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- PDB-4qtu: Structure of S. cerevisiae Bud23-Trm112 complex involved in forma... -

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Basic information

Entry
Database: PDB / ID: 4qtu
TitleStructure of S. cerevisiae Bud23-Trm112 complex involved in formation of m7G1575 on 18S rRNA (SAM bound form)
Components
  • Multifunctional methyltransferase subunit TRM112
  • Putative methyltransferase BUD23
KeywordsTRANSFERASE / Class I / Methyltransferase
Function / homology
Function and homology information


tRNA (m2G10) methyltransferase complex / Methylation / positive regulation of termination of DNA-templated transcription / 18S rRNA (guanine1575-N7)-methyltransferase / eRF1 methyltransferase complex / Eukaryotic Translation Termination / peptidyl-glutamine methylation / rRNA (guanine-N7)-methylation / tRNA methyltransferase complex / rRNA (guanine) methyltransferase activity ...tRNA (m2G10) methyltransferase complex / Methylation / positive regulation of termination of DNA-templated transcription / 18S rRNA (guanine1575-N7)-methyltransferase / eRF1 methyltransferase complex / Eukaryotic Translation Termination / peptidyl-glutamine methylation / rRNA (guanine-N7)-methylation / tRNA methyltransferase complex / rRNA (guanine) methyltransferase activity / tRNA wobble uridine modification / tRNA methylation / Major pathway of rRNA processing in the nucleolus and cytosol / ribosomal small subunit export from nucleus / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / maturation of LSU-rRNA / ribosomal large subunit biogenesis / ribosomal small subunit biogenesis / ribosome / protein heterodimerization activity / nucleolus / nucleus / cytosol / cytoplasm
Similarity search - Function
18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23, C-terminal / 18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23-like / Methyltransferase involved in Williams-Beuren syndrome / Multifunctional methyltransferase subunit Trm112 / Trm112-like / Trm112p-like protein / Methyltransferase type 11 / Methyltransferase domain / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb ...18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23, C-terminal / 18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23-like / Methyltransferase involved in Williams-Beuren syndrome / Multifunctional methyltransferase subunit Trm112 / Trm112-like / Trm112p-like protein / Methyltransferase type 11 / Methyltransferase domain / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / Single Sheet / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / 18S rRNA (guanine(1575)-N(7))-methyltransferase / Multifunctional methyltransferase subunit TRM112
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.124 Å
AuthorsLetoquart, J. / Huvelle, E. / Wacheul, L. / Bourgeois, G. / Zorbas, C. / Graille, M. / Heurgue-Hamard, V. / Lafontaine, D.L.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural and functional studies of Bud23-Trm112 reveal 18S rRNA N7-G1575 methylation occurs on late 40S precursor ribosomes.
Authors: Letoquart, J. / Huvelle, E. / Wacheul, L. / Bourgeois, G. / Zorbas, C. / Graille, M. / Heurgue-Hamard, V. / Lafontaine, D.L.
History
DepositionJul 9, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multifunctional methyltransferase subunit TRM112
B: Putative methyltransferase BUD23
C: Multifunctional methyltransferase subunit TRM112
D: Putative methyltransferase BUD23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,36027
Polymers76,2534
Non-polymers2,10723
Water3,117173
1
A: Multifunctional methyltransferase subunit TRM112
B: Putative methyltransferase BUD23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,58320
Polymers38,1262
Non-polymers1,45718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-13 kcal/mol
Surface area15270 Å2
MethodPISA
2
C: Multifunctional methyltransferase subunit TRM112
D: Putative methyltransferase BUD23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7767
Polymers38,1262
Non-polymers6505
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-13 kcal/mol
Surface area14480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.472, 53.733, 85.205
Angle α, β, γ (deg.)90.00, 94.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Multifunctional methyltransferase subunit TRM112 / rRNA MTase activator subunit / eRF1 methyltransferase subunit TRM112 / eRF1 MTase subunit TRM112 / ...rRNA MTase activator subunit / eRF1 methyltransferase subunit TRM112 / eRF1 MTase subunit TRM112 / tRNA methyltransferase 112


Mass: 15078.209 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: N3445, TRM112, YNR046W / Production host: Escherichia coli (E. coli) / References: UniProt: P53738
#2: Protein Putative methyltransferase BUD23 / rRNA MTase catalytic subunit / Bud site selection protein 23


Mass: 23048.053 Da / Num. of mol.: 2 / Fragment: fragment residues 1-202
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: BUD23, YCR047C, YCR47C / Production host: Escherichia coli (E. coli)
References: UniProt: P25627, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 4 types, 196 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2012
RadiationMonochromator: Channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.124→50 Å / Num. obs: 38373 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 37.1 Å2
Reflection shellResolution: 2.2→2.33 Å / % possible all: 94.7

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Processing

Software
NameVersionClassification
XDSdata scaling
SHARPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QTT

4qtt


Resolution: 2.124→38.307 Å / FOM work R set: 0.8226 / SU ML: 0.27 / σ(F): 1.99 / Phase error: 24.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2286 1917 5 %
Rwork0.178 --
obs0.1806 38373 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.94 Å2 / Biso mean: 44.88 Å2 / Biso min: 19.75 Å2
Refinement stepCycle: LAST / Resolution: 2.124→38.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4946 0 132 173 5251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085165
X-RAY DIFFRACTIONf_angle_d1.116963
X-RAY DIFFRACTIONf_chiral_restr0.046783
X-RAY DIFFRACTIONf_plane_restr0.005893
X-RAY DIFFRACTIONf_dihedral_angle_d15.531913
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1235-2.17660.33341230.26062338246190
2.1766-2.23550.33021390.251826352774100
2.2355-2.30120.31251310.26132526265798
2.3012-2.37550.27641390.212326372776100
2.3755-2.46040.29151370.197725972734100
2.4604-2.55890.26231380.198626242762100
2.5589-2.67530.231360.193525942730100
2.6753-2.81630.27141400.193826462786100
2.8163-2.99270.29061370.190726122749100
2.9927-3.22370.22251380.195426132751100
3.2237-3.54790.19541380.18182640277899
3.5479-4.06080.20191390.15772624276399
4.0608-5.11420.1991400.141526582798100
5.1142-38.31360.19711420.15782712285499

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