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- PDB-9zbc: Human GGPPS in the Open Hexamer Conformation -

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Basic information

Entry
Database: PDB / ID: 9zbc
TitleHuman GGPPS in the Open Hexamer 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: 2.25 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 in the Open Hexamer 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

Downloads & links

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Assembly

Deposited unit
A: Geranylgeranyl pyrophosphate synthase
B: Geranylgeranyl pyrophosphate synthase
C: Geranylgeranyl pyrophosphate synthase
E: Geranylgeranyl pyrophosphate synthase
F: Geranylgeranyl pyrophosphate synthase
G: Geranylgeranyl pyrophosphate synthase


Theoretical massNumber of molelcules
Total (without water)209,8376
Polymers209,8376
Non-polymers00
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "E" or chain "F" or chain "G" or chain "H"
d_2ens_1chain "A" or chain "B" or chain "C" or chain "D"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLNGLNLYSLYSED9 - 29610 - 297
d_12THRTHRPHEPHEFE7 - 2958 - 296
d_13GLUGLUHISHISGF6 - 2907 - 291
d_14HOHHOHHOHHOHEJ464
d_21GLNGLNLYSLYSAA9 - 29610 - 297
d_22THRTHRPHEPHEBB7 - 2958 - 296
d_23GLUGLUHISHISCC6 - 2907 - 291
d_24HOHHOHHOHHOHAG464

NCS oper: (Code: given / Matrix: (-1), (-1), (1) / Vector: 89.548319850215, 126.7453222611)

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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.: 6
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / Source method: isolated from a natural source / Formula: H2O
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 in the open conformation / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPES1
2100 mMSodium ChlorideNaCl1
35 mMMagnesium ChlorideMgCl21
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: 4436
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
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5009239
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 531400 / Algorithm: FOURIER SPACE / 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: 12.72 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004412696
ELECTRON MICROSCOPYf_angle_d0.58717178
ELECTRON MICROSCOPYf_chiral_restr0.03771918
ELECTRON MICROSCOPYf_plane_restr0.00462182
ELECTRON MICROSCOPYf_dihedral_angle_d4.93061664
Refine LS restraints NCSType: NCS constraints / Rms dev position: 3.1006960837786E-13 Å

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