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- EMDB-75307: CRYO-EM STRUCTURE OF THE A149T DIMER VARIANT OF SERINE HYDROXYMET... -

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Basic information

Entry
Database: EMDB / ID: EMD-75307
TitleCRYO-EM STRUCTURE OF THE A149T DIMER VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP
Map dataSharpened map
Sample
  • Organelle or cellular component: A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP
    • Protein or peptide: Serine hydroxymethyltransferase
Keywordsenzyme / missense variant / TRANSFERASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsBeamer LJ / Samarakoon V / Buckley DP / Owuocha LF / Durie CL / Mitchum MG
Funding support United States, 1 items
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, 2026-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75307.png

Downloads & links

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Map

FileDownload / File: emd_75307.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 224 pix.
= 226.778 Å		1.01 Å/pix.
x 224 pix.
= 226.778 Å		1.01 Å/pix.
x 224 pix.
= 226.778 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0124 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.29977936 - 0.51120085
Average (Standard dev.)0.00034820847 (±0.012881589)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 226.7776 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_75307_msk_1.map
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Additional map: Gaussian filtered map at SD 1

Fileemd_75307_additional_1.map
AnnotationGaussian filtered map at SD 1
Projections & Slices
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Half map: Half map A

Fileemd_75307_half_map_1.map
AnnotationHalf map A
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Half map: Half map B

Fileemd_75307_half_map_2.map
AnnotationHalf map B
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Sample components

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Entire : A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN C...

EntireName: A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP
Components
  • Organelle or cellular component: A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP
    • Protein or peptide: Serine hydroxymethyltransferase

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Supramolecule #1: A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN C...

SupramoleculeName: A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Glycine max (soybean) / Strain: SHMT / Location in cell: Cytoplasm
Molecular weightTheoretical: 103.6 KDa

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Macromolecule #1: Serine hydroxymethyltransferase

MacromoleculeName: Serine hydroxymethyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: glycine hydroxymethyltransferase
Source (natural)Organism: Glycine max (soybean)
Molecular weightTheoretical: 54.951082 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGMHHHHHHS SGVDLGTENL YFQSNMDPVS VWGNTPLATV DPEIHDLIEK EKRRQCRGIE LIASENFTSF AVIEALGSAL TNKYSEGMP GNRYYGGNEY IDQIENLCRS RALQAFHLDA QSWGVNVQPY SGSPANFAAY TAVLNPHDRI MGLDLPSGGH L THGYYTSG ...String:
MGMHHHHHHS SGVDLGTENL YFQSNMDPVS VWGNTPLATV DPEIHDLIEK EKRRQCRGIE LIASENFTSF AVIEALGSAL TNKYSEGMP GNRYYGGNEY IDQIENLCRS RALQAFHLDA QSWGVNVQPY SGSPANFAAY TAVLNPHDRI MGLDLPSGGH L THGYYTSG GKKISTTSIY FESLPYKVNS TTGYIDYDRL EEKALDFRPK LIICGGSAYP RDWDYKRFRE VADKCGALLL CD MAHTSGL VAAQEVNSPF EYCDIVTTTT H(LLP)SLRGPRAG MIFYRKGPKP PKKGQPENAV YDFEDKINFA VFPSLQGGP HNHQIGALAV ALKQAASPGF KAYAKQVKAN AVALGKYLMG KGYSLVTGGT ENHLVLWDLR PLGLTGNKVE KLCDLCNITV NKNAVFGDS SALAPGGVRI GAPAMTSRGL VEKDFEQIGE FLHRAVTLTL EIQKEHGKLL KDFNKGLVNN KAIEDLKADV E KFSALFDM PGFLVSEMKY KD

UniProtKB: Serine hydroxymethyltransferase

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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

Concentration0.25 mg/mL
BufferpH: 7.5 / Details: 50mM HEPES, 150mM NaCl, 0.5mM TCEP
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Details: 15mA of current used
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
SoftwareName: SerialEM
Image recordingFilm or detector model: FEI FALCON I (4k x 4k) / Number grids imaged: 1 / Number real images: 14550 / Average exposure time: 0.951 sec. / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 98700 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
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: 5739678
Details: Particles selected after 2 rounds of 2D template selections
CTF correctionSoftware - Name: cryoSPARC (ver. v4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9ybz


Details: Chains A and B only
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.7.1) / Number images used: 71315
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.7.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.7.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

9ybz

chain_id: A, residue_range: 1-471, source_name: PDB, initial_model_type: experimental model

9ybz

chain_id: B, residue_range: 1-471, source_name: PDB, initial_model_type: experimental model
SoftwareName: UCSF ChimeraX (ver. 1.11.1)
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 81.41 / Target criteria: Correlation coefficient
Output model

PDB-10nm:
CRYO-EM STRUCTURE OF THE A149T DIMER VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP

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