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- EMDB-73980: Human GGPPS Bound to Selective Inhibitor CML-07-119 in theShielde... -

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Basic information

Entry
Database: EMDB / ID: EMD-73980
TitleHuman GGPPS Bound to Selective Inhibitor CML-07-119 in theShielded Binding Site Conformation
Map dataPost-processed map (Cropped, sharpened and density modified with Resolve-CryoEM in Phenix)
Sample
  • Complex: Human GGPPS Hexamer bound to Selective inhibitor CML-07-119
    • Protein or peptide: Geranylgeranyl pyrophosphate synthase
  • Ligand: {[(2-{3-[(3-fluoro-4-methoxyphenyl)carbamoyl]phenyl}thieno[2,3-d]pyrimidin-4-yl)amino]methylene}bis(phosphonic acid)
  • Ligand: MAGNESIUM ION
KeywordsInhibitor / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.15 Å
AuthorsFerens FG / Tsantrizos YS / Lemieux MJ
Funding support Canada, 2 items
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 FG / Tsantrizos YS / Lemieux MJ
History
DepositionNov 20, 2025-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73980.png

Downloads & links

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Map

FileDownload / File: emd_73980.map.gz / Format: CCP4 / Size: 15.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed map (Cropped, sharpened and density modified with Resolve-CryoEM in Phenix)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.69 Å/pix.
x 141 pix.
= 97.149 Å		0.69 Å/pix.
x 189 pix.
= 130.221 Å		0.69 Å/pix.
x 155 pix.
= 106.795 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.689 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.974
Minimum - Maximum-7.9035015 - 14.677928
Average (Standard dev.)-0.000000000017559 (±0.5001898)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin122121146
Dimensions189155141
Spacing141189155
CellA: 97.149 Å / B: 130.22101 Å / C: 106.795 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73980_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_73980_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Raw Half-Map A

Fileemd_73980_half_map_1.map
AnnotationRaw Half-Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Raw Half-Map B

Fileemd_73980_half_map_2.map
AnnotationRaw Half-Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human GGPPS Hexamer bound to Selective inhibitor CML-07-119

EntireName: Human GGPPS Hexamer bound to Selective inhibitor CML-07-119
Components
  • Complex: Human GGPPS Hexamer bound to Selective inhibitor CML-07-119
    • Protein or peptide: Geranylgeranyl pyrophosphate synthase
  • Ligand: {[(2-{3-[(3-fluoro-4-methoxyphenyl)carbamoyl]phenyl}thieno[2,3-d]pyrimidin-4-yl)amino]methylene}bis(phosphonic acid)
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Human GGPPS Hexamer bound to Selective inhibitor CML-07-119

SupramoleculeName: Human GGPPS Hexamer bound to Selective inhibitor CML-07-119
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Geranylgeranyl pyrophosphate synthase

MacromoleculeName: Geranylgeranyl pyrophosphate synthase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Transferring alkyl or aryl groups, other than methyl groups
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.972883 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GMEKTQETVQ RILLEPYKYL LQLPGKQVRT KLSQAFNHWL KVPEDKLQII IEVTEMLHNA SLLIDDIEDN SKLRRGFPVA HSIYGIPSV INSANYVYFL GLEKVLTLDH PDAVKLFTRQ LLELHQGQGL DIYWRDNYTC PTEEEYKAMV LQKTGGLFGL A VGLMQLFS ...String:
GMEKTQETVQ RILLEPYKYL LQLPGKQVRT KLSQAFNHWL KVPEDKLQII IEVTEMLHNA SLLIDDIEDN SKLRRGFPVA HSIYGIPSV INSANYVYFL GLEKVLTLDH PDAVKLFTRQ LLELHQGQGL DIYWRDNYTC PTEEEYKAMV LQKTGGLFGL A VGLMQLFS DYKEDLKPLL NTLGLFFQIR DDYANLHSKE YSENKSFCED LTEGKFSFPT IHAIWSRPES TQVQNILRQR TE NIDIKKY CVHYLEDVGS FEYTRNTLKE LEAKAYKQID ARGGNPELVA LVKHLSKMFK EENE

UniProtKB: Geranylgeranyl pyrophosphate synthase

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Macromolecule #2: {[(2-{3-[(3-fluoro-4-methoxyphenyl)carbamoyl]phenyl}thieno[2,3-d]...

MacromoleculeName: {[(2-{3-[(3-fluoro-4-methoxyphenyl)carbamoyl]phenyl}thieno[2,3-d]pyrimidin-4-yl)amino]methylene}bis(phosphonic acid)
type: ligand / ID: 2 / Number of copies: 1 / Formula: A1C1E
Molecular weightTheoretical: 568.408 Da

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291.15 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 1 / Number real images: 10903 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 11731724
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab-initio in cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 559505
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: Ab-initio in cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 10 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9zba:
Human GGPPS Bound to Selective Inhibitor CML-07-119 in theShielded Binding Site Conformation

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