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- PDB-7f4q: Crystal structure of SAH-bound MTA1-p2 complex -

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Basic information

Entry
Database: PDB / ID: 7f4q
TitleCrystal structure of SAH-bound 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. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Transmembrane protein, putative / mRNA m(6)A methyltransferase
Similarity search - Component
Biological speciesTetrahymena thermophila SB210 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 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
B: Transmembrane protein, putative
A: MT-a70 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4793
Polymers45,0942
Non-polymers3841
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-17 kcal/mol
Surface area18180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.789, 136.789, 60.902
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: 28481.586 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: 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.65 Å3/Da / Density % sol: 66.28 %
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: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 7170 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 36.22 Å2 / Rpim(I) all: 0.093 / Net I/σ(I): 11
Reflection shellResolution: 3.4→3.46 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 433 / Rpim(I) all: 0.402

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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: 7F4O

7f4o


Resolution: 3.42→45.48 Å / SU ML: 0.4183 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 23.9758
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2628 345 4.81 %
Rwork0.2491 6825 -
obs0.2497 7170 78.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.08 Å2
Refinement stepCycle: LAST / Resolution: 3.42→45.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2756 0 26 15 2797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01562834
X-RAY DIFFRACTIONf_angle_d1.68343816
X-RAY DIFFRACTIONf_chiral_restr0.3729408
X-RAY DIFFRACTIONf_plane_restr0.0073492
X-RAY DIFFRACTIONf_dihedral_angle_d25.74961060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.42-4.30.2771120.26282447X-RAY DIFFRACTION56.92
4.31-45.480.25582330.24194378X-RAY DIFFRACTION99.83

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