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- PDB-6jp6: The X-ray structure of yeast tRNA methyltransferase complex of Tr... -

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Basic information

Entry
Database: PDB / ID: 6jp6
TitleThe X-ray structure of yeast tRNA methyltransferase complex of Trm7 and Trm734 essential for 2'-O-methylation at the first position of anticodon in specific tRNAs
Components
  • tRNA (cytidine(34)/guanosine(34)-2'-O)-methyltransferase
  • tRNA (guanosine(34)-2'-O)-methyltransferase non-catalytic subunit TRM734
KeywordsTRANSFERASE / tRNA methyltransferase / tRNA maturation
Function / homology
Function and homology information


tRNA (cytidine32/guanosine34-2'-O)-methyltransferase / wobble position ribose methylation / tRNA 2'-O-methyltransferase activity / tRNA (cytidine(32)-2'-O)-methyltransferase activity / RND1 GTPase cycle / tRNA nucleoside ribose methylation / RHOU GTPase cycle / RHOV GTPase cycle / tRNA methyltransferase activity / tRNA methylation ...tRNA (cytidine32/guanosine34-2'-O)-methyltransferase / wobble position ribose methylation / tRNA 2'-O-methyltransferase activity / tRNA (cytidine(32)-2'-O)-methyltransferase activity / RND1 GTPase cycle / tRNA nucleoside ribose methylation / RHOU GTPase cycle / RHOV GTPase cycle / tRNA methyltransferase activity / tRNA methylation / endocytic recycling / enzyme regulator activity / cytoplasmic translation / endosome / cytoplasm
Similarity search - Function
tRNA (cytidine(32)/guanosine(34)-2-O)-methyltransferase TRM7 / Ribosomal RNA large subunit methyltransferase E / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. ...tRNA (cytidine(32)/guanosine(34)-2-O)-methyltransferase TRM7 / Ribosomal RNA large subunit methyltransferase E / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase / Regulator of Ty1 transposition protein 10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.699 Å
AuthorsHirata, A. / Okada, K. / Yoshii, K. / Shiraisi, H. / Saijo, S. / Yonezawa, K. / Sihimzu, N. / Hori, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science15K06975 Japan
Japan Society for the Promotion of Science16H04763 Japan
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition.
Authors: Hirata, A. / Okada, K. / Yoshii, K. / Shiraishi, H. / Saijo, S. / Yonezawa, K. / Shimizu, N. / Hori, H.
History
DepositionMar 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 20, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA (guanosine(34)-2'-O)-methyltransferase non-catalytic subunit TRM734
B: tRNA (cytidine(34)/guanosine(34)-2'-O)-methyltransferase
C: tRNA (guanosine(34)-2'-O)-methyltransferase non-catalytic subunit TRM734
D: tRNA (cytidine(34)/guanosine(34)-2'-O)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)306,73710
Polymers305,8774
Non-polymers8616
Water4,630257
1
A: tRNA (guanosine(34)-2'-O)-methyltransferase non-catalytic subunit TRM734
B: tRNA (cytidine(34)/guanosine(34)-2'-O)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,3695
Polymers152,9382
Non-polymers4303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-39 kcal/mol
Surface area47730 Å2
MethodPISA
2
C: tRNA (guanosine(34)-2'-O)-methyltransferase non-catalytic subunit TRM734
D: tRNA (cytidine(34)/guanosine(34)-2'-O)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,3695
Polymers152,9382
Non-polymers4303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-40 kcal/mol
Surface area47950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)253.643, 110.351, 133.503
Angle α, β, γ (deg.)90.000, 90.020, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A or chain D
21chain B or chain C

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLYSLYSchain A or chain DAA1 - 10131 - 1013
12ARGARGSERSERchain A or chain DDD9 - 2599 - 259
21ARGARGSERSERchain B or chain CBB9 - 2599 - 259
22METMETLYSLYSchain B or chain CCC1 - 10131 - 1013

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Components

#1: Protein tRNA (guanosine(34)-2'-O)-methyltransferase non-catalytic subunit TRM734


Mass: 116391.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Production host: Escherichia coli (E. coli) / References: UniProt: Q08924
#2: Protein tRNA (cytidine(34)/guanosine(34)-2'-O)-methyltransferase / 2'-O-ribose RNA methyltransferase TRM7 / tRNA methylase 7


Mass: 36546.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Production host: Escherichia coli (E. coli)
References: UniProt: P38238, tRNA (cytidine32/guanosine34-2'-O)-methyltransferase
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 3.05 Å3/Da / Density % sol: 59.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG400, HEPES-NaOH, ammonium sulfate, phenol, ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.699→36.433 Å / Num. obs: 100973 / % possible obs: 99.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 44.62 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 22.2
Reflection shellResolution: 2.7→2.75 Å / Rmerge(I) obs: 0.465 / Num. unique obs: 4959

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.699→36.433 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.49
RfactorNum. reflection% reflection
Rfree0.2387 5047 5 %
Rwork0.1939 --
obs0.1962 100973 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.04 Å2 / Biso mean: 46.5571 Å2 / Biso min: 17.6 Å2
Refinement stepCycle: final / Resolution: 2.699→36.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19560 0 50 257 19867
Biso mean--52.62 37.36 -
Num. residues----2458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119996
X-RAY DIFFRACTIONf_angle_d1.22727040
X-RAY DIFFRACTIONf_chiral_restr0.0733058
X-RAY DIFFRACTIONf_plane_restr0.0083420
X-RAY DIFFRACTIONf_dihedral_angle_d15.7111942
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A11655X-RAY DIFFRACTION6.674TORSIONAL
12B11655X-RAY DIFFRACTION6.674TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6988-2.72950.29661640.25182876304091
2.7295-2.76160.31911710.250532103381100
2.7616-2.79520.33731620.256331383300100
2.7952-2.83060.33571790.259432473426100
2.8306-2.86780.32711900.253831513341100
2.8678-2.90710.27221510.239332123363100
2.9071-2.94860.29951780.234832203398100
2.9486-2.99260.29911650.231831433308100
2.9926-3.03940.30711660.219432263392100
3.0394-3.08920.26671760.222431533329100
3.0892-3.14240.25661630.216932313394100
3.1424-3.19950.27991590.217632133372100
3.1995-3.2610.29181570.218332313388100
3.261-3.32750.26281520.215931423294100
3.3275-3.39980.28571860.206331933379100
3.3998-3.47890.23621690.199632123381100
3.4789-3.56580.28141570.196432273384100
3.5658-3.66210.2341690.182231763345100
3.6621-3.76980.22871560.186532313387100
3.7698-3.89130.22791760.187631603336100
3.8913-4.03020.22861810.181732193400100
4.0302-4.19140.20691610.167232413402100
4.1914-4.38180.20681590.156631983357100
4.3818-4.61240.16621520.145532563408100
4.6124-4.90070.18641730.14231693342100
4.9007-5.27810.19891930.168632273420100
5.2781-5.80730.24991910.18832303421100
5.8073-6.64330.22451620.204932363398100
6.6433-8.35310.23961550.210232623417100
8.3531-36.43650.1921740.1973296347099

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