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- PDB-5cd1: Structure of an asymmetric tetramer of human tRNA m1A58 methyltra... -

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Basic information

Entry
Database: PDB / ID: 5cd1
TitleStructure of an asymmetric tetramer of human tRNA m1A58 methyltransferase in a complex with SAH and tRNA3Lys
Components
  • tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A
  • tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6
  • tRNA3Lys
KeywordsTRANSFERASE/RNA / class I methyltransferase fold / tRNA modification / SAM-dependent methyl transfer / TRANSFERASE-RNA complex
Function / homology
Function and homology information


mRNA (adenine-N1-)-methyltransferase activity / tRNA (adenine(58)-N1)-methyltransferase activity / tRNA (adenine58-N1)-methyltransferase / tRNA (m1A) methyltransferase complex / tRNA modification in the nucleus and cytosol / : / tRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / RNA binding / nucleoplasm / nucleus
Similarity search - Function
tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6 / Gcd10p family / : / Vcp-like ATPase; Chain A, domain 2 - #20 / tRNA (1-methyladenosine) methyltransferase catalytic subunit Gcd14 / tRNA methyltransferase complex GCD14 subunit / tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile. / Vcp-like ATPase; Chain A, domain 2 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6 / Gcd10p family / : / Vcp-like ATPase; Chain A, domain 2 - #20 / tRNA (1-methyladenosine) methyltransferase catalytic subunit Gcd14 / tRNA methyltransferase complex GCD14 subunit / tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile. / Vcp-like ATPase; Chain A, domain 2 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / : / RNA / RNA (> 10) / tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A / tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsFiner-Moore, J. / Czudnochowski, N. / O'Connell III, J.D. / Wang, A.L. / Stroud, R.M.
Funding support United States, Germany, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM51232 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM0082250 United States
German Research Foundation (DFG)CZ 205/1-1 Germany
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Crystal Structure of the Human tRNA m(1)A58 Methyltransferase-tRNA3(Lys) Complex: Refolding of Substrate tRNA Allows Access to the Methylation Target.
Authors: Finer-Moore, J. / Czudnochowski, N. / O'Connell, J.D. / Wang, A.L. / Stroud, R.M.
History
DepositionJul 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A
B: tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6
D: tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A
E: tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6
M: tRNA3Lys
N: tRNA3Lys
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,00810
Polymers224,1936
Non-polymers8154
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27790 Å2
ΔGint-181 kcal/mol
Surface area67720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.240, 137.440, 157.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A / tRNA(m1A58)-methyltransferase subunit TRMT61A / tRNA(m1A58)MTase subunit TRMT61A


Mass: 31420.627 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRMT61A, C14orf172, TRM61 / Plasmid: pET17b-6HisTrm6-Trm61
Details (production host): 3C protease cleavage site added C-terminal to the 6His tag
Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli)
References: UniProt: Q96FX7, tRNA (adenine58-N1)-methyltransferase
#2: Protein tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6 / tRNA(m1A58)-methyltransferase subunit TRM6 / tRNA(m1A58)MTase subunit TRM6


Mass: 55883.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRMT6, KIAA1153, TRM6, CGI-09 / Plasmid: pET17b-6HisTrm6-Trm61
Details (production host): 3C protease cleavage site added C-terminal to 6His tag
Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJA5
#3: RNA chain tRNA3Lys


Mass: 24792.689 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 339572
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na

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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: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 microliter protein solution (4.8 mg/ml protein, 66.4 micromolar tRNA3Lys, 2mM SAH, 1mM MgCl2 and 50mM Hepes pH7.5) mixed with 1 microliter reservoir solution (0.1M NaAcetate, pH4.8-5.0,2% ...Details: 1 microliter protein solution (4.8 mg/ml protein, 66.4 micromolar tRNA3Lys, 2mM SAH, 1mM MgCl2 and 50mM Hepes pH7.5) mixed with 1 microliter reservoir solution (0.1M NaAcetate, pH4.8-5.0,2% w/v PEG 4000, and 15% v/v MPD) over 1000 microliter reservoir solution
PH range: 4.8-5.0

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Data collection

DiffractionMean temperature: 103.15 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 5, 2014
RadiationMonochromator: double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 3.6→102.3 Å / Num. obs: 32882 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.308 / Net I/σ(I): 6.4
Reflection shellResolution: 3.6→3.69 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.87 / Mean I/σ(I) obs: 1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CCB

5ccb


Resolution: 3.6→59.392 Å / SU ML: 0.68 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2729 1636 5 %Random selection
Rwork0.2316 31075 --
obs0.2337 32711 99.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→59.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9637 3200 54 0 12891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413480
X-RAY DIFFRACTIONf_angle_d0.76318994
X-RAY DIFFRACTIONf_dihedral_angle_d14.0495387
X-RAY DIFFRACTIONf_chiral_restr0.042256
X-RAY DIFFRACTIONf_plane_restr0.0031875
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.70590.45911270.41312458X-RAY DIFFRACTION96
3.7059-3.82550.35491300.34882568X-RAY DIFFRACTION100
3.8255-3.96220.35211470.30242546X-RAY DIFFRACTION100
3.9622-4.12080.33111280.28392568X-RAY DIFFRACTION100
4.1208-4.30830.30921230.25122592X-RAY DIFFRACTION100
4.3083-4.53530.2781380.22392580X-RAY DIFFRACTION100
4.5353-4.81940.25991460.20652576X-RAY DIFFRACTION100
4.8194-5.19130.28361330.21592584X-RAY DIFFRACTION100
5.1913-5.71330.2621390.21912609X-RAY DIFFRACTION100
5.7133-6.53910.28811370.22932627X-RAY DIFFRACTION100
6.5391-8.23510.24631430.19582627X-RAY DIFFRACTION99
8.2351-59.40010.1911450.17892740X-RAY DIFFRACTION98

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