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- PDB-7f4o: Crystal structure of MTA1-p2 complex -

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Basic information

Entry
Database: PDB / ID: 7f4o
TitleCrystal structure of MTA1-p2 complex
Components
  • MT-a70 family protein
  • Transmembrane protein, putative
KeywordsDNA BINDING PROTEIN / DNA / Protein / Complex
Function / homology
Function and homology information


mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / methylation / nucleus / membrane
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
Transmembrane protein, putative / mRNA m(6)A methyltransferase
Similarity search - Component
Biological speciesTetrahymena thermophila SB210 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 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 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Transmembrane protein, putative
A: MT-a70 family protein


Theoretical massNumber of molelcules
Total (without water)45,4232
Polymers45,4232
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-17 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.409, 137.409, 61.571
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Transmembrane protein, putative


Mass: 16612.893 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote)
Gene: p2 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: I7M8B9
#2: Protein MT-a70 family protein


Mass: 28809.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote)
Gene: MTA1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q22GC0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 70.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES, pH 6.5, 15% PEG 550 MME

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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: Dec 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 12112 / % possible obs: 100 % / Redundancy: 33.2 % / Biso Wilson estimate: 51.44 Å2 / Rpim(I) all: 0.024 / Net I/σ(I): 37.5
Reflection shellResolution: 3.1→3.15 Å / Mean I/σ(I) obs: 4 / Num. unique obs: 607 / Rpim(I) all: 0.182

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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: SAD / Resolution: 3.1→44.98 Å / SU ML: 0.4589 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 26.3898
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2739 604 4.99 %
Rwork0.2491 11508 -
obs0.2504 12112 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.89 Å2
Refinement stepCycle: LAST / Resolution: 3.1→44.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2769 0 0 17 2786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01562819
X-RAY DIFFRACTIONf_angle_d1.64483794
X-RAY DIFFRACTIONf_chiral_restr0.4574405
X-RAY DIFFRACTIONf_plane_restr0.0137493
X-RAY DIFFRACTIONf_dihedral_angle_d25.66231050
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.410.32841330.30152678X-RAY DIFFRACTION91.86
3.41-3.910.33161440.26972906X-RAY DIFFRACTION100
3.91-4.920.2611930.22342882X-RAY DIFFRACTION100
4.93-44.980.22751340.2353042X-RAY DIFFRACTION99.78

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