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- PDB-7f4s: Crystal structure of TthMTA1-PteMTA9 complex -

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Basic information

Entry
Database: PDB / ID: 7f4s
TitleCrystal structure of TthMTA1-PteMTA9 complex
Components
  • MT-a70 family protein
  • MTA9
KeywordsDNA BINDING PROTEIN / Protein Complex
Function / homology
Function and homology information


mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / mRNA modification / methylation / RNA binding / nucleus
Similarity search - Function
MT-A70-like / MT-A70 / MT-A70-like family profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chromosome undetermined scaffold_82, whole genome shotgun sequence / mRNA m(6)A methyltransferase
Similarity search - Component
Biological speciesTetrahymena thermophila SB210 (eukaryote)
Paramecium tetraurelia strain d4-2 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsChen, J. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32022047 China
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for MTA1c-mediated DNA N6-adenine methylation
Authors: Chen, J. / Hu, R. / Chen, Y. / Lin, X. / Xiang, W. / Chen, H. / Yao, C. / Liu, L.
History
DepositionJun 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MT-a70 family protein
B: MT-a70 family protein
C: MT-a70 family protein
D: MTA9
E: MTA9
F: MTA9


Theoretical massNumber of molelcules
Total (without water)152,2216
Polymers152,2216
Non-polymers00
Water3,819212
1
A: MT-a70 family protein
D: MTA9


Theoretical massNumber of molelcules
Total (without water)50,7402
Polymers50,7402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-21 kcal/mol
Surface area19280 Å2
MethodPISA
2
B: MT-a70 family protein
F: MTA9


Theoretical massNumber of molelcules
Total (without water)50,7402
Polymers50,7402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-17 kcal/mol
Surface area20350 Å2
MethodPISA
3
C: MT-a70 family protein
E: MTA9


Theoretical massNumber of molelcules
Total (without water)50,7402
Polymers50,7402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-22 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.699, 75.647, 142.471
Angle α, β, γ (deg.)90.000, 99.158, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein MT-a70 family protein / MTA1MTase


Mass: 23113.408 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote)
Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q22GC0
#2: Protein MTA9


Mass: 27627.061 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium tetraurelia strain d4-2 (eukaryote)
Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0E887
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris-HCl, pH 7.5, 0.2 M LiCl, 14% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.09→50 Å / Num. obs: 32542 / % possible obs: 99.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 64.21 Å2 / Rpim(I) all: 0.154 / Net I/σ(I): 5.25
Reflection shellResolution: 3.09→3.15 Å / Mean I/σ(I) obs: 1.29 / Num. unique obs: 1471 / Rpim(I) all: 0.498

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F4R

7f4r


Resolution: 3.09→44.93 Å / SU ML: 0.4986 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 35.6492
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3156 2809 8.63 %
Rwork0.3037 29733 -
obs0.3047 32542 57.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.4 Å2
Refinement stepCycle: LAST / Resolution: 3.09→44.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8934 0 0 212 9146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01059065
X-RAY DIFFRACTIONf_angle_d1.654112226
X-RAY DIFFRACTIONf_chiral_restr0.32431400
X-RAY DIFFRACTIONf_plane_restr0.00451551
X-RAY DIFFRACTIONf_dihedral_angle_d27.09673260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.150.410850.513659X-RAY DIFFRACTION2.19
3.15-3.20.4064130.4306132X-RAY DIFFRACTION5.51
3.2-3.270.4176300.429317X-RAY DIFFRACTION12.07
3.27-3.330.4266530.3919550X-RAY DIFFRACTION21.2
3.33-3.40.3896780.3679832X-RAY DIFFRACTION32.18
3.4-3.480.3261980.33961030X-RAY DIFFRACTION39.43
3.48-3.570.36311120.33541185X-RAY DIFFRACTION44.74
3.57-3.670.32041170.3321229X-RAY DIFFRACTION47.56
3.67-3.780.37681190.31831255X-RAY DIFFRACTION48.23
3.78-3.90.34751220.31761283X-RAY DIFFRACTION50.02
3.9-4.040.30621360.28691462X-RAY DIFFRACTION56.01
4.04-4.20.28281650.27481694X-RAY DIFFRACTION63.86
4.2-4.390.2711740.26591884X-RAY DIFFRACTION73.84
4.39-4.620.23892040.2532125X-RAY DIFFRACTION81.63
4.62-4.910.27932090.26762242X-RAY DIFFRACTION86.46
4.91-5.290.31312220.2822404X-RAY DIFFRACTION91.47
5.29-5.820.31272450.30572562X-RAY DIFFRACTION97.77
5.82-6.660.35392440.34212540X-RAY DIFFRACTION98.83
6.66-8.380.3282340.33492543X-RAY DIFFRACTION96.66
8.38-44.930.33052290.30992405X-RAY DIFFRACTION93.17

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