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- PDB-7yrj: S-adenosylmethionine sensor upstream of mTORC1 -

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Basic information

Entry
Database: PDB / ID: 7yrj
TitleS-adenosylmethionine sensor upstream of mTORC1
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 / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
SINEFUNGIN / S-adenosylmethionine sensor upstream of mTORC1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsZhang, H. / Li, X.Z. / Wen, Y.N.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: S-adenosylmethionine sensor upstream of mTORC1
Authors: Zhang, H. / Li, X.Z. / Wen, Y.N.
History
DepositionAug 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 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_ec / _entity_src_gen.gene_src_common_name ..._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 / _pdbx_entry_details.has_protein_modification / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)111,1968
Polymers109,6714
Non-polymers1,5264
Water3,099172
1
B: S-adenosylmethionine sensor upstream of mTORC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7992
Polymers27,4181
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: S-adenosylmethionine sensor upstream of mTORC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7992
Polymers27,4181
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: S-adenosylmethionine sensor upstream of mTORC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7992
Polymers27,4181
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: S-adenosylmethionine sensor upstream of mTORC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7992
Polymers27,4181
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.333, 78.896, 100.096
Angle α, β, γ (deg.)90.000, 96.400, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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.: 4
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: Chemical
ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion
Details: Sodium citrate tribasic dihydrate, Polyethylene glycol 3350

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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: 2.35→99.47 Å / Num. obs: 40916 / % possible obs: 98.1 % / Redundancy: 6.1 % / Biso Wilson estimate: 34.57 Å2 / CC1/2: 0.997 / Net I/σ(I): 7.8
Reflection shellResolution: 2.35→2.47 Å / Num. unique obs: 5694 / CC1/2: 0.929

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alphafold2

Resolution: 2.35→63.93 Å / SU ML: 0.315 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.8845
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2914 2043 5.02 %
Rwork0.2397 38667 -
obs0.2423 40710 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.37 Å2
Refinement stepCycle: LAST / Resolution: 2.35→63.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6709 0 108 172 6989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00266973
X-RAY DIFFRACTIONf_angle_d0.57249451
X-RAY DIFFRACTIONf_chiral_restr0.03981065
X-RAY DIFFRACTIONf_plane_restr0.00511192
X-RAY DIFFRACTIONf_dihedral_angle_d5.1469931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40.33861400.30142286X-RAY DIFFRACTION86.83
2.4-2.460.31931370.30922568X-RAY DIFFRACTION97.87
2.46-2.530.35531300.30012595X-RAY DIFFRACTION99.05
2.53-2.60.3641290.28992612X-RAY DIFFRACTION98.67
2.6-2.690.40631400.27852615X-RAY DIFFRACTION98.67
2.69-2.780.331470.27222573X-RAY DIFFRACTION98.69
2.78-2.890.33631520.25232541X-RAY DIFFRACTION96.49
2.89-3.030.3131300.24712613X-RAY DIFFRACTION98.92
3.03-3.190.29481280.25722616X-RAY DIFFRACTION99.28
3.19-3.390.28391290.25312623X-RAY DIFFRACTION98.99
3.39-3.650.29961040.22692589X-RAY DIFFRACTION96.94
3.65-4.010.23081440.20382629X-RAY DIFFRACTION98.97
4.01-4.590.24941530.19432570X-RAY DIFFRACTION97.08
4.6-5.790.26751360.20632639X-RAY DIFFRACTION99.32
5.79-63.930.29911440.25192598X-RAY DIFFRACTION95.24
Refinement TLS params.Method: refined / Origin x: 27.9596629036 Å / Origin y: 4.3673143016 Å / Origin z: -24.5322730588 Å
111213212223313233
T0.2314163611 Å2-0.00468644317754 Å2-0.00291606771862 Å2-0.282633092886 Å2-0.0128381594254 Å2--0.393725822665 Å2
L0.0490793771825 °2-0.0573746948804 °2-0.0235120855624 °2-0.001389713195 °2-0.0932089497282 °2--0.129080787562 °2
S0.00223796772392 Å °0.0179399315942 Å °-0.0338513598898 Å °-0.00156938897972 Å °-0.00261862499706 Å °0.0184843339192 Å °0.00660868305649 Å °-0.00714813485001 Å °0.00436998062973 Å °
Refinement TLS groupSelection details: all

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