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- PDB-3gdh: Methyltransferase domain of human Trimethylguanosine Synthase 1 (... -

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Basic information

Entry
Database: PDB / ID: 3gdh
TitleMethyltransferase domain of human Trimethylguanosine Synthase 1 (TGS1) bound to m7GTP and adenosyl-homocysteine (active form)
ComponentsTrimethylguanosine synthase homolog
KeywordsTRANSFERASE / m7G / cap / dimethyltransferase / UsnRNA / snoRNA / telomerase / Cytoplasm / Methyltransferase / Nucleus / Phosphoprotein / Polymorphism / Transcription / Transcription regulation
Function / homology
Function and homology information


ribonucleoprotein complex biogenesis / RNA cap trimethylguanosine synthase activity / RNA methyltransferase activity / 7-methylguanosine cap hypermethylation / small nuclear ribonucleoprotein complex / spliceosomal snRNP assembly / Cajal body / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression ...ribonucleoprotein complex biogenesis / RNA cap trimethylguanosine synthase activity / RNA methyltransferase activity / 7-methylguanosine cap hypermethylation / small nuclear ribonucleoprotein complex / spliceosomal snRNP assembly / Cajal body / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Transferases; Transferring one-carbon groups; Methyltransferases / Activation of gene expression by SREBF (SREBP) / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Circadian Clock / snRNP Assembly / nucleolus / extracellular space / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
RNA cap guanine-N2 methyltransferase / RNA cap guanine-N2 methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE / S-1,2-PROPANEDIOL / R-1,2-PROPANEDIOL / S-ADENOSYL-L-HOMOCYSTEINE / Trimethylguanosine synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsMonecke, T. / Dickmanns, A. / Ficner, R.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Structural basis for m7G-cap hypermethylation of small nuclear, small nucleolar and telomerase RNA by the dimethyltransferase TGS1.
Authors: Monecke, T. / Dickmanns, A. / Ficner, R.
History
DepositionFeb 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trimethylguanosine synthase homolog
B: Trimethylguanosine synthase homolog
C: Trimethylguanosine synthase homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,38014
Polymers80,2313
Non-polymers3,14811
Water7,368409
1
A: Trimethylguanosine synthase homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8195
Polymers26,7441
Non-polymers1,0754
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Trimethylguanosine synthase homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7434
Polymers26,7441
Non-polymers9993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Trimethylguanosine synthase homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8195
Polymers26,7441
Non-polymers1,0754
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)156.248, 156.248, 100.309
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Trimethylguanosine synthase homolog / Nuclear receptor coactivator 6-interacting protein / PRIP-interacting protein with ...Nuclear receptor coactivator 6-interacting protein / PRIP-interacting protein with methyltransferase motif / PIPMT / PIMT / CLL-associated antigen KW-2 / Hepatocellular carcinoma-associated antigen 137


Mass: 26743.785 Da / Num. of mol.: 3 / Fragment: UNP residues 618-853
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGS1, HCA137, NCOA6IP, PIMT / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q96RS0, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 5 types, 420 molecules

#2: Chemical ChemComp-MGP / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE


Mass: 538.215 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H19N5O14P3
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical
ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O2
#5: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O

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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: 2.94 Å3/Da / Density % sol: 58.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6 / Details: PEG 8000, pH 6, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 5, 2008
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 61489 / % possible obs: 99.8 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 16.464
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2-2.072.40.359100
2.07-2.152.40.281100
2.15-2.252.40.205100
2.25-2.372.40.149100
2.37-2.522.40.121100
2.52-2.712.40.089100
2.71-2.992.40.062100
2.99-3.422.50.043100
3.42-4.312.50.03299.7
4.31-302.50.02798.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 2→30 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.27 / σ(F): 1.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.213 3134 5.1 %
Rwork0.18 --
obs0.182 61430 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.39 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 33.42 Å2
Baniso -1Baniso -2Baniso -3
1--1.089 Å20 Å20 Å2
2---1.089 Å2-0 Å2
3---2.178 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4974 0 202 409 5585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055302
X-RAY DIFFRACTIONf_angle_d0.9147228
X-RAY DIFFRACTIONf_dihedral_angle_d17.3942042
X-RAY DIFFRACTIONf_chiral_restr0.06766
X-RAY DIFFRACTIONf_plane_restr0.004912
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0320.2851620.2382563X-RAY DIFFRACTION100
2.032-2.0660.2821390.2352698X-RAY DIFFRACTION100
2.066-2.1010.2741230.2282664X-RAY DIFFRACTION100
2.101-2.1390.2751550.2172671X-RAY DIFFRACTION100
2.139-2.1810.2461250.2122665X-RAY DIFFRACTION100
2.181-2.2250.2411560.1962611X-RAY DIFFRACTION100
2.225-2.2730.2271430.2022687X-RAY DIFFRACTION100
2.273-2.3260.2971330.1982633X-RAY DIFFRACTION100
2.326-2.3840.2451530.2012658X-RAY DIFFRACTION100
2.384-2.4490.2431260.2032675X-RAY DIFFRACTION100
2.449-2.5210.261280.1952668X-RAY DIFFRACTION100
2.521-2.6020.2181620.22657X-RAY DIFFRACTION100
2.602-2.6950.2721410.1932636X-RAY DIFFRACTION100
2.695-2.8030.241370.1912664X-RAY DIFFRACTION100
2.803-2.930.2151370.1852658X-RAY DIFFRACTION100
2.93-3.0850.2261390.1762645X-RAY DIFFRACTION100
3.085-3.2780.2221500.1762660X-RAY DIFFRACTION100
3.278-3.530.1891520.1612658X-RAY DIFFRACTION100
3.53-3.8850.171160.152672X-RAY DIFFRACTION100
3.885-4.4460.1671450.1372630X-RAY DIFFRACTION100
4.446-5.5950.1521600.1382653X-RAY DIFFRACTION100
5.595-29.6590.1741520.1662570X-RAY DIFFRACTION98

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