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- PDB-7cv9: RNA methyltransferase METTL4 -

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Basic information

Entry
Database: PDB / ID: 7cv9
TitleRNA methyltransferase METTL4
ComponentsMethyltransferase-like protein 2
KeywordsNUCLEAR PROTEIN / RNA methyltransferase
Function / homology
Function and homology information


nucleic acid metabolic process / 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
S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase-like protein 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.455 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,9557
Polymers95,9102
Non-polymers1,0455
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-15 kcal/mol
Surface area31680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.603, 93.545, 96.612
Angle α, β, γ (deg.)90.000, 104.780, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 or (resid 3 and (name...
21(chain C and (resid 2 through 39 or (resid 40...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 or (resid 3 and (name...A2
121(chain A and (resid 2 or (resid 3 and (name...A3
131(chain A and (resid 2 or (resid 3 and (name...A2 - 414
141(chain A and (resid 2 or (resid 3 and (name...A2 - 414
151(chain A and (resid 2 or (resid 3 and (name...A2 - 414
161(chain A and (resid 2 or (resid 3 and (name...A2 - 414
171(chain A and (resid 2 or (resid 3 and (name...A2 - 414
211(chain C and (resid 2 through 39 or (resid 40...C2 - 39
221(chain C and (resid 2 through 39 or (resid 40...C40
231(chain C and (resid 2 through 39 or (resid 40...C2 - 414
241(chain C and (resid 2 through 39 or (resid 40...C2 - 414
251(chain C and (resid 2 through 39 or (resid 40...C2 - 414
261(chain C and (resid 2 through 39 or (resid 40...C2 - 414

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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-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.9 Å3/Da / Density % sol: 57.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1600 mM Magnesium sulfate 100 mM MES/ Sodium hydroxide pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / 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: 2.45→30.03 Å / Num. obs: 39010 / % possible obs: 97.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 41.51 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.046 / Rrim(I) all: 0.114 / Χ2: 1.241 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.5440.39235360.8390.1980.4420.8288.6
2.54-2.644.20.36137910.8850.1790.4050.85895.8
2.64-2.764.50.30838610.9280.1520.3440.87196.8
2.76-2.94.80.25939150.950.1250.2890.93598.5
2.9-3.095.40.21839000.9760.0990.240.99398.9
3.09-3.325.70.15839770.9860.070.1731.05299
3.32-3.665.60.12339470.990.0550.1351.14999.4
3.66-4.196.20.0940090.9950.0380.0981.36399.6
4.19-5.276.40.06939990.9960.0290.0741.20299.7
5.27-306.50.07440750.9910.0310.082.42499.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: SAD / Resolution: 2.455→30 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 29.54 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2541 1992 5.11 %
Rwork0.2111 36980 -
obs0.2133 38972 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.75 Å2 / Biso mean: 55.6137 Å2 / Biso min: 24.03 Å2
Refinement stepCycle: final / Resolution: 2.455→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5639 0 96 22 5757
Biso mean--42.36 43.15 -
Num. residues----707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055905
X-RAY DIFFRACTIONf_angle_d0.9748031
X-RAY DIFFRACTIONf_chiral_restr0.054871
X-RAY DIFFRACTIONf_plane_restr0.0061017
X-RAY DIFFRACTIONf_dihedral_angle_d9.2473448
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2930X-RAY DIFFRACTION11.694TORSIONAL
12C2930X-RAY DIFFRACTION11.694TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4554-2.51680.38051110.3245224583
2.5168-2.58480.37071500.3164251993
2.5848-2.66080.30361470.2998261597
2.6608-2.74660.30181400.2738263097
2.7466-2.84470.31891570.2699258797
2.8447-2.95850.32871690.2654264399
2.9585-3.0930.30911230.2479270199
3.093-3.25590.26331450.2263268699
3.2559-3.45970.27241440.2275270399
3.4597-3.72630.24771420.2059271299
3.7263-4.10050.22991510.18262673100
4.1005-4.69190.20041380.15992735100
4.6919-5.90390.18791410.16882740100
5.9039-300.23181340.1882791100
Refinement TLS params.Method: refined / Origin x: -15.5653 Å / Origin y: 31.0272 Å / Origin z: 16.857 Å
111213212223313233
T0.2782 Å2-0.0193 Å20.0656 Å2-0.2791 Å20.0342 Å2--0.2947 Å2
L0.4631 °2-0.0365 °20.4248 °2-1.8735 °20.591 °2--2.0923 °2
S0.0242 Å °-0.019 Å °0.0028 Å °0.1158 Å °-0.0494 Å °0.1079 Å °-0.0924 Å °0.036 Å °0.0242 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allC2 - 414
2X-RAY DIFFRACTION1allA2 - 414
3X-RAY DIFFRACTION1allS501
4X-RAY DIFFRACTION1allH502
5X-RAY DIFFRACTION1allB1 - 25
6X-RAY DIFFRACTION1allD1 - 3

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