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- PDB-7dpe: RNA methyltransferase METTL4 -

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Basic information

Entry
Database: PDB / ID: 7dpe
TitleRNA methyltransferase METTL4
Components
  • DNA (5'-D(*GP*CP*CP*GP*CP*GP*TP*GP*AP*TP*CP*AP*CP*GP*CP*GP*GP*C)-3')
  • Methyltransferase-like protein 2
KeywordsTRANSFERASE/DNA / Methyltransferase / TRANSFERASE-DNA complex
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / nucleic acid binding / nucleus
Similarity search - Function
MT-A70-like / MT-A70 / MT-A70-like family profile. / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / Methyltransferase-like protein 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.751 Å
AuthorsLuo, Q. / Ma, J.B.
CitationJournal: To Be Published
Title: Structure of RNA m6A methyltransferase METTL4 in complex with DNA at 2.75 Angstroms resolutioon
Authors: Luo, Q. / Ma, J.B.
History
DepositionDec 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*GP*CP*CP*GP*CP*GP*TP*GP*AP*TP*CP*AP*CP*GP*CP*GP*GP*C)-3')
A: Methyltransferase-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2267
Polymers53,4742
Non-polymers7535
Water75742
1
A: Methyltransferase-like protein 2
hetero molecules

A: Methyltransferase-like protein 2
hetero molecules

B: DNA (5'-D(*GP*CP*CP*GP*CP*GP*TP*GP*AP*TP*CP*AP*CP*GP*CP*GP*GP*C)-3')

B: DNA (5'-D(*GP*CP*CP*GP*CP*GP*TP*GP*AP*TP*CP*AP*CP*GP*CP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)108,45314
Polymers106,9474
Non-polymers1,50610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_557-x,y,-z+21
Buried area5640 Å2
ΔGint-15 kcal/mol
Surface area38610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.655, 93.494, 70.885
Angle α, β, γ (deg.)90.000, 107.190, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain DNA (5'-D(*GP*CP*CP*GP*CP*GP*TP*GP*AP*TP*CP*AP*CP*GP*CP*GP*GP*C)-3')


Mass: 5518.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#2: Protein Methyltransferase-like protein 2


Mass: 47955.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g19340, F18O14.6 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8LFA9, Transferases; Transferring one-carbon groups; Methyltransferases
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.68 Å3/Da / Density % sol: 54.16 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium malonate pH5.0 and 12% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 14645 / % possible obs: 99.4 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.032 / Rrim(I) all: 0.081 / Χ2: 0.492 / Net I/σ(I): 5 / Num. measured all: 81664
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.853.80.31714380.7970.1730.3630.30397.2
2.85-2.964.50.28114340.9190.1410.3160.34398.4
2.96-3.150.22114640.9610.1050.2450.37399.5
3.1-3.265.30.14214590.9930.0640.1560.4399.9
3.26-3.465.60.11114580.9930.0490.1220.46499.8
3.46-3.735.60.09814690.9910.0440.1080.49499.4
3.73-4.116.30.08114630.9940.0340.0880.53499.7
4.11-4.76.60.06714740.9960.0270.0720.56499.9
4.7-5.916.20.06314850.9960.0270.0680.54799.8
5.91-306.60.05815010.9980.0240.0630.66100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMACv1.0refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: SAD / Resolution: 2.751→29.324 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 26.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2616 757 5.17 %
Rwork0.2103 --
obs0.213 14631 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 216.66 Å2 / Biso mean: 95.1262 Å2 / Biso min: 29.17 Å2
Refinement stepCycle: final / Resolution: 2.751→29.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 365 50 42 3235
Biso mean--69.19 79.26 -
Num. residues----354
Refinement TLS params.Method: refined / Origin x: -2.775 Å / Origin y: 12.299 Å / Origin z: 83.38 Å
111213212223313233
T0.6174 Å2-0.0351 Å2-0.1624 Å2-0.5701 Å20.0818 Å2--0.5021 Å2
L2.4606 °2-0.5137 °2-0.7657 °2-1.9308 °2-0.2368 °2--2.7843 °2
S0.0009 Å °-0.6409 Å °-0.3038 Å °0.7407 Å °-0.068 Å °-0.8289 Å °0.0282 Å °0.1429 Å °0.1035 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 18
2X-RAY DIFFRACTION1A3 - 411
3X-RAY DIFFRACTION1A501
4X-RAY DIFFRACTION1A502
5X-RAY DIFFRACTION1A503
6X-RAY DIFFRACTION1A504
7X-RAY DIFFRACTION1A505
8X-RAY DIFFRACTION1A601 - 632
9X-RAY DIFFRACTION1B101 - 110

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