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- PDB-5ccb: Crystal structure of human m1A58 methyltransferase in a complex w... -

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Basic information

Entry
Database: PDB / ID: 5ccb
TitleCrystal structure of human m1A58 methyltransferase in a complex with tRNA3Lys and SAH
Components
  • (tRNA (adenine(58)-N(1))-methyltransferase ...) x 2
  • tRNA3Lys
KeywordsTRANSFERASE/RNA / tRNA A58 modification / methyl transferase-tRNA complex / class I methyltransferase fold / S-adenosyl-L-methionine cofactor / 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: 2 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 1, 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 / Database references / Category: pdbx_audit_support / struct_ref_seq_dif
Item: _pdbx_audit_support.funding_organization / _struct_ref_seq_dif.details
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
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.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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)112,5045
Polymers112,0973
Non-polymers4072
Water7,494416
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)225,00810
Polymers224,1936
Non-polymers8154
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area30220 Å2
ΔGint-194 kcal/mol
Surface area69160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.180, 137.180, 177.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-418-

HOH

21B-542-

HOH

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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): plasmid 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 site C-terminal to the 6His-tag
Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UJA5, tRNA (adenine58-N1)-methyltransferase

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RNA chain , 1 types, 1 molecules N

#3: RNA chain tRNA3Lys


Mass: 24792.689 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, 418 molecules

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


Mass: 18.015 Da / Num. of mol.: 416 / 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: 3.71 Å3/Da / Density % sol: 66.89 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1microliter protein solution (4.8 mg/ml protein, 66.4 micromolar tRNA3Lys, 2 mM s-adenosyl-L-homocysteine, 1mM MgCl2 and 50 mM Hepes pH7.5) and 1 microliter reservoir solution (0.1 M ...Details: 1microliter protein solution (4.8 mg/ml protein, 66.4 micromolar tRNA3Lys, 2 mM s-adenosyl-L-homocysteine, 1mM MgCl2 and 50 mM Hepes pH7.5) and 1 microliter reservoir solution (0.1 M NaAcetate, pH 4.8-5.0, 2% w/v PEG 4000, 15% v/v MPD) suspended 1000 microliters 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: 2→97 Å / Num. obs: 113960 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 18.6
Reflection shellResolution: 2→2.5 Å / Redundancy: 7.6 % / Rmerge(I) obs: 2.23 / Mean I/σ(I) obs: 1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PWY

2pwy


Resolution: 2→74.373 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 5683 4.99 %random selection
Rwork0.1988 ---
obs0.2 113874 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→74.373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5088 1642 27 416 7173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057083
X-RAY DIFFRACTIONf_angle_d0.8559961
X-RAY DIFFRACTIONf_dihedral_angle_d14.7152871
X-RAY DIFFRACTIONf_chiral_restr0.0461176
X-RAY DIFFRACTIONf_plane_restr0.003984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02280.39371890.36163549X-RAY DIFFRACTION100
2.0228-2.04660.37061750.33063567X-RAY DIFFRACTION100
2.0466-2.07150.33821670.32223574X-RAY DIFFRACTION100
2.0715-2.09770.32791930.30243544X-RAY DIFFRACTION100
2.0977-2.12530.33641690.2983557X-RAY DIFFRACTION100
2.1253-2.15450.27911800.28393595X-RAY DIFFRACTION100
2.1545-2.18520.28791880.27253575X-RAY DIFFRACTION100
2.1852-2.21790.29282090.26373552X-RAY DIFFRACTION100
2.2179-2.25250.27931990.26863566X-RAY DIFFRACTION100
2.2525-2.28940.33032060.25163538X-RAY DIFFRACTION100
2.2894-2.32890.2952090.25173546X-RAY DIFFRACTION100
2.3289-2.37130.26421650.23593582X-RAY DIFFRACTION100
2.3713-2.41690.24261940.22783584X-RAY DIFFRACTION100
2.4169-2.46620.25911840.23323586X-RAY DIFFRACTION100
2.4662-2.51990.2651890.2163567X-RAY DIFFRACTION100
2.5199-2.57850.23571850.2173600X-RAY DIFFRACTION100
2.5785-2.6430.23671910.20913619X-RAY DIFFRACTION100
2.643-2.71440.26421690.22253580X-RAY DIFFRACTION100
2.7144-2.79430.241940.21213607X-RAY DIFFRACTION100
2.7943-2.88450.24361850.21033586X-RAY DIFFRACTION100
2.8845-2.98760.24931920.21583618X-RAY DIFFRACTION100
2.9876-3.10720.23191940.20633610X-RAY DIFFRACTION100
3.1072-3.24860.25181890.19823618X-RAY DIFFRACTION100
3.2486-3.41990.22922010.19733615X-RAY DIFFRACTION100
3.4199-3.63420.20371890.18813610X-RAY DIFFRACTION100
3.6342-3.91470.18291930.17163665X-RAY DIFFRACTION100
3.9147-4.30870.16211790.16043702X-RAY DIFFRACTION100
4.3087-4.9320.16242040.15123667X-RAY DIFFRACTION100
4.932-6.21340.19531910.1783737X-RAY DIFFRACTION100
6.2134-74.42440.20622110.18193875X-RAY DIFFRACTION99

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