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- EMDB-79087: Cryo-EM structure of Sr01-080, a denovo designed borneol dehydrogenase -

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Basic information

Entry
Database: EMDB / ID: EMD-79087
TitleCryo-EM structure of Sr01-080, a denovo designed borneol dehydrogenase
Map dataEM half map of the 01_80 tetramer complex
Sample
  • Cell: 01_80
    • Protein or peptide: Sr01-080
KeywordsDehydrogenase / De novo designed protein / borneol dehydrogenase / oxidoreductase
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsMiles U / McShan A / McManus C / Kamerlin SCL / Di Geronimo Quintero B
Funding support United States, 2 items
OrganizationGrant numberCountry
Other government United States
Other private United States
CitationJournal: To Be Published
Title: Full-Atom MPNN Based Redesign of Plant Dehydrogenase Enables Thermostability Enhancement Without Loss of Stereoselectivity
Authors: Miles U / McShan A / McManus C / Kamerlin SCL / Di Geronimo Quintero B
History
DepositionSep 15, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_79087.png

Downloads & links

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Map

FileDownload / File: emd_79087.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM half map of the 01_80 tetramer complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 256 pix.
= 294.144 Å		1.15 Å/pix.
x 256 pix.
= 294.144 Å		1.15 Å/pix.
x 256 pix.
= 294.144 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.149 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.278
Minimum - Maximum-9.00569 - 9.286241
Average (Standard dev.)0.0014572679 (±0.1175112)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 294.144 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: EM half map of the 01 80 tetramer complex

Fileemd_79087_half_map_1.map
AnnotationEM half map of the 01_80 tetramer complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: None

Fileemd_79087_half_map_2.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 01_80

EntireName: 01_80
Components
  • Cell: 01_80
    • Protein or peptide: Sr01-080

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Supramolecule #1: 01_80

SupramoleculeName: 01_80 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Tetrameric complex of 4 01_80 units
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Sr01-080

MacromoleculeName: Sr01-080 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 28.21609 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHGR LEGKVAIVTG GASGIGRSTV ELFHEEGAKV VIADIREEEG QALAEKLGDD VTFQHCDVTD EEQVKALVEA TVERWGGVD IMFSNAGIVE GPNSIADVDK ADFERLMGIN LVGAFLTAKY AAEVMKPQKS GVIIFTASAC TEIAGIAGFA Y TASKYGVV ...String:
MGHHHHHHGR LEGKVAIVTG GASGIGRSTV ELFHEEGAKV VIADIREEEG QALAEKLGDD VTFQHCDVTD EEQVKALVEA TVERWGGVD IMFSNAGIVE GPNSIADVDK ADFERLMGIN LVGAFLTAKY AAEVMKPQKS GVIIFTASAC TEIAGIAGFA Y TASKYGVV GLMKELAFEL GKYGIRANAV SPFLVLTGIP PGGSKGVEEF AKLYEKVGTL KGKILTADDV AKTVLYLASD EA SFVSGVN LLVDGGYTVV NPTFVNVVNA

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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

Concentration5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
125.0 mMNaClSodium Chloride
20.0 mMC4H11NO3Tris

Details: 125 mM NaCl, 10 mM Tris HCl (pH = 8.0)
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK III
DetailsThis samples was monodisperse

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 2564 / Average exposure time: 8.0 sec. / Average electron dose: 52.88 e/Å2
Details: Images were collected as movies with 80 images collected per movie at 100 ms of exposure for a total of 8.0 sec of exposure per micrograph
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 100000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 3922227
Details: Particles were picked using Blob Picker in CryoSPARC with min particle diameter 80 A, max particle diameter 120 A, and min separation distance 40 A. 5974094 picks were reduced with an ...Details: Particles were picked using Blob Picker in CryoSPARC with min particle diameter 80 A, max particle diameter 120 A, and min separation distance 40 A. 5974094 picks were reduced with an Inspect Picks Job to 4494189, and an Extract Mics. (G) job reduced picks further to 3922227.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio model generated in CryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC
Details: Non-uniform refinement in CryosPARC with D2 symmetry and refinement mask excluding neighboring particles in psuedo-filaments present in micrographs.
Number images used: 743562
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: Ab-initio model generated in CryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: Non-uniform refinement in CryoSPARC
Final 3D classificationNumber classes: 5 / Avg.num./class: 156481
Details: Classes 0-4 contained 44.9%, 14.2%, 36.3%, 0.0%, and 4.6% of 782,408 particles. Classes 0-2 were retained for downstream processing.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsInitial fitting was done in chimeraX, and refined through sequential Real space refinement protocol in PHENIX and manual refinement with ISOLDE
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-38rr:
Cryo-EM structure of Sr01-080, a denovo designed borneol dehydrogenase

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