[English] 日本語
Yorodumi
- PDB-1d8e: Zinc-depleted FTase complexed with K-RAS4B peptide substrate and ... -

+
Open data


ID or keywords:

Loading...

-
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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Non-polymers , 3 types, 77 molecules

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


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 / Water


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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more