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- PDB-2vdu: Structure of trm8-trm82, THE YEAST TRNA m7G methylation complex -

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Basic information

Entry
Database: PDB / ID: 2vdu
TitleStructure of trm8-trm82, THE YEAST TRNA m7G methylation complex
Components
  • TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE
  • TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE-ASSOCIATED WD REPEAT PROTEIN TRM82
KeywordsTRANSFERASE / S-ADENOSYL-L-METHIONINE / TRNA PROCESSING / PHOSPHORYLATION / METHYLTRANSFERASE / M7G / TRNA / SPOUT MT / WD REPEAT
Function / homology
Function and homology information


tRNA (m7G46) methyltransferase complex / tRNA (guanine-N7)-methylation / RNA (guanine-N7)-methylation / tRNA (guanine46-N7)-methyltransferase / tRNA (guanine(46)-N7)-methyltransferase activity / tRNA methyltransferase complex / tRNA modification / tRNA methylation / enzyme activator activity / tRNA binding ...tRNA (m7G46) methyltransferase complex / tRNA (guanine-N7)-methylation / RNA (guanine-N7)-methylation / tRNA (guanine46-N7)-methyltransferase / tRNA (guanine(46)-N7)-methyltransferase activity / tRNA methyltransferase complex / tRNA modification / tRNA methylation / enzyme activator activity / tRNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit / tRNA (guanine-N-7) methyltransferase catalytic subunit Trm8, eukaryote / SAM-dependent methyltransferase TRMB-type domain profile. / tRNA (guanine-N-7) methyltransferase, Trmb type / Putative methyltransferase / Vaccinia Virus protein VP39 / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat ...tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit / tRNA (guanine-N-7) methyltransferase catalytic subunit Trm8, eukaryote / SAM-dependent methyltransferase TRMB-type domain profile. / tRNA (guanine-N-7) methyltransferase, Trmb type / Putative methyltransferase / Vaccinia Virus protein VP39 / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit TRM82 / tRNA (guanine-N(7)-)-methyltransferase
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsLeulliot, N. / Chaillet, M. / Durand, D. / Ulryck, N. / Blondeau, K. / Van Tilbeurgh, H.
CitationJournal: Structure / Year: 2008
Title: Structure of the Yeast tRNA M7G Methylation Complex.
Authors: Leulliot, N. / Chaillet, M. / Durand, D. / Ulryck, N. / Blondeau, K. / Van Tilbeurgh, H.
History
DepositionOct 11, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE-ASSOCIATED WD REPEAT PROTEIN TRM82
D: TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE-ASSOCIATED WD REPEAT PROTEIN TRM82
E: TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE
F: TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,5506
Polymers162,3604
Non-polymers1902
Water4,666259
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-49.4 kcal/mol
Surface area59830 Å2
MethodPQS
2
B: TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE-ASSOCIATED WD REPEAT PROTEIN TRM82
E: TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2753
Polymers81,1802
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-15.2 kcal/mol
Surface area30960 Å2
MethodPQS
3
D: TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE-ASSOCIATED WD REPEAT PROTEIN TRM82
F: TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2753
Polymers81,1802
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-15.6 kcal/mol
Surface area30930 Å2
MethodPQS
Unit cell
Length a, b, c (Å)53.376, 107.676, 127.749
Angle α, β, γ (deg.)90.00, 91.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE-ASSOCIATED WD REPEAT PROTEIN TRM82


Mass: 51383.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GOLD (DE3) / References: UniProt: Q03774
#2: Protein TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE / TRM8 / TRNA(M7G46)-METHYLTRANSFERASE


Mass: 29796.221 Da / Num. of mol.: 2 / Fragment: 46-END, RESIDUES 39-286
Source method: isolated from a genetically manipulated source
Details: 46 N-TERMNIAL TRUNCATION
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GOLD (DE3)
References: UniProt: Q12009, tRNA (guanine46-N7)-methyltransferase
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL 46 RESIDUE TRUNCATION CTERM HIS TAG

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 45.56 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97953
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97953 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 26954 / % possible obs: 98.2 % / Observed criterion σ(I): 1.5 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.2
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.5 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.4→20 Å / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2764 --
Rwork0.228 --
obs-26954 99.1 %
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9302 0 10 259 9571

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