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- PDB-32jy: Structure of the pathogenic variant G423S of Human SHMT2 -

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Basic information

Entry
Database: PDB / ID: 32jy
TitleStructure of the pathogenic variant G423S of Human SHMT2
ComponentsSerine hydroxymethyltransferase, mitochondrial
KeywordsTRANSFERASE
Function / homology
Function and homology information


formate biosynthetic process / hydroxytrimethyllysine aldolase activity / BRISC complex / glycine metabolic process / L-allo-threonine aldolase activity / response to vitamin B6 / regulation of mitochondrial translation / regulation of oxidative phosphorylation / L-serine metabolic process / L-serine biosynthetic process ...formate biosynthetic process / hydroxytrimethyllysine aldolase activity / BRISC complex / glycine metabolic process / L-allo-threonine aldolase activity / response to vitamin B6 / regulation of mitochondrial translation / regulation of oxidative phosphorylation / L-serine metabolic process / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / : / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to type I interferon / tetrahydrofolate interconversion / protein K63-linked deubiquitination / regulation of aerobic respiration / amino acid binding / RHOG GTPase cycle / mitochondrial nucleoid / one-carbon metabolic process / Mitochondrial protein degradation / protein tetramerization / pyridoxal phosphate binding / protein homotetramerization / mitochondrial inner membrane / mitochondrial matrix / positive regulation of cell population proliferation / chromatin binding / mitochondrion / extracellular exosome / identical protein binding / nucleus / cytoplasm
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
1-BUTANOL / 1,4-BUTANEDIOL / 1,3-PROPANDIOL / Serine hydroxymethyltransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGiardina, G. / Boumis, G. / Di Matteo, A. / Breccia, S.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission20205534European Union
CitationJournal: To Be Published
Title: Structural and functional defects of mitochondrial serine hydroxymethyltransferase genetic variants responsible for a novel neurodevelopmental syndrome
Authors: Giardina, G. / Boumis, G. / Di Matteo, A. / Breccia, S.
History
DepositionJul 13, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase, mitochondrial
B: Serine hydroxymethyltransferase, mitochondrial
C: Serine hydroxymethyltransferase, mitochondrial
D: Serine hydroxymethyltransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,5718
Polymers216,2694
Non-polymers3024
Water14,160786
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.339, 126.009, 135.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A1_
21B4_
12A1_
22C5_
13A1_
23D7_
14B4_
24C5_
15B4_
25D7_
16C5_
26D7_

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 1 / Auth seq-ID: 43 - 504 / Label seq-ID: 25 - 486

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999954, 0.003675, 0.008913), (0.009322, 0.132675, 0.991116), (0.00246, 0.991153, -0.132703)9.4286, -41.09889, 46.97513
3given(-0.999494, -0.026009, -0.01832), (0.021722, -0.137233, -0.990301), (0.023242, -0.990197, 0.137729)11.88435, 101.08866, 88.12177
4given(0.999805, 0.014766, 0.013089), (0.014709, -0.999882, 0.004447), (0.013153, -0.004254, -0.999904)-0.99073, 59.8621, 135.43806
5given(0.999706, 0.022318, 0.009444), (0.022272, -0.999739, 0.005049), (0.009555, -0.004837, -0.999943)-1.03269, 59.6568, 135.48531
6given(-0.999593, -0.023998, -0.015437), (0.018583, -0.136957, -0.990403), (0.021653, -0.990286, 0.137347)11.56478, 101.04337, 88.21986
7given(-0.998684, -0.036325, -0.036207), (-0.040995, 0.141136, 0.989141), (-0.030821, 0.989324, -0.142439)13.06302, -40.86192, 47.58298

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Serine hydroxymethyltransferase, mitochondrial / SHMT / Glycine hydroxymethyltransferase / Serine methylase


Mass: 54067.242 Da / Num. of mol.: 4 / Mutation: G423S
Source method: isolated from a genetically manipulated source
Details: crystallized construct: SHMT2 Isoform 3 differences from canonical isoform: 1-21 missing and additional residues (GSH) at the N-ter belonging to cleaved His-tag
Source: (gene. exp.) Homo sapiens (human) / Gene: SHMT2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P34897, glycine hydroxymethyltransferase

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Non-polymers , 5 types, 790 molecules

#2: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical ChemComp-1BO / 1-BUTANOL / BUTAN-1-OL


Mass: 74.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 786 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: MORPHEUS screen (Molecular Dimensions) condition D4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→46.1 Å / Num. obs: 191505 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.038 / Rrim(I) all: 0.135 / Χ2: 0.98 / Net I/σ(I): 11.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 12.1 % / Rmerge(I) obs: 1.432 / Num. unique obs: 9374 / CC1/2: 0.863 / Rpim(I) all: 0.445 / Rrim(I) all: 1.555 / Χ2: 0.87

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimless0.7.7data scaling
XDSdata reduction
MOLREP11.7.03phasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.1 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.471 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25768 9508 5 %RANDOM
Rwork0.23813 ---
obs0.23912 181829 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.861 Å2
Baniso -1Baniso -2Baniso -3
1-5.95 Å20 Å2-0 Å2
2---2.76 Å20 Å2
3----3.19 Å2
Refinement stepCycle: 1 / Resolution: 1.8→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14022 0 20 786 14828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01214335
X-RAY DIFFRACTIONr_bond_other_d0.0010.01613681
X-RAY DIFFRACTIONr_angle_refined_deg1.741.83219392
X-RAY DIFFRACTIONr_angle_other_deg0.6241.76131401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59951780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.1395144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.919102400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0890.22140
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217145
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023407
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9343.3067147
X-RAY DIFFRACTIONr_mcbond_other2.9343.3067147
X-RAY DIFFRACTIONr_mcangle_it4.1425.9338915
X-RAY DIFFRACTIONr_mcangle_other4.1425.9338916
X-RAY DIFFRACTIONr_scbond_it3.7683.7697188
X-RAY DIFFRACTIONr_scbond_other3.7673.7697189
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8356.72610477
X-RAY DIFFRACTIONr_long_range_B_refined7.32433.7916644
X-RAY DIFFRACTIONr_long_range_B_other7.30133.7516504
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.87

Ens-IDDom-IDNumberRms dev position (Å)
1134972.73
2234983.15
3334814.78
4434943.02
5534823.69
6634983.88
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 696 -
Rwork0.404 13282 -
obs--99.89 %

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