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

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Basic information

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


Methylation / tRNA (m2G10) methyltransferase complex / positive regulation of termination of DNA-templated transcription / 18S rRNA (guanine1575-N7)-methyltransferase / eRF1 methyltransferase complex / Eukaryotic Translation Termination / rRNA (guanine-N7)-methylation / tRNA methyltransferase complex / rRNA (guanine) methyltransferase activity / tRNA wobble uridine modification ...Methylation / tRNA (m2G10) methyltransferase complex / positive regulation of termination of DNA-templated transcription / 18S rRNA (guanine1575-N7)-methyltransferase / eRF1 methyltransferase complex / Eukaryotic Translation Termination / rRNA (guanine-N7)-methylation / tRNA methyltransferase complex / rRNA (guanine) methyltransferase activity / tRNA wobble uridine modification / tRNA methylation / 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 LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / 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
18S rRNA (guanine(1575)-N(7))-methyltransferase / Multifunctional methyltransferase subunit TRM112
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 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 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)77,17811
Polymers76,2534
Non-polymers9267
Water4,864270
1
A: Multifunctional methyltransferase subunit TRM112
B: Putative methyltransferase BUD23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9878
Polymers38,1262
Non-polymers8606
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint0 kcal/mol
Surface area14470 Å2
MethodPISA
2
C: Multifunctional methyltransferase subunit TRM112
D: Putative methyltransferase BUD23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1923
Polymers38,1262
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-14 kcal/mol
Surface area14180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.420, 53.880, 83.760
Angle α, β, γ (deg.)90.00, 95.32, 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, 277 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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.1943.91
2
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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSOLEIL PROXIMA 110.9801
SYNCHROTRONSOLEIL PROXIMA 121.2822, 1.2828, 1.2757
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELNov 14, 2012
PSI PILATUS 6M2PIXELNov 14, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Channel cut cryogenically cooled monochromator crystalSINGLE WAVELENGTHMx-ray1
2Channel cut cryogenically cooled monochromator crystalMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.98011
21.28221
31.28281
41.27571
ReflectionResolution: 2→50 Å / Num. all: 46211 / Num. obs: 44594 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 37.61 Å2 / Rsym value: 0.045 / Net I/σ(I): 18.3
Reflection shellResolution: 2→2.12 Å / % possible all: 96.5

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Processing

Software
NameVersionClassification
XDSdata scaling
SHARPphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→37.05 Å / FOM work R set: 0.8321 / SU ML: 0.52 / σ(F): 2 / Phase error: 24.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 2228 5 %
Rwork0.1911 --
obs0.1937 44585 99.21 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.006 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 90.17 Å2 / Biso mean: 43.32 Å2 / Biso min: 20.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.3891 Å20 Å2-3.8283 Å2
2---3.1623 Å20 Å2
3---2.7732 Å2
Refinement stepCycle: LAST / Resolution: 2→37.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4736 0 34 270 5040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084867
X-RAY DIFFRACTIONf_angle_d1.0446577
X-RAY DIFFRACTIONf_chiral_restr0.071745
X-RAY DIFFRACTIONf_plane_restr0.004848
X-RAY DIFFRACTIONf_dihedral_angle_d17.6891810
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0005-2.0440.32081250.25712404252991
2.044-2.09150.29771390.234426362775100
2.0915-2.14380.30871400.232426512791100
2.1438-2.20180.27861380.218926302768100
2.2018-2.26660.27281400.21652650279099
2.2666-2.33970.28441400.210926612801100
2.3397-2.42330.25281380.19726312769100
2.4233-2.52030.27911390.211426382777100
2.5203-2.6350.24971410.20426732814100
2.635-2.77390.26671400.195626622802100
2.7739-2.94760.23171390.192726452784100
2.9476-3.17510.27511410.195126812822100
3.1751-3.49440.23151400.190326612801100
3.4944-3.99950.2041420.170727002842100
3.9995-5.03690.21071410.158726822823100
5.0369-37.05610.24051450.20142752289799

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