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- PDB-3q87: Structure of E. cuniculi Mtq2-Trm112 complex responible for the m... -

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Basic information

Entry
Database: PDB / ID: 3q87
TitleStructure of E. cuniculi Mtq2-Trm112 complex responible for the methylation of eRF1 translation termination factor
Components
  • N6 adenine specific DNA methylase
  • Putative uncharacterized protein ECU08_1170
KeywordsTRANSFERASE ACTIVATOR/TRANSFERASE / SAM-methyltransferase / methyltransferase / methylation / TRANSFERASE ACTIVATOR-TRANSFERASE complex
Function / homology
Function and homology information


methyltransferase activity / methylation / nucleic acid binding / metal ion binding
Similarity search - Function
Trm112-like / Trm112p-like protein / Methyltransferase small domain / Methyltransferase small domain / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / Single Sheet / Vaccinia Virus protein VP39 ...Trm112-like / Trm112p-like protein / Methyltransferase small domain / Methyltransferase small domain / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / Single Sheet / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / Uncharacterized protein
Similarity search - Component
Biological speciesEncephalitozoon cuniculi (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.997 Å
AuthorsLiger, D. / Mora, L. / Lazar, N. / Figaro, S. / Henri, J. / Scrima, N. / Buckingham, R.H. / van Tilbeurgh, H. / Heurgue-Hamard, V. / Graille, M.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Mechanism of activation of methyltransferases involved in translation by the Trm112 'hub' protein
Authors: Liger, D. / Mora, L. / Lazar, N. / Figaro, S. / Henri, J. / Scrima, N. / Buckingham, R.H. / van Tilbeurgh, H. / Heurgue-Hamard, V. / Graille, M.
History
DepositionJan 6, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 3, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Dec 25, 2019Group: Data collection / Database references / Refinement description
Category: refine / reflns_shell / struct_ref_seq_dif
Item: _refine.ls_R_factor_all / _reflns_shell.pdbx_Rsym_value / _struct_ref_seq_dif.details
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein ECU08_1170
B: N6 adenine specific DNA methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8734
Polymers33,4092
Non-polymers4642
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-13 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.115, 74.316, 96.754
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 Putative uncharacterized protein ECU08_1170 / Trm112 activator protein


Mass: 14175.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Plasmid: pET21-a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8SUP0
#2: Protein N6 adenine specific DNA methylase / Methyltransferase superfamily / Mtq2 catalytic subunit


Mass: 19233.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Plasmid: pET21-a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8SRR4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.27 Å3/Da / Density % sol: 45.72 %
Crystal growTemperature: 310 K / Method: vapor diffusion / pH: 7.5
Details: 20% PEG4000, 10% isopropanol, 100mM Hepes, pH 7.5, VAPOR DIFFUSION, temperature 310K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.214 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.214 Å / Relative weight: 1
ReflectionResolution: 1.997→50 Å / Num. all: 34474 / Num. obs: 33750 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 24.64 Å2 / Rsym value: 0.089 / Net I/σ(I): 8.3
Reflection shellResolution: 2→2.22 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.482 / % possible all: 96.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.997→48.377 Å / Occupancy max: 1 / Occupancy min: 0.22 / FOM work R set: 0.8156 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2558 1964 4.99 %Random
Rwork0.2024 ---
obs0.2051 21198 98.88 %-
all-39356 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.901 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso max: 102.19 Å2 / Biso mean: 30.2186 Å2 / Biso min: 9.96 Å2
Baniso -1Baniso -2Baniso -3
1-2.1432 Å20 Å20 Å2
2---1.0093 Å2-0 Å2
3----1.1339 Å2
Refinement stepCycle: LAST / Resolution: 1.997→48.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 28 136 2419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072318
X-RAY DIFFRACTIONf_angle_d1.1063126
X-RAY DIFFRACTIONf_chiral_restr0.072363
X-RAY DIFFRACTIONf_plane_restr0.004399
X-RAY DIFFRACTIONf_dihedral_angle_d17.029887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9971-2.0470.36761250.32952464X-RAY DIFFRACTION92
2.047-2.10240.32081400.29192680X-RAY DIFFRACTION99
2.1024-2.16430.31521410.26462680X-RAY DIFFRACTION99
2.1643-2.23410.31291420.25442697X-RAY DIFFRACTION99
2.2341-2.3140.28221430.22722710X-RAY DIFFRACTION100
2.314-2.40660.28651390.21312667X-RAY DIFFRACTION100
2.4066-2.51610.25831440.21122699X-RAY DIFFRACTION100
2.5161-2.64880.26111480.19432716X-RAY DIFFRACTION100
2.6488-2.81470.28151430.21362679X-RAY DIFFRACTION100
2.8147-3.0320.28191430.19262696X-RAY DIFFRACTION100
3.032-3.33710.25261380.19522674X-RAY DIFFRACTION100
3.3371-3.81980.18461400.16622687X-RAY DIFFRACTION99
3.8198-4.81180.20811420.15232655X-RAY DIFFRACTION99
4.8118-48.39120.20891360.17792688X-RAY DIFFRACTION99

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