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- EMDB-70421: The structure of a Fungal Cyanide Hydratase from Gloeocercospora ... -

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Basic information

Entry
Database: EMDB / ID: EMD-70421
TitleThe structure of a Fungal Cyanide Hydratase from Gloeocercospora sorghi
Map dataThe structure of a Fungal Cyanide Hydratase from Gloeocercospora sorghi
Sample
  • Complex: Quaternary lef-handed helix of cyanide hydratase dimers
    • Protein or peptide: Cyanide hydratase
KeywordsCynH / nitrilase / biorremediation / oligomer / HYDROLASE
Function / homology
Function and homology information


cyanide hydratase / cyanide catabolic process / cyanide hydratase activity / nitrilase activity
Similarity search - Function
Cyanide hydratase / Nitrilases / cyanide hydratase active site signature. / Nitrilase/Cyanide hydratase / Nitrilases / cyanide hydratase signature 1. / Nitrilase/cyanide hydratase, conserved site / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase
Similarity search - Domain/homology
Biological speciesMicrodochium sorghi (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.04 Å
AuthorsJusto Arevalo S / Valle-Riestra F V / Balan A / Farah CS
Funding support Brazil, 3 items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2022/00943-1 Brazil
Sao Paulo Research Foundation (FAPESP)2021/10577-0 Brazil
Sao Paulo Research Foundation (FAPESP)2024/02456-6 Brazil
CitationJournal: Structure / Year: 2026
Title: The single-particle cryo-EM structures of a bacterial cyanide dihydratase and a fungal cyanide hydratase.
Authors: Santiago Justo Arevalo / Valeria Valle-Riestra Felice / Mikaela Barahona Acuña / Katia Ordinola Flores / Mauro Quiñones Aguilar / Andrea Balan / Chuck Shaker Farah /
Abstract: Cyanide is widely used in industries due to its affinity for metals, a property that also underlies its toxicity. Industries, therefore, must reduce cyanide concentration before the final disposal of ...Cyanide is widely used in industries due to its affinity for metals, a property that also underlies its toxicity. Industries, therefore, must reduce cyanide concentration before the final disposal of wastewater. Physical, chemical, and biological methods have been developed for this; however, knowledge about the structure of enzymes involved in cyanide degradation remains limited. Structural characterization of these proteins could facilitate the development of enzymes with enhanced bioremediation potential. Here, we present the single-particle cryo-electron microscopy structures of a cyanide dihydratase from Bacillus safensis and a cyanide hydratase from Gloeocercospora sorghi at 2.2 Å and 2.0 Å resolution, respectively. We provide a comprehensive description and comparative analysis alongside all previously determined nitrilase structures. Importantly, our full-length structures reveal new features in the C-terminal as well as specific intermolecular interactions between protomer interfaces and within the helix lumen. Finally, our findings offer insights into the reaction mechanisms of these two enzymes.
History
DepositionApr 29, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70421.png

Downloads & links

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Map

FileDownload / File: emd_70421.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe structure of a Fungal Cyanide Hydratase from Gloeocercospora sorghi
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 450 pix.
= 393.66 Å		0.87 Å/pix.
x 450 pix.
= 393.66 Å		0.87 Å/pix.
x 450 pix.
= 393.66 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8748 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.71427 - 3.9677384
Average (Standard dev.)0.0026779335 (±0.12803565)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 393.66 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70421_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map with the helical axis aligend to the...

Fileemd_70421_additional_1.map
AnnotationMap with the helical axis aligend to the Z-axis. This map could have a slightly less resolution compared to the main map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of the structure of a Fungal...

Fileemd_70421_half_map_1.map
AnnotationHalf map of the structure of a Fungal Cyanide Hydratase from Gloeocercospora sorghi
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of the structure of a Fungal...

Fileemd_70421_half_map_2.map
AnnotationHalf map of the structure of a Fungal Cyanide Hydratase from Gloeocercospora sorghi
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Quaternary lef-handed helix of cyanide hydratase dimers

EntireName: Quaternary lef-handed helix of cyanide hydratase dimers
Components
  • Complex: Quaternary lef-handed helix of cyanide hydratase dimers
    • Protein or peptide: Cyanide hydratase

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Supramolecule #1: Quaternary lef-handed helix of cyanide hydratase dimers

SupramoleculeName: Quaternary lef-handed helix of cyanide hydratase dimers
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: wild type CynH from Gloeocercospora sorghi
Source (natural)Organism: Microdochium sorghi (fungus)
Molecular weightTheoretical: 981.582 KDa

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Macromolecule #1: Cyanide hydratase

MacromoleculeName: Cyanide hydratase / type: protein_or_peptide / ID: 1 / Details: Monomer of CynH / Number of copies: 20 / Enantiomer: LEVO / EC number: cyanide hydratase
Source (natural)Organism: Microdochium sorghi (fungus)
Molecular weightTheoretical: 40.946137 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPINKYKAAV VTSEPVWENL EGGVVKTIEF INEAGKAGCK LIAFPEVWIP GYPYWMWKVN YLQSLPMLKA YRENSIAMDS SEMRRIRAA ARDNQIYVSI GVSEIDHATL YLTQVLISPL GDVINHRRKI KPTHVEKLVY GDGSGDSFEP VTQTEIGRLG Q LNCWENMN ...String:
MPINKYKAAV VTSEPVWENL EGGVVKTIEF INEAGKAGCK LIAFPEVWIP GYPYWMWKVN YLQSLPMLKA YRENSIAMDS SEMRRIRAA ARDNQIYVSI GVSEIDHATL YLTQVLISPL GDVINHRRKI KPTHVEKLVY GDGSGDSFEP VTQTEIGRLG Q LNCWENMN PFLKSLAVAR GEQIHVAAWP VYPDLSKQVH PDPATNYADP ASDLVTPAYA IETGTWVLAP FQRISVEGLK RH TPPGVEP ETDATPYNGH ARIFRPDGSL YAKPAVDFDG LMYVDIDLNE SHLTKALADF AGHYMRPDLI RLLVDTRRKE LVT EVGGGD NGGIQSYSTM ARLGLDRPLE EEDYRQGTDA GETEKASSNG HA

UniProtKB: Cyanide hydratase

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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

Concentration1.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
100.0 mMNaClsodium chloride
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 5928 / Average exposure time: 4.39 sec. / Average electron dose: 55.59 e/Å2
Details: Number of processing frames fractions collected were 30
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: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 742870
CTF correctionSoftware - Name: cisTEM (ver. 1.0.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Initial model constructed by cryosparc
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 209895
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final 3D classificationNumber classes: 2 / Avg.num./class: 104947 / Software - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9ofa:
The structure of a Fungal Cyanide Hydratase from Gloeocercospora sorghi

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