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- PDB-7vkk: Crystal structure of D. melanogaster SAMTOR V66W/E67P mutant -

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Basic information

Entry
Database: PDB / ID: 7vkk
TitleCrystal structure of D. melanogaster SAMTOR V66W/E67P mutant
ComponentsS-adenosylmethionine sensor upstream of mTORC1
KeywordsTRANSFERASE / SAMTOR / SAM
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: 3.55 Å
AuthorsZhang, T. / Ding, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31530013 China
CitationJournal: Sci Adv / Year: 2022
Title: Molecular mechanism of S -adenosylmethionine sensing by SAMTOR in mTORC1 signaling.
Authors: Tang, X. / Zhang, Y. / Wang, G. / Zhang, C. / Wang, F. / Shi, J. / Zhang, T. / Ding, J.
History
DepositionSep 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-adenosylmethionine sensor upstream of mTORC1
B: S-adenosylmethionine sensor upstream of mTORC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6417
Polymers70,1342
Non-polymers5065
Water00
1
A: S-adenosylmethionine sensor upstream of mTORC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3824
Polymers35,0671
Non-polymers3143
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15150 Å2
MethodPISA
2
B: S-adenosylmethionine sensor upstream of mTORC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2593
Polymers35,0671
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-18 kcal/mol
Surface area13170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.494, 168.494, 168.494
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

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


Mass: 35067.242 Da / Num. of mol.: 2 / Fragment: trasnferase / Mutation: V66W, E67P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Samtor, CG3570 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9W138, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN

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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: 2.84 Å3/Da / Density % sol: 56.72 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 5
Details: 1.8 M Ammonium sulfate, 0.1 M Bis-Tris, pH 6.5, and 2% (v/v) PEG monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.55→37.68 Å / Num. obs: 9792 / % possible obs: 99.8 % / Redundancy: 6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.168 / Net I/σ(I): 7.9
Reflection shellResolution: 3.55→3.68 Å / Rmerge(I) obs: 0.813 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 950 / CC1/2: 0.686

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VKR

7vkr


Resolution: 3.55→37.68 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.894 / SU B: 75.369 / SU ML: 0.511 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.643 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2748 485 5 %RANDOM
Rwork0.2255 ---
obs0.2279 9250 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 152.71 Å2 / Biso mean: 84.687 Å2 / Biso min: 61.74 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 3.55→37.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3843 0 28 0 3871
Biso mean--88.47 --
Num. residues----521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193956
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.9625407
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.935515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.70623.265147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.34515556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7721520
X-RAY DIFFRACTIONr_chiral_restr0.0720.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212980
LS refinement shellResolution: 3.55→3.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 32 -
Rwork0.271 665 -
all-697 -
obs--96.4 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.34080.52250.07371.5887-0.71881.07750.1671-0.0797-0.04650.094-0.1677-0.00260.10530.0060.00060.1396-0.0118-0.04480.032-0.01430.1237-10.0621-40.863950.3071
20.66880.40340.7460.73550.58340.9067-0.01270.11030.04580.0486-0.0428-0.1917-0.01820.06130.05550.016-0.0065-0.03090.06940.01620.26437.5316-14.240947.1356
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 297
2X-RAY DIFFRACTION2B41 - 287

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