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- PDB-12yi: The GNMT N-Terminal Domain Orchestrates Folate-Dependent Regulati... -

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Basic information

Entry
Database: PDB / ID: 12yi
TitleThe GNMT N-Terminal Domain Orchestrates Folate-Dependent Regulation of Cellular Methylation Dynamics
ComponentsGlycine N-methyltransferase
KeywordsTRANSFERASE / GLYCINE N-METHYLTRANSFERASE / GNMT / METHYLTRANSFERASE
Function / homology
Function and homology information


glycine N-methyltransferase / glycine N-methyltransferase activity / : / L-methionine metabolic process / Glyoxylate metabolism and glycine degradation / Metabolism of ingested SeMet, Sec, MeSec into H2Se / : / Developmental Lineage of Pancreatic Acinar Cells / S-adenosylmethionine metabolic process / S-adenosyl-L-methionine binding ...glycine N-methyltransferase / glycine N-methyltransferase activity / : / L-methionine metabolic process / Glyoxylate metabolism and glycine degradation / Metabolism of ingested SeMet, Sec, MeSec into H2Se / : / Developmental Lineage of Pancreatic Acinar Cells / S-adenosylmethionine metabolic process / S-adenosyl-L-methionine binding / folic acid binding / regulation of gluconeogenesis / glycogen metabolic process / glycine binding / one-carbon metabolic process / methylation / protein homotetramerization / identical protein binding / cytosol
Similarity search - Function
Glycine/Sarcosine N-methyltransferase / Glycine N-methyltransferase (EC 2.1.1.20 and EC 2.1.1.156) family profile. / Methyltransferase domain 25 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Glycine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKraz, I. / Lorton, B.M. / Harijan, R.K. / Hedge, S. / Bonanno, J.B. / Shechter, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM135614 United States
CitationJournal: To Be Published
Title: The GNMT N-Terminal Domain Orchestrates Folate-Dependent Regulation of Cellular Methylation Dynamics
Authors: Kraz, I. / Lorton, B.M. / Harijan, R.K. / Hedge, S. / Bonanno, J.B. / Shechter, D.
History
DepositionApr 22, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 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: Glycine N-methyltransferase
B: Glycine N-methyltransferase
C: Glycine N-methyltransferase
D: Glycine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,0968
Polymers130,7164
Non-polymers3804
Water17,853991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14940 Å2
ΔGint-99 kcal/mol
Surface area46290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.067, 144.147, 98.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glycine N-methyltransferase


Mass: 32679.098 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNMT / Plasmid: pcDNA3.3 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q14749, glycine N-methyltransferase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 991 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 49 %
Description: crystal and data appear orthorhombic however data proved to be from monoclinic with beta angle very near 90.0 degrees.
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium formate and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97933 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.65→98.13 Å / Num. obs: 145249 / % possible obs: 97 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.027 / Rrim(I) all: 0.052 / Χ2: 0.71 / Net I/σ(I): 13.5 / Num. measured all: 499083
Reflection shellResolution: 1.65→1.68 Å / % possible obs: 91.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.219 / Num. measured all: 22380 / Num. unique obs: 6827 / CC1/2: 0.945 / Rpim(I) all: 0.143 / Rrim(I) all: 0.263 / Χ2: 0.44 / Net I/σ(I) obs: 3.6

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→19.97 Å / Cross valid method: FREE R-VALUE / σ(F): 5.49 / Phase error: 31.1 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.22 7278 5.02 %
Rwork0.1696 --
obs0.2036 145115 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8816 0 20 991 9827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089055
X-RAY DIFFRACTIONf_angle_d0.87812291
X-RAY DIFFRACTIONf_dihedral_angle_d9.2791249
X-RAY DIFFRACTIONf_chiral_restr0.0491356
X-RAY DIFFRACTIONf_plane_restr0.0051571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.680.34483160.33066570X-RAY DIFFRACTION88
1.68-1.710.32763260.32196911X-RAY DIFFRACTION92
1.71-1.740.37953650.32826906X-RAY DIFFRACTION92
1.74-1.780.33193710.32156856X-RAY DIFFRACTION92
1.78-1.820.34783380.31866936X-RAY DIFFRACTION92
1.82-1.860.33093300.32066957X-RAY DIFFRACTION93
1.86-1.90.40313750.33956813X-RAY DIFFRACTION91
1.9-1.960.34413520.32296841X-RAY DIFFRACTION91
1.96-2.010.30153620.29616917X-RAY DIFFRACTION93
2.01-2.080.29913860.27816930X-RAY DIFFRACTION93
2.08-2.150.2893810.27326974X-RAY DIFFRACTION93
2.15-2.240.30513400.26146949X-RAY DIFFRACTION93
2.24-2.340.25783340.25626715X-RAY DIFFRACTION90
2.34-2.460.23583430.23236963X-RAY DIFFRACTION93
2.46-2.620.26423660.21866954X-RAY DIFFRACTION93
2.62-2.820.25834120.20756925X-RAY DIFFRACTION92
2.82-3.10.25723460.17686780X-RAY DIFFRACTION91
3.1-3.550.21763040.14717090X-RAY DIFFRACTION95
3.55-4.460.1833340.11057004X-RAY DIFFRACTION92
4.46-19.970.19713640.12467079X-RAY DIFFRACTION93

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