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- PDB-8rdx: PGGtase I in complex with probe BAY-6092 -

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Basic information

Entry
Database: PDB / ID: 8rdx
TitlePGGtase I in complex with probe BAY-6092
Components
  • Geranylgeranyl transferase type-1 subunit beta
  • Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
KeywordsTRANSFERASE / inhibitor
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 / 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 geranylgeranyltransferase type I / protein farnesylation / 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 / negative regulation of nitric-oxide synthase biosynthetic process / microtubule associated complex / heterocyclic compound binding / 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 / response to organic cyclic compound / receptor tyrosine kinase binding / microtubule binding / molecular adaptor activity / positive regulation of cell population proliferation / negative regulation of apoptotic process / zinc ion binding / cytoplasm
Similarity search - Function
Geranylgeranyl transferase type-1 subunit beta / 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 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid
Similarity search - Domain/homology
: / DIPHOSPHATE / Geranylgeranyl transferase type-1 subunit beta / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.67 Å
AuthorsSteuber, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Cell Chem Biol / Year: 2024
Title: Discovery of YAP1/TAZ pathway inhibitors through phenotypic screening with potent anti-tumor activity via blockade of Rho-GTPase signaling.
Authors: Graham, K. / Lienau, P. / Bader, B. / Prechtl, S. / Naujoks, J. / Lesche, R. / Weiske, J. / Kuehnlenz, J. / Brzezinka, K. / Potze, L. / Zanconato, F. / Nicke, B. / Montebaur, A. / Bone, W. / ...Authors: Graham, K. / Lienau, P. / Bader, B. / Prechtl, S. / Naujoks, J. / Lesche, R. / Weiske, J. / Kuehnlenz, J. / Brzezinka, K. / Potze, L. / Zanconato, F. / Nicke, B. / Montebaur, A. / Bone, W. / Golfier, S. / Kaulfuss, S. / Kopitz, C. / Pilari, S. / Steuber, H. / Hayat, S. / Kamburov, A. / Steffen, A. / Schlicker, A. / Buchgraber, P. / Braeuer, N. / Font, N.A. / Heinrich, T. / Kuhnke, L. / Nowak-Reppel, K. / Stresemann, C. / Steigemann, P. / Walter, A.O. / Blotta, S. / Ocker, M. / Lakner, A. / von Nussbaum, F. / Mumberg, D. / Eis, K. / Piccolo, S. / Lange, M.
#1: Journal: Biorxiv / Year: 2023
Title: Novel YAP1/TAZ pathway inhibitors identified through phenotypic screening with potent anti-tumor activity via blockade of GGTase-I / Rho-GTPase signaling
Authors: Graham, K. / Lienau, P. / Bader, B. / Prechtl, S. / Naujoks, J. / Lesche, R. / Weiske, J. / Kuehnlenz, J. / Brzezinka, K. / Potze, L. / Zanconato, F. / Nicke, B. / Montebaur, A. / Bone, W. / ...Authors: Graham, K. / Lienau, P. / Bader, B. / Prechtl, S. / Naujoks, J. / Lesche, R. / Weiske, J. / Kuehnlenz, J. / Brzezinka, K. / Potze, L. / Zanconato, F. / Nicke, B. / Montebaur, A. / Bone, W. / Golfier, S. / Kaulfuss, S. / Kopitz, C. / Pilari, S. / Steuber, H. / Hayat, S. / Kamburov, A. / Steffen, A. / Schlicker, A. / Buchgraber, P. / Braeuer, N. / Font, N. / Heinrich, T. / Kuhnke, L. / Reppel, K. / Stresemann, C. / Steigemann, P. / Walter, A. / Blotta, S. / Ocker, M. / Lakner, A. / Mumberg, D. / Eis, K. / Piccolo, S. / Lange, M.
History
DepositionDec 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / citation_author

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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: Geranylgeranyl transferase type-1 subunit beta
C: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
D: Geranylgeranyl transferase type-1 subunit beta
E: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
F: Geranylgeranyl transferase type-1 subunit beta
G: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
H: Geranylgeranyl transferase type-1 subunit beta
I: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
J: Geranylgeranyl transferase type-1 subunit beta
K: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
L: Geranylgeranyl transferase type-1 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)466,93036
Polymers462,33812
Non-polymers4,59224
Water1086
1
A: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
B: Geranylgeranyl transferase type-1 subunit beta
hetero molecules


