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- EMDB-66311: GaTPS1-GGSPP -

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Basic information

Entry
Database: EMDB / ID: EMD-66311
TitleGaTPS1-GGSPP
Map data
Sample
  • Complex: GaTPS1-GGSPP
    • Protein or peptide: sesterterterpenes synthase
  • Ligand: phosphonooxy-[(10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]sulfanyl-phosphinic acid
  • Ligand: MAGNESIUM ION
  • Ligand: water
Keywordsterpene synthase / Lyase / BIOSYNTHETIC PROTEIN
Biological speciesGentianella arenaria (plant) / Gentianella (plant)
Methodsingle particle reconstruction / Resolution: 2.64 Å
AuthorsGuo K / Kaituo W
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82204245 China
CitationJournal: To Be Published
Title: Discovery and Biosynthesis of Gentianellane-Type Sesterterpenoids as Potent Anti-Liver Fibrosis Agents
Authors: Guo K
History
DepositionSep 23, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66311.png

Downloads & links

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Map

FileDownload / File: emd_66311.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 288 pix.
= 244.8 Å		0.85 Å/pix.
x 288 pix.
= 244.8 Å		0.85 Å/pix.
x 288 pix.
= 244.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.27417263 - 0.6205048
Average (Standard dev.)-0.00044222394 (±0.012525707)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 244.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66311_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66311_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GaTPS1-GGSPP

EntireName: GaTPS1-GGSPP
Components
  • Complex: GaTPS1-GGSPP
    • Protein or peptide: sesterterterpenes synthase
  • Ligand: phosphonooxy-[(10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]sulfanyl-phosphinic acid
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: GaTPS1-GGSPP

SupramoleculeName: GaTPS1-GGSPP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Gentianella arenaria (plant)

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Macromolecule #1: sesterterterpenes synthase

MacromoleculeName: sesterterterpenes synthase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gentianella (plant)
Molecular weightTheoretical: 64.001074 KDa
Recombinant expressionOrganism: Escherichia coli B (bacteria)
SequenceString: GSRPLVNFPE KISGDRFMSS FTHLDQKVHE GYAKEIQSLK DEVKNMLLKE CKAVDKLYLI DNIERLGLSY HFEDEIDEQL QLLFDQNES IKDDRYSDLS TIALRFRLFR QHGYPISSDV FKQFTFGNGT FKTALQSDSR GILNLYDAAY VSTRNDVILD E AVRFTTDK ...String:
GSRPLVNFPE KISGDRFMSS FTHLDQKVHE GYAKEIQSLK DEVKNMLLKE CKAVDKLYLI DNIERLGLSY HFEDEIDEQL QLLFDQNES IKDDRYSDLS TIALRFRLFR QHGYPISSDV FKQFTFGNGT FKTALQSDSR GILNLYDAAY VSTRNDVILD E AVRFTTDK LQRQSTRGAY IDKLVKHALE QSLHRGVPRL EARHFIDAYE HDEMKNVSLL KLAKLDFNFL QLLYKQELNE SL RWWKEID AATNVPYARN RLVESYFWAL VMFYEPKYSK ARLMVTKYLA TGTFIDDTYD AYGSRDELEI FTSAIQRWDY SEA DRLPGY MKKAYTIFLN TYVEFEEYAN QQGRPYAFHY LQEGWKEYSR SSNMQSRWFF NPEELPLFDE YMVHGLITGA GRVN ACVCA LLMESGTEDA FQWLFQYPPI LYAGNTIYRL VNDLAGYQVE KETGIPNSID CYMKEFKVSE EEAKMRLTEM VENAW KDFN EEYMNRRKQT TPPIGEEIWT LLINQTRIMD VAYKNGVDGW TNSQDSLKHF LNGLLVDPIP I

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Macromolecule #2: phosphonooxy-[(10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetra...

MacromoleculeName: phosphonooxy-[(10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]sulfanyl-phosphinic acid
type: ligand / ID: 2 / Number of copies: 1 / Formula: GGS
Molecular weightTheoretical: 466.509 Da
Chemical component information

ChemComp-GGS:
phosphonooxy-[(10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]sulfanyl-phosphinic acid

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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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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 393355 / Resolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Software - Name: cryoSPARC / Number images used: 537371
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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