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- PDB-5ccx: Structure of the product complex of tRNA m1A58 methyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 5ccx
TitleStructure of the product complex of tRNA m1A58 methyltransferase with tRNA3Lys as substrate
Components
  • (tRNA (adenine(58)-N(1))-methyltransferase ...) x 2
  • tRNA3Lys
KeywordsTRANSFERASE/RNA / tRNA modification / Sam-dependent methyltransferase class I / methyltransferase fold / HIV-1 primer / TRANSFERASE-RNA complex
Function / homology
Function and homology information


mRNA (adenine-N1-)-methyltransferase activity / tRNA (adenine58-N1)-methyltransferase / tRNA (m1A) methyltransferase complex / tRNA (adenine(58)-N1)-methyltransferase activity / tRNA modification in the nucleus and cytosol / tRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / mRNA processing / 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: 2.1 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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
N: tRNA3Lys
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5185
Polymers112,1113
Non-polymers4072
Water5,567309
1
A: tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A
B: tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6
N: tRNA3Lys
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)225,03610
Polymers224,2216
Non-polymers8154
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area31380 Å2
ΔGint-195 kcal/mol
Surface area68740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.770, 136.770, 177.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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TRNA (adenine(58)-N(1))-methyltransferase ... , 2 types, 2 molecules AB

#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.: 1
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): modified to contain a 3C protease cleavage site 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.: 1
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): modified to contain a 3C protease cleavage site C-terminal to the 6His tag
Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJA5

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RNA chain , 1 types, 1 molecules N

#3: RNA chain tRNA3Lys


Mass: 24806.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 339572

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Non-polymers , 3 types, 311 molecules

#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 3.69 Å3/Da / Density % sol: 66.71 %
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 SAM, 1mM MgCl2 and 50mM Hepes pH 7.5) plus 1 microliter reservoir solution (0.1 M NaAcetate, pH 4.8-5.0, 2% ...Details: 1 microliter protein solution (4.8 mg/ml protein, 66.4 micromolar tRNA3Lys, 2mM SAM, 1mM MgCl2 and 50mM Hepes pH 7.5) plus 1 microliter reservoir solution (0.1 M NaAcetate, pH 4.8-5.0, 2% w/v PEG 4000 and 15% v/v MPD) over 1000 microliters reservoir solution
PH range: 4.8-5.0

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 14, 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: 2.1→108 Å / Num. obs: 98180 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 16.7
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 8.2 % / Rmerge(I) obs: 2.59 / Mean I/σ(I) obs: 0.9 / % possible all: 100

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Processing

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

5ccb


Resolution: 2.1→54.13 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.237 4963 5.06 %random selection
Rwork0.207 ---
obs0.208 98079 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→54.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5092 1642 27 309 7070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047172
X-RAY DIFFRACTIONf_angle_d0.69910099
X-RAY DIFFRACTIONf_dihedral_angle_d14.1732899
X-RAY DIFFRACTIONf_chiral_restr0.0391189
X-RAY DIFFRACTIONf_plane_restr0.003995
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.35821330.33213064X-RAY DIFFRACTION100
2.1239-2.14890.34631750.32583079X-RAY DIFFRACTION100
2.1489-2.17510.3881620.32633068X-RAY DIFFRACTION100
2.1751-2.20260.34441530.30913070X-RAY DIFFRACTION100
2.2026-2.23160.30251630.30133041X-RAY DIFFRACTION100
2.2316-2.26210.3391830.29533058X-RAY DIFFRACTION100
2.2621-2.29450.31921620.28973056X-RAY DIFFRACTION100
2.2945-2.32870.35491730.2873095X-RAY DIFFRACTION100
2.3287-2.36510.27891490.27843057X-RAY DIFFRACTION100
2.3651-2.40390.3231650.27153103X-RAY DIFFRACTION100
2.4039-2.44530.30351580.25723049X-RAY DIFFRACTION100
2.4453-2.48980.2811560.2573099X-RAY DIFFRACTION100
2.4898-2.53770.31721630.25053061X-RAY DIFFRACTION100
2.5377-2.58950.26651650.24843084X-RAY DIFFRACTION100
2.5895-2.64580.23871840.23343057X-RAY DIFFRACTION100
2.6458-2.70730.28341610.24293082X-RAY DIFFRACTION100
2.7073-2.7750.28581620.24053097X-RAY DIFFRACTION100
2.775-2.85010.28641670.23253110X-RAY DIFFRACTION100
2.8501-2.93390.30321750.22233078X-RAY DIFFRACTION100
2.9339-3.02860.28321510.23093095X-RAY DIFFRACTION100
3.0286-3.13680.26531830.20473078X-RAY DIFFRACTION100
3.1368-3.26240.21591540.20913118X-RAY DIFFRACTION100
3.2624-3.41090.24171720.20613117X-RAY DIFFRACTION100
3.4109-3.59070.2281690.19683123X-RAY DIFFRACTION100
3.5907-3.81560.21651630.18283125X-RAY DIFFRACTION100
3.8156-4.11010.19571600.16793152X-RAY DIFFRACTION100
4.1101-4.52350.19421780.1573139X-RAY DIFFRACTION100
4.5235-5.17760.20831630.16033180X-RAY DIFFRACTION100
5.1776-6.52150.20991840.1933221X-RAY DIFFRACTION100
6.5215-54.14870.17251770.1873360X-RAY DIFFRACTION99

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