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- PDB-9zba: Human GGPPS Bound to Selective Inhibitor CML-07-119 in theShielde... -

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Basic information

Entry
Database: PDB / ID: 9zba
TitleHuman GGPPS Bound to Selective Inhibitor CML-07-119 in theShielded Binding Site Conformation
ComponentsGeranylgeranyl pyrophosphate synthase
KeywordsTRANSFERASE/INHIBITOR / Inhibitor / complex / isoprenoid / synthesis / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


isoprenoid metabolic process / geranylgeranyl diphosphate synthase / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / Transferases; Transferring alkyl or aryl groups, other than methyl groups / (2E,6E)-farnesyl diphosphate synthase / Lanosterol biosynthesis / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase activity / isoprenoid biosynthetic process ...isoprenoid metabolic process / geranylgeranyl diphosphate synthase / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / Transferases; Transferring alkyl or aryl groups, other than methyl groups / (2E,6E)-farnesyl diphosphate synthase / Lanosterol biosynthesis / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase activity / isoprenoid biosynthetic process / trans, trans-farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / Activation of gene expression by SREBF (SREBP) / Z disc / perinuclear region of cytoplasm / metal ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
: / Geranylgeranyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.15 Å
AuthorsFerens, F.G. / Tsantrizos, Y.S. / Lemieux, M.J.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2023-04396 Canada
Canadian Institutes of Health Research (CIHR)PJT-159743 Canada
CitationJournal: To Be Published
Title: Human GGPPS Bound to Selective Inhibitor CML-07-119 in the Shielded Binding Site Conformation
Authors: Ferens, F.G. / Tsantrizos, Y.S. / Lemieux, M.J.
History
DepositionNov 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Geranylgeranyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6145
Polymers34,9731
Non-polymers6414
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Geranylgeranyl pyrophosphate synthase / GGPP synthase / GGPPSase / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase ...GGPP synthase / GGPPSase / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl diphosphate synthase / Farnesyltranstransferase / Geranylgeranyl diphosphate synthase / Geranyltranstransferase


Mass: 34972.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GGPS1 / Production host: Escherichia coli (E. coli)
References: UniProt: O95749, Transferases; Transferring alkyl or aryl groups, other than methyl groups, dimethylallyltranstransferase, geranylgeranyl diphosphate synthase, (2E,6E)-farnesyl diphosphate synthase
#2: Chemical ChemComp-A1C1E / {[(2-{3-[(3-fluoro-4-methoxyphenyl)carbamoyl]phenyl}thieno[2,3-d]pyrimidin-4-yl)amino]methylene}bis(phosphonic acid)


Mass: 568.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H19FN4O8P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human GGPPS Hexamer bound to Selective inhibitor CML-07-119
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10903
EM imaging opticsEnergyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
9PHENIX2.0_5729model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 11731724
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 559505 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 14.87 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00662403
ELECTRON MICROSCOPYf_angle_d0.53213245
ELECTRON MICROSCOPYf_chiral_restr0.0338355
ELECTRON MICROSCOPYf_plane_restr0.0036409
ELECTRON MICROSCOPYf_dihedral_angle_d7.9632312

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