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- PDB-7l4n: Crystal structure of the DRM2 (C397R)-CCG DNA complex -

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Basic information

Entry
Database: PDB / ID: 7l4n
TitleCrystal structure of the DRM2 (C397R)-CCG DNA complex
Components
  • DNA (5'-D(*AP*TP*TP*CP*CP*TP*AP*AP*TP*(C49)P*CP*GP*AP*AP*TP*TP*TP*A)-3')
  • DNA (5'-D(*TP*AP*AP*AP*TP*TP*CP*GP*GP*AP*TP*TP*AP*GP*GP*AP*AP*T)-3')
  • DNA (cytosine-5)-methyltransferase DRM2
KeywordsDNA BINDING PROTEIN/DNA / DNA methyltransferase / complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


: / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA methylation-dependent heterochromatin formation / : / defense response to fungus / DNA binding / nucleoplasm / nucleus
Similarity search - Function
SAM-dependent methyltransferase DRM / SAM-dependent methyltransferase DRM-type domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / DNA (cytosine-5)-methyltransferase DRM2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.247 Å
AuthorsFang, J. / Song, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM119721 United States
CitationJournal: Sci Adv / Year: 2021
Title: Substrate deformation regulates DRM2-mediated DNA methylation in plants.
Authors: Fang, J. / Leichter, S.M. / Jiang, J. / Biswal, M. / Lu, J. / Zhang, Z.M. / Ren, W. / Zhai, J. / Cui, Q. / Zhong, X. / Song, J.
History
DepositionDec 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (cytosine-5)-methyltransferase DRM2
B: DNA (5'-D(*TP*AP*AP*AP*TP*TP*CP*GP*GP*AP*TP*TP*AP*GP*GP*AP*AP*T)-3')
C: DNA (5'-D(*AP*TP*TP*CP*CP*TP*AP*AP*TP*(C49)P*CP*GP*AP*AP*TP*TP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2455
Polymers51,7693
Non-polymers4772
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-33 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.292, 231.692, 54.347
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA (cytosine-5)-methyltransferase DRM2 / Protein DOMAINS REARRANGED METHYLASE 2


Mass: 40676.547 Da / Num. of mol.: 1 / Mutation: C397R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DRM2, At5g14620/At5g14630, T15N1.110/T15N1.120 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9M548, DNA (cytosine-5-)-methyltransferase

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*TP*AP*AP*AP*TP*TP*CP*GP*GP*AP*TP*TP*AP*GP*GP*AP*AP*T)-3')


Mass: 5578.653 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#3: DNA chain DNA (5'-D(*AP*TP*TP*CP*CP*TP*AP*AP*TP*(C49)P*CP*GP*AP*AP*TP*TP*TP*A)-3')


Mass: 5513.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)

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Non-polymers , 3 types, 345 molecules

#4: 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
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.6 Å3/Da / Density % sol: 65.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2% v/v Tacsimate(pH 6.0), 0.1 M BIS-TRIS (pH 6.5) and 20% w/v Polyethylene glycol 3,350.
PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.247→50 Å / Num. obs: 35193 / % possible obs: 97.6 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.06 / Rrim(I) all: 0.166 / Χ2: 0.499 / Net I/σ(I): 3.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.336.81.61934820.4430.6431.7540.41698.4
2.33-2.427.11.24235170.5540.4821.3390.42298.9
2.42-2.537.10.91635070.6920.3590.9880.42598.9
2.53-2.677.10.735440.8180.2720.7540.43599
2.67-2.837.50.49835330.9050.1880.5350.44898.6
2.83-3.057.20.31935040.9530.1240.3440.45398
3.05-3.367.40.16935190.9880.0640.1810.48997.7
3.36-3.857.50.10534980.9940.040.1130.57196.8
3.85-4.857.40.06935080.9960.0260.0750.64396
4.85-507.30.05335810.9980.020.0570.67293.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ONJ

