cell proliferation / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / cardiac muscle cell proliferation / Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / alpha-tubulin binding / Estrogen-stimulated signaling through PRKCZ / glial cell proliferation / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / positive regulation of cell cycle / FRS-mediated FGFR1 signaling / p38MAPK events / Signaling by FGFR3 in disease / protein-membrane adaptor activity / Tie2 Signaling / striated muscle cell differentiation / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / Downstream signal transduction / GRB2 events in ERBB2 signaling / homeostasis of number of cells within a tissue / Insulin receptor signalling cascade / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / response to glucocorticoid / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / small monomeric GTPase / FCERI mediated MAPK activation / wound healing / liver development / RAF activation / Signaling by ERBB2 TMD/JMD mutants / female pregnancy
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 alpha-alpha toroid domain / 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 alpha-alpha toroid domain / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Small GTPase, Ras-type / Small GTPase Ras domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
ACETIC ACID / FARNESYL / GTPase KRas / GTPase KRas / Protein farnesyltransferase subunit beta / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLong, S.B. / Casey, P.J. / Beese, L.S.
Citation
Journal: Nature / Year: 2002
Title: Reaction path of protein farnesyltransferase at atomic resolution
Authors: Long, S.B. / Casey, P.J. / Beese, L.S.
#1: Journal: Structure / Year: 2000
Title: The Basis for K-Ras4B Binding Specificity to Protein Farnesyltransferase Revealed by 2 A 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 2.25 A Resolution
Authors: Park, H.W. / Boduluri, S.R. / Moomaw, J.F. / Casey, P.J. / Beese, L.S.
#3: Journal: Biochemistry / Year: 1998
Title: Co-Crystal Structure of Protein Farnesyltransferase Complexed with a Farnesyl Diphosphate Substrate
Authors: Long, S.B. / Casey, P.J. / Beese, L.S.
History
DepositionFeb 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Aug 16, 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_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_asym_id / _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_asym_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.pdbx_leaving_atom_flag / _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_asym_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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: Farnesylated K-Ras4B peptide product
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5117
Polymers94,1193
Non-polymers3924
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-65 kcal/mol
Surface area29470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.239, 171.239, 69.361
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
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 / CAAX FARNESYLTRANSFERASE ALPHA SUBUNIT / RAS PROTEINS PRENYLTRANSFERASE ALPHA / FTASE-ALPHA


Mass: 44098.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q04631, squalene synthase
#2: Protein Protein Farnesyltransferase beta subunit / CAAX FARNESYLTRANSFERASE BETA SUBUNIT / RAS PROTEINS PRENYLTRANSFERASE BETA / FTASE-BETA


Mass: 48722.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q02293, squalene synthase

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Farnesylated K-Ras4B peptide product / TRANSFORMING PROTEIN P21B


Mass: 1298.723 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN HOMO SAPIENS.
References: UniProt: P01118, UniProt: P01116*PLUS

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Non-polymers , 4 types, 425 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-FAR / FARNESYL


Mass: 206.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.12 Å3/Da / Density % sol: 60.54 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: PEG 8000, Ammonium Acetate, Magnesium Chloride, DTT, Tris-HCl, pH 5.70, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 7 / Details: Park, H.W., (1997) Science, 275, 1800.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 mg/mlFTase1drop
220 mM1dropKCl
310 mM1dropZnCl
410 mMdithiothreitol1drop
520 mMTris-HCl1drop
613-15 %(w/v)PEG80001drop
7200 mMammonium acetate1drop
813-15 %(w/v)PEG80001reservoir
9200 mMammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 26, 1999 / 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: 2.1→50 Å / Num. obs: 67840 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.93 % / Biso Wilson estimate: 28.9 Å2 / Rsym value: 0.086 / Net I/σ(I): 21
Reflection shellResolution: 2.1→2.12 Å / Redundancy: 5.62 % / Mean I/σ(I) obs: 2.47 / Num. unique all: 2216 / Rsym value: 0.637 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 50 Å / % possible obs: 100 % / Num. measured all: 402441 / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 2.8

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Processing

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

1d8d


Resolution: 2.1→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
RfactorNum. reflection% reflectionSelection details
Rfree0.202 3073 5 %FROM STARTING MODEL: PDB ENTRY 1D8D
Rwork0.164 ---
all0.1659 67840 --
obs0.164 61433 90.5 %-
Displacement parametersBiso mean: 34.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.364 Å2-0.03 Å20 Å2
2---1.364 Å20 Å2
3---6.841 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5983 0 24 421 6428
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.4
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_d1.34
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.651.5
X-RAY DIFFRACTIONx_mcangle_it2.612
X-RAY DIFFRACTIONx_scbond_it2.952
X-RAY DIFFRACTIONx_scangle_it4.512.5
LS refinement shellResolution: 2.1→2.2 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.273 334 5.2 %
Rwork0.235 6119 -
obs-6453 76.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1parhcsdx.protophcsdx.pro
X-RAY DIFFRACTION2param19.soltoph19.sol
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor all: 0.1659 / Rfactor obs: 0.164 / Rfactor Rfree: 0.202 / Rfactor Rwork: 0.164
Solvent computation
*PLUS
Displacement parameters
*PLUS
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_deg1.34
LS refinement shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.235

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