  • defined by author&software
  • 77.8 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)77,8226
Polymers77,0562
Non-polymers7654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-66 kcal/mol
Surface area25560 Å2
MethodPISA
2
C: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
D: Geranylgeranyl transferase type-1 subunit beta
hetero molecules


  • defined by author&software
  • 77.8 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)77,8226
Polymers77,0562
Non-polymers7654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-63 kcal/mol
Surface area25540 Å2
MethodPISA
3
E: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
F: Geranylgeranyl transferase type-1 subunit beta
hetero molecules


  • defined by author&software
  • 77.8 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)77,8226
Polymers77,0562
Non-polymers7654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-63 kcal/mol
Surface area25740 Å2
MethodPISA
4
G: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
H: Geranylgeranyl transferase type-1 subunit beta
hetero molecules


  • defined by author&software
  • 77.8 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)77,8226
Polymers77,0562
Non-polymers7654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-64 kcal/mol
Surface area25700 Å2
MethodPISA
5
I: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
J: Geranylgeranyl transferase type-1 subunit beta
hetero molecules


  • defined by author&software
  • 77.8 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)77,8226
Polymers77,0562
Non-polymers7654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-60 kcal/mol
Surface area25510 Å2
MethodPISA
6
K: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
L: Geranylgeranyl transferase type-1 subunit beta
hetero molecules


  • defined by author&software
  • 77.8 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)77,8226
Polymers77,0562
Non-polymers7654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-60 kcal/mol
Surface area25650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)270.891, 269.263, 185.248
Angle α, β, γ (deg.)90.00, 131.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein
Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha


Mass: 37871.570 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fnta / Production host: Spodoptera (butterflies/moths) / References: UniProt: Q04631
#2: Protein
Geranylgeranyl transferase type-1 subunit beta


Mass: 39184.699 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pggt1b / Production host: Spodoptera (butterflies/moths) / References: UniProt: P53610

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Non-polymers , 5 types, 30 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-DPO / DIPHOSPHATE / Pyrophosphate


Mass: 173.943 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: O7P2
#6: Chemical
ChemComp-A1HZ4 / (5~{R})-5-(2-methoxyphenyl)-9-[(2~{R})-3,3,3-tris(fluoranyl)-2-methoxy-2-phenyl-propanoyl]-3,9-diazaspiro[5.5]undecan-2-one


Mass: 490.515 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C26H29F3N2O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4.85 Å3/Da / Density % sol: 74.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.2 M K-Na-tartrate, 100 mM (NH4)2SO4, 100 mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.67→48.21 Å / Num. obs: 105402 / % possible obs: 97.4 % / Redundancy: 3.86 % / CC1/2: 0.999 / Net I/σ(I): 20.64
Reflection shellResolution: 3.67→3.89 Å / Mean I/σ(I) obs: 5.8 / Num. unique obs: 15220 / CC1/2: 0.955

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.67→48.21 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.928 / SU B: 17.344 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18907 2100 2 %RANDOM
Rwork0.13713 ---
obs0.13817 103301 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.179 Å2
Baniso -1Baniso -2Baniso -3
1--4.55 Å20 Å2-2.46 Å2
2--9.17 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 3.67→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31959 0 276 6 32241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01333003
X-RAY DIFFRACTIONr_bond_other_d0.0010.01729521
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.64544830
X-RAY DIFFRACTIONr_angle_other_deg1.31.57867942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.00753948
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54221.5621927
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.328155455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2315270
X-RAY DIFFRACTIONr_chiral_restr0.0730.24146
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0237108
X-RAY DIFFRACTIONr_gen_planes_other0.0020.027476
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.7298.47115828
X-RAY DIFFRACTIONr_mcbond_other6.7258.4715827
X-RAY DIFFRACTIONr_mcangle_it10.09112.70319764
X-RAY DIFFRACTIONr_mcangle_other10.09112.70319765
X-RAY DIFFRACTIONr_scbond_it7.3478.9717175
X-RAY DIFFRACTIONr_scbond_other7.3478.97117176
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.26613.25525066
X-RAY DIFFRACTIONr_long_range_B_refined13.36999.4839605
X-RAY DIFFRACTIONr_long_range_B_other13.36999.48139606
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.672→3.767 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 117 -
Rwork0.213 5738 -
obs--74.35 %

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