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- PDB-7f4m: Crystal structure of SAM-bound MTA1-p1-p2 complex -

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Basic information

Entry
Database: PDB / ID: 7f4m
TitleCrystal structure of SAM-bound 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


RNA N6-methyladenosine methyltransferase complex / methyltransferase activity / nucleus / membrane
Similarity search - Function
MT-A70-like / MT-A70 / MT-A70-like family profile. / Myb-like DNA-binding domain / SANT/Myb domain / Homeobox-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Transmembrane protein, putative / MT-a70 family protein / Myb-like domain-containing protein
Similarity search - Component
Biological speciesTetrahymena thermophila SB210 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.58 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

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,0908
Polymers161,2936
Non-polymers7972
Water43224
1
B: Transmembrane protein, putative
C: MT-a70 family protein
F: p1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0454
Polymers80,6473
Non-polymers3981
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-40 kcal/mol
Surface area19410 Å2
MethodPISA
2
D: MT-a70 family protein
E: p1 protein
A: Transmembrane protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0454
Polymers80,6473
Non-polymers3981
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-37 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.517, 85.786, 162.903
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: 16612.893 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: 28481.586 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: 35552.168 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: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 1.81 Å3/Da / Density % sol: 32.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / 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 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 13242 / % possible obs: 100 % / Redundancy: 10.9 % / Biso Wilson estimate: 29.86 Å2 / Rpim(I) all: 0.033 / Net I/σ(I): 20.3
Reflection shellResolution: 3.4→3.46 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 806 / Rpim(I) all: 0.334

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F4L

7f4l


Resolution: 3.58→48.23 Å / SU ML: 0.4052 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 25.0006
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2761 692 5.23 %
Rwork0.2507 12550 -
obs0.252 13242 92.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.61 Å2
Refinement stepCycle: LAST / Resolution: 3.58→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6115 0 54 24 6193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01276278
X-RAY DIFFRACTIONf_angle_d1.35978444
X-RAY DIFFRACTIONf_chiral_restr0.1856908
X-RAY DIFFRACTIONf_plane_restr0.00711082
X-RAY DIFFRACTIONf_dihedral_angle_d23.69992398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.58-3.860.3031850.27651642X-RAY DIFFRACTION61.5
3.86-4.240.31421330.26442674X-RAY DIFFRACTION99.57
4.24-4.860.28431600.23872677X-RAY DIFFRACTION100
4.86-6.120.28931500.26012728X-RAY DIFFRACTION99.97
6.12-48.230.21511640.22892829X-RAY DIFFRACTION99.44

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