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- PDB-1d8e: Zinc-depleted FTase complexed with K-RAS4B peptide substrate and ... -

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Basic information

Entry
Database: PDB / ID: 1d8e
TitleZinc-depleted FTase complexed with K-RAS4B peptide substrate and FPP analog.
Components
  • (FARNESYLTRANSFERASE ...) x 2
  • K-RAS4B PEPTIDE SUBSTRATE
KeywordsTRANSFERASE / FTASE / PFT / PFTASE / FARNESYLTRANSFERASE / FARNESYL TRANSFERASE / CAAX / RAS / CANCER
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 / positive regulation of tubulin deacetylation / protein farnesyltransferase ...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 / positive regulation of tubulin deacetylation / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / Rab geranylgeranyltransferase activity / regulation of fibroblast proliferation / protein geranylgeranylation / positive regulation of skeletal muscle acetylcholine-gated channel clustering / : / farnesyltranstransferase activity / microtubule associated complex / forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / type I pneumocyte differentiation / epithelial tube branching involved in lung morphogenesis / enzyme-linked receptor protein signaling pathway / Rac protein signal transduction / : / skeletal muscle cell differentiation / 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 / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / alpha-tubulin binding / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / glial cell proliferation / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of cell cycle / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / positive regulation of glial cell proliferation / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / homeostasis of number of cells within a tissue / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / striated muscle cell differentiation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / CD209 (DC-SIGN) signaling / Ras activation upon Ca2+ influx through NMDA receptor / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / small monomeric GTPase / VEGFR2 mediated cell proliferation / response to cytokine / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / wound healing / Constitutive Signaling by EGFRvIII / regulation of long-term neuronal synaptic plasticity / Signaling by high-kinase activity BRAF mutants / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / visual learning / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / 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
ACETATE ION / Chem-FII / GTPase KRas / Protein farnesyltransferase subunit beta / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsLong, S.B. / Casey, P.J. / Beese, L.S.
Citation
Journal: Structure Fold.Des. / 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.
#1: 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.
#2: 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
DepositionOct 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FARNESYLTRANSFERASE (ALPHA SUBUNIT)
B: FARNESYLTRANSFERASE (BETA SUBUNIT)
P: K-RAS4B PEPTIDE SUBSTRATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5385
Polymers94,1193
Non-polymers4182
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9120 Å2
ΔGint-25 kcal/mol
Surface area29390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.411, 171.411, 69.663
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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FARNESYLTRANSFERASE ... , 2 types, 2 molecules AB

#1: Protein FARNESYLTRANSFERASE (ALPHA SUBUNIT) / FTASE


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


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

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide K-RAS4B PEPTIDE SUBSTRATE


Mass: 1298.723 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This synthetic peptide is derived from human K-Ras4B, residues 178-188
References: UniProt: P01116

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Non-polymers , 3 types, 77 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
Details: non-reactive FPP analog (FPT Inhibitor II, Calbiochem) Manne, V. et al. & Biller, S.A. (1995) Drug Dev. Res. 34,pg 121-137
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsThe peptide adopts a non-catalytic beta-turn conformation in the absence of zinc. Please refer to ...The peptide adopts a non-catalytic beta-turn conformation in the absence of zinc. Please refer to the 2.0A resolution structure in the presence of zinc, 1D8D. residues 1-54 of chain A are disordered residues 1-16 and 424-437 of chain b are disordered residues 1-5 of chain P are disordered

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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: 3.14 Å3/Da / Density % sol: 60.79 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: Peg 8000, ammonium acetate, DTT , pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃
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: 96 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 22662 / Num. obs: 21199 / % possible obs: 89.3 % / Observed criterion σ(I): 0 / Redundancy: 4.01 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.9
Reflection shellResolution: 3→3.03 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.289 / Num. unique all: 770 / % possible all: 96
Reflection
*PLUS
Num. measured all: 85082
Reflection shell
*PLUS
% possible obs: 82.2 % / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementResolution: 3→50 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 984 5 %DERIVED from those for 1d8d
Rwork0.196 ---
all0.219 21612 --
obs0.199 19588 82.8 %-
Displacement parametersBiso mean: 45.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5995 0 28 75 6098
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d20.9
X-RAY DIFFRACTIONx_improper_angle_d1.32
X-RAY DIFFRACTIONx_mcbond_it1.681.5
X-RAY DIFFRACTIONx_mcangle_it2.832
X-RAY DIFFRACTIONx_scbond_it2.452
X-RAY DIFFRACTIONx_scangle_it3.782.5
LS refinement shellResolution: 3→3.14 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.347 87 4.4 %
Rwork0.289 1870 -
obs--66.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOP.SOL
X-RAY DIFFRACTION3TOPH19.SOL
X-RAY DIFFRACTION4
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
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_deg1.32

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