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- PDB-1jcr: CRYSTAL STRUCTURE OF RAT PROTEIN FARNESYLTRANSFERASE COMPLEXED WI... -

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Basic information

Entry
Database: PDB / ID: 1jcr
TitleCRYSTAL STRUCTURE OF RAT PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH THE NON-SUBSTRATE TETRAPEPTIDE INHIBITOR CVFM AND FARNESYL DIPHOSPHATE SUBSTRATE
Components
  • (PROTEIN FARNESYLTRANSFERASE, ...Farnesyltransferase) x 2
  • SYNTHETIC TETRAPEPTIDE CVFM
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / FTASE / PFT / PFTASE / FT / FPT / FARNESYLTRANSFERASE / FARNESYL TRANSFERASE / FARNESYL PROTEIN TRANSFERASE / CAAX / RAS / CANCER / TRANSFERASE-TRANSFERASE INHIBITOR 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 / enzyme-linked receptor protein signaling pathway / positive regulation of nitric-oxide synthase biosynthetic process / positive regulation of Rac protein signal transduction / alpha-tubulin binding / response to inorganic substance / positive regulation of cell cycle / response to cytokine / wound healing / lipid metabolic process / receptor tyrosine kinase binding / response to organic cyclic compound / positive regulation of fibroblast proliferation / fibroblast proliferation / microtubule binding / cell population proliferation / molecular adaptor activity / negative regulation of cell population proliferation / positive regulation of cell population proliferation / negative regulation of apoptotic process / zinc ion binding / 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
ACETIC ACID / FARNESYL DIPHOSPHATE / 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 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: 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN FARNESYLTRANSFERASE, ALPHA SUBUNIT
B: PROTEIN FARNESYLTRANSFERASE, BETA SUBUNIT
C: SYNTHETIC TETRAPEPTIDE CVFM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8877
Polymers93,3193
Non-polymers5684
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-75 kcal/mol
Surface area29050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.225, 171.225, 69.332
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: 44098.145 Da / Num. of mol.: 1 / Fragment: ALPHA SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q04631, 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: 48722.281 Da / Num. of mol.: 1 / Fragment: BETA SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q02293, Transferases; Transferring alkyl or aryl groups, other than methyl groups

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide SYNTHETIC TETRAPEPTIDE CVFM


Mass: 498.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: NON-SUBSTRATE INHIBITOR

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Non-polymers , 4 types, 434 molecules

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


Mass: 60.052 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 3.14 Å3/Da / Density % sol: 60.85 %
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: May 19, 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→50 Å / Num. all: 78430 / Num. obs: 68579 / % possible obs: 87.3 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.4
Reflection shellResolution: 2→2.02 Å / Redundancy: 3.28 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 2.48 / Num. unique all: 2615 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 78430 / % possible obs: 100 % / Num. measured all: 277944 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
Lowest resolution: 2.07 Å / Rmerge(I) obs: 0.397

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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: 1D8D

1d8d


Resolution: 2→50 Å / Rfactor Rfree error: 0.003 / 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
Rfree0.206 3652 5.1 %FROM PDB ENTRY 1D8D
Rwork0.166 ---
all0.168 78430 --
obs0.166 72300 92.1 %-
Displacement parametersBiso mean: 35.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.178 Å2-0.036 Å20 Å2
2---2.178 Å20 Å2
3---1.625 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5981 0 33 430 6444
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_d20.7
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_mcbond_it1.951.5
X-RAY DIFFRACTIONx_mcangle_it3.042
X-RAY DIFFRACTIONx_scbond_it3.552
X-RAY DIFFRACTIONx_scangle_it5.382.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.276 392 5.1 %
Rwork0.245 7237 -
obs-7629 77.1 %
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: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.4
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: 0.276 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.245 / Rfactor obs: 0.245

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