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- PDB-3pz4: Crystal structure of FTase(ALPHA-subunit; BETA-subunit DELTA C10)... -

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Basic information

Entry
Database: PDB / ID: 3pz4
TitleCrystal structure of FTase(ALPHA-subunit; BETA-subunit DELTA C10) in complex with BMS3 and lipid substrate FPP
Components
  • Protein farnesyltransferase subunit betaFarnesyltransferase
  • Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein prenylation / 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 geranylgeranyltransferase type I / protein farnesylation / 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 geranylgeranyltransferase type I / protein farnesylation / 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
Chem-3PZ / FARNESYL DIPHOSPHATE / Protein farnesyltransferase subunit beta / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGuo, Z. / Bon, R.S. / Stigter, E.A. / Waldmann, H. / Alexandrov, K. / Blankenfeldt, W. / Goody, R.S.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2011
Title: Structure-Guided Development of Selective RabGGTase Inhibitors.
Authors: Bon, R.S. / Guo, Z. / Stigter, E.A. / Wetzel, S. / Menninger, S. / Wolf, A. / Choidas, A. / Alexandrov, K. / Blankenfeldt, W. / Goody, R.S. / Waldmann, H.
History
DepositionDec 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 15, 2014Group: Database references / Refinement description / Source and taxonomy
Revision 1.3Sep 13, 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_ref_seq_dif / 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.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_ref_seq_dif.details / _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/geranylgeranyltransferase type-1 subunit alpha
B: Protein farnesyltransferase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8875
Polymers91,9112
Non-polymers9753
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-12 kcal/mol
Surface area28130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.746, 170.746, 69.085
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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Protein , 2 types, 2 molecules AB

#1: Protein Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha / CAAX farnesyltransferase subunit alpha / FTase-alpha / Ras proteins prenyltransferase subunit alpha ...CAAX farnesyltransferase subunit alpha / FTase-alpha / Ras proteins prenyltransferase subunit alpha / Type I protein geranyl-geranyltransferase subunit alpha / GGTase-I-alpha


Mass: 44293.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: coexpression of engineered alpha-subunit from pGATEV and beta-subunit from pET30a
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fnta, Ggta, Rabggta / Plasmid: pGATEV and pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON-PLUS RIL (DE3)
References: UniProt: Q04631, protein farnesyltransferase, protein geranylgeranyltransferase type I
#2: Protein Protein farnesyltransferase subunit beta / Farnesyltransferase / FTase-beta / CAAX farnesyltransferase subunit beta / Ras proteins prenyltransferase subunit beta


Mass: 47618.148 Da / Num. of mol.: 1 / Fragment: UNP residues 2-427
Source method: isolated from a genetically manipulated source
Details: coexpression of engineered alpha-subunit from pGATEV and beta-subunit from pET30a
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fntb, Ggtb, Rabggtb / Plasmid: pGATEV and pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON-PLUS RIL (DE3) / References: UniProt: Q02293, protein farnesyltransferase

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Non-polymers , 4 types, 309 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE / Farnesyl pyrophosphate


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2
#5: Chemical ChemComp-3PZ / (3R)-3-benzyl-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepine-7-carbonitrile


Mass: 527.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H29N5O3S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 3.16 Å3/Da / Density % sol: 61.11 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% (w/v) PEG 4000, 0.2 M MgCl2, 0.1 M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 29, 2008
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 67245 / Num. obs: 67104 / % possible obs: 99.8 % / Observed criterion σ(I): 5 / Redundancy: 6.2 % / Biso Wilson estimate: 36 Å2 / Rsym value: 0.06 / Net I/σ(I): 24
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 6.5 / Num. unique all: 8682 / Rsym value: 0.359 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EU5

3eu5


Resolution: 2.1→29.91 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.9 / SU B: 15.485 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2674 3365 5 %RANDOM
Rwork0.22521 ---
obs0.22733 63737 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.501 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20.6 Å20 Å2
2--1.21 Å20 Å2
3----1.81 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5839 0 63 306 6208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226075
X-RAY DIFFRACTIONr_bond_other_d00.024129
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.9598252
X-RAY DIFFRACTIONr_angle_other_deg4.1473.0019963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.125716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18723.987311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.967151016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.681542
X-RAY DIFFRACTIONr_chiral_restr0.1130.2873
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026756
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021252
X-RAY DIFFRACTIONr_nbd_refined0.2720.21865
X-RAY DIFFRACTIONr_nbd_other0.2560.24684
X-RAY DIFFRACTIONr_nbtor_refined0.1960.22975
X-RAY DIFFRACTIONr_nbtor_other0.110.22911
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2360.2405
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.120.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2940.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3050.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4650.226
X-RAY DIFFRACTIONr_mcbond_it1.8391.53583
X-RAY DIFFRACTIONr_mcbond_other6.2051.51440
X-RAY DIFFRACTIONr_mcangle_it3.14125782
X-RAY DIFFRACTIONr_scbond_it2.80632492
X-RAY DIFFRACTIONr_scangle_it4.7254.52470
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 255 -
Rwork0.314 4673 -
obs--99.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.08550.06310.06330.15970.07330.2054-0.0061-0.00020.0204-0.0083-0.00390.0136-0.03730.01280.01-0.0108-0.00070.0055-0.02820.00180.00953.7319-37.7349-2.4781
20.09290.01160.02880.04240.0150.1923-0.00220.00260.00440.0038-0.0006-0.0111-0.01020.0370.0029-0.0118-0.0005-0.0015-0.01950.00210.021861.8574-50.16689.6111
30.0344-0.48280.02346.7788-0.3290.0160.00480.2576-0.0036-0.17220.02980.07050.1336-0.0672-0.0346-0.0001-0.00050.0001-0.00010.0010.000551.4779-50.91014.0944
4000000000000000-0.02580.0017-0.0035-0.0259-0.001-0.025452.4021-47.07329.7471
52.4184-4.7116-3.38529.1796.59514.7386-0.0261-0.09710.0113-0.19150.08780.0537-0.14330.2375-0.06160.00040.00050-0.0001-0.00040.000255.8508-45.71353.6637
60.04220.00990.01530.01330.00560.0660.0002-0.00080.00210.00040-0.0007-0.00470.0098-0.0002-0.0074-0.0039-0.0003-0.0110.00210.02757.4591-45.16914.507
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 369
2X-RAY DIFFRACTION2B21 - 423
3X-RAY DIFFRACTION3B429
4X-RAY DIFFRACTION4B1
5X-RAY DIFFRACTION5B428
6X-RAY DIFFRACTION6A378 - 514
7X-RAY DIFFRACTION6B430 - 598

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