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- PDB-7cv7: RNA methyltransferase METTL4 -

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Basic information

Entry
Database: PDB / ID: 7cv7
TitleRNA methyltransferase METTL4
ComponentsMethyltransferase-like protein 2
KeywordsNUCLEAR PROTEIN / RNA methyltransferase
Function / homology
Function and homology information


RNA methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) activity / nucleic acid metabolic process / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / nucleic acid binding / nucleus / cytosol
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-ADENOSYLMETHIONINE / Methyltransferase-like protein 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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 1.2May 29, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase-like protein 2
B: Methyltransferase-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7074
Polymers95,9102
Non-polymers7972
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-15 kcal/mol
Surface area31560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.931, 93.719, 96.365
Angle α, β, γ (deg.)90.000, 104.380, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 18 or (resid 19...
21(chain B and (resid 2 through 29 or (resid 30...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALASERSER(chain A and (resid 2 through 18 or (resid 19...AA2 - 182 - 18
12ASPASPASPASP(chain A and (resid 2 through 18 or (resid 19...AA1919
13ALAALAVALVAL(chain A and (resid 2 through 18 or (resid 19...AA2 - 4142 - 414
14ALAALAVALVAL(chain A and (resid 2 through 18 or (resid 19...AA2 - 4142 - 414
15ALAALAVALVAL(chain A and (resid 2 through 18 or (resid 19...AA2 - 4142 - 414
16ALAALAVALVAL(chain A and (resid 2 through 18 or (resid 19...AA2 - 4142 - 414
21ALAALAVALVAL(chain B and (resid 2 through 29 or (resid 30...BB2 - 292 - 29
22ARGARGARGARG(chain B and (resid 2 through 29 or (resid 30...BB3030
23ALAALALYSLYS(chain B and (resid 2 through 29 or (resid 30...BB2 - 4132 - 413
24ALAALALYSLYS(chain B and (resid 2 through 29 or (resid 30...BB2 - 4132 - 413
25ALAALALYSLYS(chain B and (resid 2 through 29 or (resid 30...BB2 - 4132 - 413
26ALAALALYSLYS(chain B and (resid 2 through 29 or (resid 30...BB2 - 4132 - 413

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Components

#1: Protein Methyltransferase-like protein 2


Mass: 47955.102 Da / Num. of mol.: 2
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-SAM / S-ADENOSYLMETHIONINE


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


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3.31 Å3/Da / Density % sol: 62.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium malonate pH 5.5 and 6% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97916 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 46526 / % possible obs: 98.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.039 / Rrim(I) all: 0.074 / Χ2: 1.619 / Net I/σ(I): 11.5 / Num. measured all: 159846
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.383.10.59742780.740.3820.7111.13591.1
2.38-2.483.20.49545040.8350.3160.5891.13195
2.48-2.593.20.39346400.8930.2490.4671.17398.4
2.59-2.733.30.29746690.940.1860.3511.24699.4
2.73-2.93.40.19646870.9740.1220.2311.29499.4
2.9-3.123.50.12747480.990.0780.1491.40199.4
3.12-3.433.60.07747190.9960.0460.091.53299.8
3.43-3.933.70.05547160.9970.0330.0642.0399.9
3.93-4.953.60.04147490.9980.0250.0482.54899.7
4.95-303.70.03948160.9970.0240.0462.28799.2

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Processing

Software
NameVersionClassification
REFMAC7.0.076refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→29.625 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 34.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2509 2380 5.12 %
Rwork0.22 --
obs0.2216 46473 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.06 Å2 / Biso mean: 72.4227 Å2 / Biso min: 32.54 Å2
Refinement stepCycle: final / Resolution: 2.3→29.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5509 0 54 57 5620
Biso mean--58.98 60.44 -
Num. residues----703
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2854X-RAY DIFFRACTION9.343TORSIONAL
12B2854X-RAY DIFFRACTION9.343TORSIONAL
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.57230.82230.17034.08730.40573.0964-0.00520.0043-0.0127-0.0418-0.16520.0789-0.0198-0.03040.13570.660.07440.06680.42480.01080.3964-17.5027-4.4092-32.7105
22.21711.15280.27574.56190.5293.08980.1208-0.13660.01040.5817-0.14810.10930.3722-0.1120.04280.3052-0.0017-0.01650.36350.02630.4246-13.9413-27.8697-1.0578
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 2:414)A2 - 414
2X-RAY DIFFRACTION2(chain B and resseq 2:413)B2 - 413

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