4onj


Resolution: 2.247→49.202 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2095 1994 5.68 %
Rwork0.18 33105 -
obs0.1817 35099 97.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.03 Å2 / Biso mean: 47.1145 Å2 / Biso min: 22.79 Å2
Refinement stepCycle: final / Resolution: 2.247→49.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 733 32 343 3918
Biso mean--36.52 49.03 -
Num. residues----388
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.247-2.30340.34191300.3186217391
2.3034-2.36570.30141450.2835239298
2.3657-2.43530.25451400.261233399
2.4353-2.51390.31271450.2429239999
2.5139-2.60370.25251440.2388238999
2.6037-2.7080.27171440.237239299
2.708-2.83120.25651430.2177237199
2.8312-2.98050.25931420.2177236398
2.9805-3.16720.26721440.2012238098
3.1672-3.41170.19591430.169237497
3.4117-3.75490.1871410.1608234697
3.7549-4.29790.18191440.1396237296
4.2979-5.41390.15651440.1347239596
5.4139-49.2020.16111450.1502242693
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)
11.6949-0.184-0.4682.7346-0.06952.41440.13960.0122-0.28130.1786-0.20570.10590.40920.14680.01070.4911-0.02710.00040.30260.03330.398312.012621.1697-6.037
20.30610.03610.13591.3581-0.55461.0588-0.03040.02220.0330.1714-0.03010.05260.3204-0.07230.07780.3668-0.0091-0.01160.29050.00610.293313.784730.61416.2627
30.9399-0.0401-0.5470.19310.0511.89640.00220.0384-0.0609-0.0782-0.0209-0.0010.15340.03670.00010.30860.0310.00890.28690.01640.274318.649230.1068-11.461
41.66910.14-0.8861.57080.62992.6842-0.05080.1257-0.308-0.12590.0381-0.37140.50210.664-0.01820.43870.12620.03830.64350.06580.48139.604426.823-28.2361
50.8958-0.2597-0.01810.49120.39091.38090.00030.1110.1167-0.07670.0181-0.0226-0.13530.0697-0.01940.31690.00910.00580.27550.02530.271717.009344.3735-9.6989
61.2378-1.0169-0.3882.00260.22181.5125-0.1221-0.20620.07210.20960.0532-0.03860.07510.09320.03370.2689-0.0192-0.01110.2988-0.00120.274518.012144.10088.0909
73.9350.75490.80141.701-0.58592.4453-0.0357-0.348-0.41340.0805-0.1898-0.40450.02380.04680.10660.4385-0.0490.05910.4450.06090.474338.940852.886-12.6006
82.2568-0.4434-0.55013.0051-1.00243.58820.42280.0072-0.4665-1.2136-0.7757-0.1230.73050.38840.16170.61350.16430.00790.41840.02530.57737.247625.2816-6.7186
92.3841.4459-2.22735.97682.23048.5734-0.73180.2037-0.7421-0.2996-1.07810.40660.41940.56480.66671.4910.2174-0.29350.6857-0.07371.705934.11932.8986-8.9207
103.77070.2561-0.40683.26720.02730.72230.8626-0.6408-0.30720.9746-1.092-0.29970.2951.2131-0.07911.18830.1023-0.11830.63420.28211.49838.98297.7261-3.4764
111.27070.7171-0.05232.7138-2.14051.75560.215-0.152-0.2134-0.1143-0.5094-0.7153-0.18260.39120.22430.35020.0390.06510.44250.10330.465438.597237.7877-9.8214
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 276 through 295 )A276 - 295
2X-RAY DIFFRACTION2chain 'A' and (resid 296 through 320 )A296 - 320
3X-RAY DIFFRACTION3chain 'A' and (resid 321 through 400 )A321 - 400
4X-RAY DIFFRACTION4chain 'A' and (resid 401 through 434 )A401 - 434
5X-RAY DIFFRACTION5chain 'A' and (resid 435 through 547 )A435 - 547
6X-RAY DIFFRACTION6chain 'A' and (resid 548 through 626 )A548 - 626
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 5 )B1 - 5
8X-RAY DIFFRACTION8chain 'B' and (resid 6 through 15 )B6 - 15
9X-RAY DIFFRACTION9chain 'B' and (resid 16 through 18 )B16 - 18
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 5 )C1 - 5
11X-RAY DIFFRACTION11chain 'C' and (resid 6 through 18 )C6 - 18

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