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- PDB-10nm: CRYO-EM STRUCTURE OF THE A149T DIMER VARIANT OF SERINE HYDROXYMET... -

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Entry
Database: PDB / ID: 10nm
TitleCRYO-EM STRUCTURE OF THE A149T DIMER VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / enzyme / missense variant
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / : / tetrahydrofolate interconversion / methyltransferase activity / pyridoxal phosphate binding / methylation
Similarity search - Function
Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / : / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsBeamer, L.J. / Samarakoon, V. / Buckley, D.P. / Owuocha, L.F. / Durie, C.L. / Mitchum, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)IOS 2152548 United States
CitationJournal: FEBS J / Year: 2026
Title: Oligomeric defects in soybean serine hydroxymethyltransferase 8: tetramer destabilization by A149T and other variants associated with soybean cyst nematode resistance.
Authors: Vindya Samarakoon / David P Buckley / Luckio F Owuocha / Clarissa L Durie / Melissa G Mitchum / Lesa J Beamer /
Abstract: Serine hydroxymethyltransferase (SHMT) is a conserved enzyme in folate-mediated one-carbon metabolism, where it contributes to nucleotide biosynthesis, methylation capacity, and cellular stress ...Serine hydroxymethyltransferase (SHMT) is a conserved enzyme in folate-mediated one-carbon metabolism, where it contributes to nucleotide biosynthesis, methylation capacity, and cellular stress responses. Amino acid polymorphisms of soybean SHMT8 are known to affect the resistance of soybean to its primary pathogen, the soybean cyst nematode (SCN). A set of SHMT8 variants from ethyl methanesulfonate (EMS)-mutagenized soybean populations has been identified with varying resistance phenotypes, but their biochemical consequences remain poorly understood. Here, we use biochemical and structural studies to assess the impacts of the A149T variant on soybean SHMT8. Despite the conservative nature of the substitution, A149T reduces folate binding, pyridoxal-5'-phosphate-dependent catalysis, and thermal stability. High-resolution crystal structures (1.9-2.3 Å resolution) reveal only very minor structural changes. However, while the usual tetrameric assembly of the enzyme is retained at the high protein concentration in crystals, multiple other methods including a 2.9 Å cryo-electron microscopy (cryo-EM) structure show that the A149T variant is predominantly a dimer. Significant structural changes in the dimer are consistent with the observed biochemical impacts of the variant and help explain the well-known reduction in activity associated with dimerization of SHMT in other systems. We also find destabilization of the tetrameric assembly in other SHMT8 variants associated with changes in SCN resistance, suggesting that weakened oligomerization may be a common consequence of such mutations. Together, these results highlight quaternary structure as a critical determinant of SHMT8 activity and stability and suggest a potential mechanistic link between enzyme biochemistry and soybean defense.
History
DepositionJan 28, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
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Revision 2.0Apr 22, 2026Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase


Theoretical massNumber of molelcules
Total (without water)109,9022
Polymers109,9022
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Serine hydroxymethyltransferase


Mass: 54951.082 Da / Num. of mol.: 2 / Mutation: A149T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: SHMT / Production host: Escherichia coli (E. coli)
References: UniProt: K4FZF8, glycine hydroxymethyltransferase
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.1036 MDa / Experimental value: YES
Source (natural)Organism: Glycine max (soybean) / Strain: SHMT / Cellular location: Cytoplasm
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5 / Details: 50mM HEPES, 150mM NaCl, 0.5mM TCEP
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15mA of current used / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Calibrated magnification: 98700 X / Nominal defocus max: 2300 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.951 sec. / Electron dose: 80 e/Å2 / Film or detector model: FEI FALCON I (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14550
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.7.1particle selection
2SerialEMimage acquisition
4cryoSPARCv4.7.1CTF correction
7UCSF ChimeraX1.11.1model fitting
9cryoSPARCv4.7.1initial Euler assignment
10cryoSPARCv4.7.1final Euler assignment
11cryoSPARCv4.7.1classification
12cryoSPARCv4.7.13D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5739678
Details: Particles selected after 2 rounds of 2D template selections
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71315 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 81.41 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model building

3D fitting-ID: 1 / Accession code: 9YBZ / Chain residue range: 1-471 / Initial refinement model-ID: 1 / Pdb chain residue range: 1-471 / PDB-ID: 9YBZ

9ybz

/ Source name: PDB / Type: experimental model

IDPdb chain-IDChain-ID
1AA
2BB
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 81.41 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00366587
ELECTRON MICROSCOPYf_angle_d0.71428989
ELECTRON MICROSCOPYf_chiral_restr0.04591022
ELECTRON MICROSCOPYf_plane_restr0.00631171
ELECTRON MICROSCOPYf_dihedral_angle_d7.526973

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