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- PDB-7cv6: RNA methyltransferase METTL4 -

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Basic information

Entry
Database: PDB / ID: 7cv6
TitleRNA methyltransferase METTL4
ComponentsMethyltransferase-like protein 2
KeywordsNUCLEAR PROTEIN / RNA methyltransferase
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / nucleic acid binding
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
2'-O-methyladenosine 5'-(dihydrogen phosphate) / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase-like protein 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsLuo, Q. / Ma, J.
CitationJournal: Nat Commun / Year: 2022
Title: Structural insights into molecular mechanism for N6-adenosine methylation by MT-A70 family methyltransferase METTL4
Authors: Luo, Q. / Mo, J. / Chen, H. / Hu, Z. / Wang, B. / Wu, J. / Liang, Z. / Xie, W. / Du, K. / Peng, M. / Li, Y. / Li, T. / Zhang, Y. / Shi, X. / Shen, W.H. / Shi, Y. / Dong, A. / Wang, H. / Ma, J.
History
DepositionAug 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 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: Methyltransferase-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0624
Polymers47,9551
Non-polymers1,1073
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint1 kcal/mol
Surface area16680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.821, 130.022, 141.322
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: 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) / Strain (production host): BL21(DE3)
References: UniProt: Q8LFA9, Transferases; Transferring one-carbon groups; Methyltransferases
#2: 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
#3: Chemical ChemComp-A2M / 2'-O-methyladenosine 5'-(dihydrogen phosphate)


Type: RNA linking / Mass: 361.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N5O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 4.49 Å3/Da / Density % sol: 72.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.49 M NaH2PO4 and 0.91 M K2HPO4,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 14468 / % possible obs: 82.5 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.049 / Rrim(I) all: 0.132 / Χ2: 1.017 / Net I/σ(I): 6.3 / Num. measured all: 83220
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.112.40.49380.0080.2610.4820.854.7
3.11-3.232.80.410720.1160.2460.4740.82661.2
3.23-3.383.20.39912850.2890.2290.4640.82175.1
3.38-3.563.40.38314720.4170.2120.4410.87684.2
3.56-3.784.50.33615800.7860.1640.3760.93291.5
3.78-4.074.70.26516090.8910.1240.2950.91592.3
4.07-4.486.50.21915890.9550.0850.2361.11590.9
4.48-5.127.70.12515170.9920.0440.1330.9986.5
5.12-6.448.30.14217020.990.0490.1510.95495.4
6.44-3010.70.04917040.9990.0150.0511.19891.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IL2

5il2


Resolution: 3.01→30 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.862 / SU B: 23.18 / SU ML: 0.401 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.552 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3001 515 4.5 %RANDOM
Rwork0.2404 ---
obs0.2431 10914 64.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 233.08 Å2 / Biso mean: 92.298 Å2 / Biso min: 11.19 Å2
Baniso -1Baniso -2Baniso -3
1--3.38 Å2-0 Å20 Å2
2---2.59 Å2-0 Å2
3---5.97 Å2
Refinement stepCycle: final / Resolution: 3.01→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2865 0 74 19 2958
Biso mean--139.2 40.35 -
Num. residues----347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193039
X-RAY DIFFRACTIONr_bond_other_d0.0020.022739
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.9824125
X-RAY DIFFRACTIONr_angle_other_deg1.01936353
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0495344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84223.649148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.27715502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6721517
X-RAY DIFFRACTIONr_chiral_restr0.0820.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213284
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02669
LS refinement shellResolution: 3.01→3.083 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.349 12 -
Rwork0.347 178 -
obs--14.84 %

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