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- PDB-7f4l: Crystal structure of MTA1-p1-p2 complex -

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Basic information

Entry
Database: PDB / ID: 7f4l
TitleCrystal structure of MTA1-p1-p2 complex
Components
  • MT-a70 family protein
  • Transmembrane protein, putative
  • p1 protein
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. / Myb-like DNA-binding domain / SANT/Myb domain / Vaccinia Virus protein VP39 / Homeobox-like domain superfamily / 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 / Myb-like domain-containing protein
Similarity search - Component
Biological speciesTetrahymena thermophila SB210 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.72 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 20, 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
C: MT-a70 family protein
D: MT-a70 family protein
E: p1 protein
F: p1 protein
A: Transmembrane protein, putative


Theoretical massNumber of molelcules
Total (without water)162,8886
Polymers162,8886
Non-polymers00
Water1,04558
1
B: Transmembrane protein, putative
C: MT-a70 family protein
F: p1 protein


Theoretical massNumber of molelcules
Total (without water)81,4443
Polymers81,4443
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-37 kcal/mol
Surface area19440 Å2
MethodPISA
2
D: MT-a70 family protein
E: p1 protein
A: Transmembrane protein, putative


Theoretical massNumber of molelcules
Total (without water)81,4443
Polymers81,4443
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-38 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.765, 86.487, 160.989
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Transmembrane protein, putative


Mass: 16800.477 Da / Num. of mol.: 2
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.: 2
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: Protein p1 protein


Mass: 35833.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote)
Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q22VV9
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 1.77 Å3/Da / Density % sol: 30.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.05M HEPES, pH 7.0, 16% PEG 4000

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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: 2.72→50 Å / Num. obs: 31234 / % possible obs: 100 % / Redundancy: 21.6 % / Biso Wilson estimate: 38.78 Å2 / Rpim(I) all: 0.03 / Net I/σ(I): 31
Reflection shellResolution: 2.72→2.77 Å / Num. unique obs: 1558 / Rpim(I) all: 0.24

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.72→48 Å / SU ML: 0.3413 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.7431
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2538 1554 4.98 %
Rwork0.2399 29679 -
obs0.2406 31233 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.97 Å2
Refinement stepCycle: LAST / Resolution: 2.72→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6084 0 0 58 6142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0186188
X-RAY DIFFRACTIONf_angle_d1.77128322
X-RAY DIFFRACTIONf_chiral_restr0.4415896
X-RAY DIFFRACTIONf_plane_restr0.00741076
X-RAY DIFFRACTIONf_dihedral_angle_d26.85582346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.80.33541010.3062162X-RAY DIFFRACTION79.6
2.8-2.90.34611180.2932654X-RAY DIFFRACTION96.89
2.9-3.020.2931480.28542694X-RAY DIFFRACTION99.93
3.02-3.160.31761490.27562726X-RAY DIFFRACTION99.97
3.16-3.320.29311380.26342760X-RAY DIFFRACTION99.97
3.32-3.530.26231400.25252699X-RAY DIFFRACTION100
3.53-3.80.27371570.23342734X-RAY DIFFRACTION100
3.81-4.190.24351560.20992743X-RAY DIFFRACTION100
4.19-4.790.20231500.19192776X-RAY DIFFRACTION100
4.79-6.040.22931350.22952807X-RAY DIFFRACTION100
6.04-480.21231620.23512924X-RAY DIFFRACTION99.77

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