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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: To Be Published
Title: CRYO-EM STRUCTURE OF THE A149T DIMER VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP
Authors: Beamer LJ / Samarakoon V / Buckley DP / Owuocha LF
History
DepositionJan 28, 2026-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 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
Brightness
Contrast
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

Slices (1/3)

Slices (1/2)

Slices (2/3)

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
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_75307_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_75307_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: 54.375457 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH HSSGLVPRGS NMDPVSVWGN TPLATVDPEI HDLIEKEKRR QCRGIELIAS ENFTSFAVIE ALGSALTNKY SEGMPGNRY YGGNEYIDQI ENLCRSRALQ AFHLDAQSWG VNVQPYSGSP ANFAAYTAVL NPHDRIMGLD LPSGGHLTHG Y YTSGGKKI ...String:
MGSSHHHHHH HSSGLVPRGS NMDPVSVWGN TPLATVDPEI HDLIEKEKRR QCRGIELIAS ENFTSFAVIE ALGSALTNKY SEGMPGNRY YGGNEYIDQI ENLCRSRALQ AFHLDAQSWG VNVQPYSGSP ANFAAYTAVL NPHDRIMGLD LPSGGHLTHG Y YTSGGKKI STTSIYFESL PYKVNSTTGY IDYDRLEEKA LDFRPKLIIC GGSAYPRDWD YKRFREVADK CGALLLCDMA HT SGLVAAQ EVNSPFEYCD IVTTTTH(LLP)SL RGPRAGMIFY RKGPKPPKKG QPENAVYDFE DKINFAVFPS LQGGPHNHQ IGALAVALKQ AASPGFKAYA KQVKANAVAL GKYLMGKGYS LVTGGTENHL VLWDLRPLGL TGNKVEKLCD LCNITVNKNA VFGDSSALA PGGVRIGAPA MTSRGLVEKD FEQIGEFLHR AVTLTLEIQK EHGKLLKDFN KGLVNNKAIE DLKADVEKFS A LFDMPGFL VSEMKYKD

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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