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- PDB-8gmy: Structure of methyltransferase -

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Basic information

Entry
Database: PDB / ID: 8gmy
TitleStructure of methyltransferase
ComponentsS-adenosylmethionine sensor upstream of mTORC1
KeywordsTRANSFERASE / a protein / SIGNALING PROTEIN
Function / homology
Function and homology information


amino acid sensor activity / cellular response to methionine / S-adenosyl-L-methionine binding / negative regulation of TORC1 signaling / cellular response to amino acid starvation / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / protein-containing complex binding
Similarity search - Function
S-adenosylmethionine-dependent methyltransferase Bmt2-like / 25S rRNA (adenine(2142)-N(1))-methyltransferase, Bmt2 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-adenosylmethionine sensor upstream of mTORC1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZhang, H. / Li, X.Z. / Wen, Y.N.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Structure of methyltransferase
Authors: Zhang, H. / Li, X.Z. / Wen, Y.N.
History
DepositionAug 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2025Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_entry_details / struct_keywords / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_keywords.pdbx_keywords / _struct_keywords.text / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: S-adenosylmethionine sensor upstream of mTORC1


Theoretical massNumber of molelcules
Total (without water)27,4181
Polymers27,4181
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11370 Å2
Unit cell
Length a, b, c (Å)98.436, 98.436, 41.628
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein S-adenosylmethionine sensor upstream of mTORC1 / dSamtor / Probable methyltransferase BMT2 homolog


Mass: 27417.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Samtor, CG3570 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9W138, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / Details: PEG550 MME, MES/Sodiumhydroxid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→49.22 Å / Num. obs: 25095 / % possible obs: 98.8 % / Redundancy: 11.7 % / Biso Wilson estimate: 23.89 Å2 / CC1/2: 1 / Net I/σ(I): 22.6
Reflection shellResolution: 1.7→1.8 Å / Num. unique obs: 3392 / CC1/2: 0.846

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alphafold2

Resolution: 1.7→32.22 Å / SU ML: 0.1996 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.2867
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2429 1306 5.21 %
Rwork0.2149 23765 -
obs0.2164 25071 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.74 Å2
Refinement stepCycle: LAST / Resolution: 1.7→32.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 0 151 1926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711814
X-RAY DIFFRACTIONf_angle_d0.91162451
X-RAY DIFFRACTIONf_chiral_restr0.0579269
X-RAY DIFFRACTIONf_plane_restr0.0081315
X-RAY DIFFRACTIONf_dihedral_angle_d5.6148242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.770.25651290.28182410X-RAY DIFFRACTION90.74
1.77-1.850.31291590.24542588X-RAY DIFFRACTION98.42
1.85-1.950.28951150.24532695X-RAY DIFFRACTION99.89
1.95-2.070.27091690.23342628X-RAY DIFFRACTION100
2.07-2.230.25931550.22612636X-RAY DIFFRACTION100
2.23-2.460.25491440.23122684X-RAY DIFFRACTION100
2.46-2.810.291520.23392669X-RAY DIFFRACTION100
2.81-3.540.23971360.21222693X-RAY DIFFRACTION100
3.55-32.220.19931470.18632762X-RAY DIFFRACTION99.9

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