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- PDB-1kzo: PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH FARNESYLATED K-RAS4B P... -

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Basic information

Entry
Database: PDB / ID: 1kzo
TitlePROTEIN FARNESYLTRANSFERASE COMPLEXED WITH FARNESYLATED K-RAS4B PEPTIDE PRODUCT AND FARNESYL DIPHOSPHATE SUBSTRATE BOUND SIMULTANEOUSLY
Components
  • (Protein Farnesyltransferase ...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 / PRODUCT / SUBSTRATE / 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 / 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 / forebrain astrocyte development / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / enzyme-linked receptor protein signaling pathway / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of nitric-oxide synthase biosynthetic process / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / alpha-tubulin binding / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / response to inorganic substance / Signalling to RAS / glial cell proliferation / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of cell cycle / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / protein-membrane adaptor activity / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / homeostasis of number of cells within a tissue / positive regulation of glial cell proliferation / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / striated muscle cell differentiation / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Ras activation upon Ca2+ influx through NMDA receptor / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / small monomeric GTPase / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / response to cytokine / FCERI mediated MAPK activation / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / visual learning / wound healing / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / lipid metabolic process
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 / Small GTPase, Ras-type / small GTPase Ras family 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 / FARNESYL DIPHOSPHATE / 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: 2.2 Å
AuthorsLong, S.B. / Casey, P.J. / Beese, L.S.
Citation
Journal: Nature / Year: 2002
Title: The 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 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.
#3: Journal: Biochemistry / Year: 1998
Title: Co-Crystal Structure of Mammalian Protein Farnesyltransferase 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_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.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_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 alpha subunit
B: Protein Farnesyltransferase beta subunit
C: Farnesylated K-Ras4B peptide product
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8337
Polymers94,1193
Non-polymers7144
Water7,710428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint-66 kcal/mol
Surface area29230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.199, 171.199, 69.444
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 PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS.
References: UniProt: P01118, UniProt: P01116*PLUS

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Non-polymers , 5 types, 432 molecules

#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-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#7: Chemical ChemComp-FAR / FARNESYL / Farnesol


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


Mass: 18.015 Da / Num. of mol.: 428 / 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: 3.12 Å3/Da / Density % sol: 60.57 %
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: 5.7 / Details: Long, S.B., (2000) Structure, 8, 209.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112-16 %(w/v)PEG80001reservoir
2600 mMammonium acetate1reservoir
320 mMdithiothreitol1reservoir

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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: Mar 7, 2000 / 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: 2.2→50 Å / Num. obs: 56209 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 4.51 % / Biso Wilson estimate: 32.8 Å2 / Rsym value: 0.089 / Net I/σ(I): 16.1
Reflection shellResolution: 2.2→2.23 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 1705 / Rsym value: 0.63 / % possible all: 87.9
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Num. measured all: 253335 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Rmerge(I) obs: 0.56

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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: 2.2→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
Rfree0.204 2497 4.9 %FROM STARTING MODEL: PDB ENTRY 1D8D
Rwork0.159 ---
all0.162 56209 --
obs0.159 50630 85.6 %-
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.184 Å20.74 Å20 Å2
2---0.184 Å20 Å2
3---1.711 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5994 0 44 428 6466
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d20.9
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_mcbond_it1.911.5
X-RAY DIFFRACTIONx_mcangle_it3.032
X-RAY DIFFRACTIONx_scbond_it3.52
X-RAY DIFFRACTIONx_scangle_it5.262.5
LS refinement shellResolution: 2.2→2.3 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.28 224 5.2 %
Rwork0.257 4055 -
obs-4279 58.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1parhcsdx.protophcsdx.pro
X-RAY DIFFRACTION2param19.soltoph19.sol
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor all: 0.162 / Rfactor obs: 0.159 / Rfactor Rfree: 0.204 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.255

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