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- EMDB-12739: Structure of the borneol dehydrogenase 2 of Salvia officinalis -

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Basic information

Entry
Database: EMDB / ID: EMD-12739
TitleStructure of the borneol dehydrogenase 2 of Salvia officinalis
Map data
Sample
  • Complex: Homotetrameric complex of borneol dehydrogenase
    • Protein or peptide: borneol dehydrogenase
  • Ligand: water
KeywordsTERPENOID / ALCOHOL / OXIDOREDUCTASE / BORNEOL / ROSSMANN-LIKE FOLD
Biological speciesSalvia officinalis (garden sage)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.04 Å
AuthorsDimos N / Helmer CPO
Funding support Germany, Austria, 6 items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research031B050B Germany
Austrian Science FundP31001-B29 Austria
German Research Foundation (DFG)INST 335/588-1 Germany
German Research Foundation (DFG)INST 335/589-1 Germany
German Research Foundation (DFG)INST 335/590-1 Germany
German Research Foundation (DFG)HA 2549/15-2 Germany
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: CryoEM analysis of small plant biocatalysts at sub-2 Å resolution.
Authors: Nicole Dimos / Carl P O Helmer / Andrea M Chánique / Markus C Wahl / Robert Kourist / Tarek Hilal / Bernhard Loll /
Abstract: Enzyme catalysis has emerged as a key technology for developing efficient, sustainable processes in the chemical, biotechnological and pharmaceutical industries. Plants provide large and diverse ...Enzyme catalysis has emerged as a key technology for developing efficient, sustainable processes in the chemical, biotechnological and pharmaceutical industries. Plants provide large and diverse pools of biosynthetic enzymes that facilitate complex reactions, such as the formation of intricate terpene carbon skeletons, with exquisite specificity. High-resolution structural analysis of these enzymes is crucial in order to understand their mechanisms and modulate their properties by targeted engineering. Although cryo-electron microscopy (cryoEM) has revolutionized structural biology, its applicability to high-resolution structural analysis of comparatively small enzymes has so far been largely unexplored. Here, it is shown that cryoEM can reveal the structures of plant borneol dehydrogenases of ∼120 kDa at or below 2 Å resolution, paving the way for the rapid development of new biocatalysts that can provide access to bioactive terpenes and terpenoids.
History
DepositionApr 12, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7o6p
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12739.png

Downloads & links

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Map

FileDownload / File: emd_12739.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 319.488 Å		0.83 Å/pix.
x 384 pix.
= 319.488 Å		0.83 Å/pix.
x 384 pix.
= 319.488 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum-0.0 - 2.983127
Average (Standard dev.)0.0042650164 (±0.04200584)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 319.488 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8320.8320.832
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z319.488319.488319.488
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0002.9830.004

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Supplemental data

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Sample components

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Entire : Homotetrameric complex of borneol dehydrogenase

EntireName: Homotetrameric complex of borneol dehydrogenase
Components
  • Complex: Homotetrameric complex of borneol dehydrogenase
    • Protein or peptide: borneol dehydrogenase
  • Ligand: water

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Supramolecule #1: Homotetrameric complex of borneol dehydrogenase

SupramoleculeName: Homotetrameric complex of borneol dehydrogenase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Salvia officinalis (garden sage)

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Macromolecule #1: borneol dehydrogenase

MacromoleculeName: borneol dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Salvia officinalis (garden sage)
Molecular weightTheoretical: 32.267602 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MATGAANVES PQSLPLRLLG RVALVTGGSS GIGESIVLLF RKHGAKVCIA DVQDNQGQRL CETLGGSSD IAFCHCDVTI EDDVKRAVDF TVDKFGTLDI MVNNAGVSGP PCPDIRDFEL SAFDRVFDIN VRGVFIGMKH A ARIMIPAK ...String:
MGSSHHHHHH SSGLVPRGSH MATGAANVES PQSLPLRLLG RVALVTGGSS GIGESIVLLF RKHGAKVCIA DVQDNQGQRL CETLGGSSD IAFCHCDVTI EDDVKRAVDF TVDKFGTLDI MVNNAGVSGP PCPDIRDFEL SAFDRVFDIN VRGVFIGMKH A ARIMIPAK KGSIISISSV ASTMGGLGPH AYTGSKHAVL GLTKNVAAEL GKHGIRVNCV SPYAVATSLA LAHLPEAERT ED TWDDFRR FVADNANLQG VELTMEDVAN AVVFLASDEA RYVSGMNLMV DGGFTSTNHA LQVFRP

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 268 / 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

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1439 / Average exposure time: 40.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 155724
CTF correctionSoftware - Name: cryoSPARC (ver. 2.19) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.19) / Number images used: 173781
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 2.19)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.19)
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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