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- PDB-7l4k: Crystal structure of the DRM2-CCG DNA complex -

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Basic information

Entry
Database: PDB / ID: 7l4k
TitleCrystal structure of the DRM2-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 constitutive heterochromatin formation / defense response to fungus / methylation / 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: 2.61 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
Revision 1.2Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_entry_details.has_protein_modification

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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)52,2836
Polymers51,7153
Non-polymers5693
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-33 kcal/mol
Surface area20190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.968, 231.582, 54.344
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: 40622.496 Da / Num. of mol.: 1
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, 60 molecules

#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.59 Å3/Da / Density % sol: 65.72 %
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: 5.0.2 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.61→49.2 Å / Num. obs: 23003 / % possible obs: 99.5 % / Redundancy: 5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.091 / Rrim(I) all: 0.212 / Net I/σ(I): 7.6 / Num. measured all: 115890 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.61-2.734.31.6391182727530.4090.8591.860.899.3
9.04-49.24.60.03527435960.9980.0170.0429.795.8

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ONJ

4onj


Resolution: 2.61→41.318 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2403 1995 8.69 %
Rwork0.2132 20961 -
obs0.2156 22956 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.49 Å2 / Biso mean: 58.6855 Å2 / Biso min: 24.65 Å2
Refinement stepCycle: final / Resolution: 2.61→41.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2816 733 38 57 3644
Biso mean--52.54 49.42 -
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 (%)
2.61-2.67530.35661360.3594142898
2.6753-2.74760.38651420.3382149299
2.7476-2.82840.36411410.32131487100
2.8284-2.91970.34431410.3071470100
2.9197-3.0240.36681430.31381517100
3.024-3.1450.30071390.29091453100
3.145-3.28810.27711410.2577148499
3.2881-3.46140.26131430.2372150599
3.4614-3.67810.27481420.2214148699
3.6781-3.96190.23031430.2018150299
3.9619-4.36020.18611440.1637150199
4.3602-4.99020.18741440.155153099
4.9902-6.28360.20031460.1771152199
6.2836-41.3180.16391500.1555158596
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)
18.04690.61021.19033.7281.3984.7860.68110.3484-0.74870.2378-0.2337-0.15280.7031-0.0189-0.34150.57850.05520.01250.30640.00710.452713.294220.679-5.5568
21.55460.0291-0.51210.89550.12191.86290.005-0.0156-0.16270.0545-0.05-0.04550.26620.0260.05580.37170.057-0.01390.31710.04380.362717.336529.8752-7.3286
33.48480.7504-0.50514.31861.00583.532-0.0187-0.198-0.5849-0.2859-0.0587-0.64390.40910.81510.12990.52360.15520.02040.75130.09390.644439.751327.0923-27.6484
41.4776-0.1779-0.55050.53140.52380.74030.1450.36490.0645-0.2821-0.1738-0.1249-0.41980.07290.0150.48390.04020.01520.51230.03760.400825.216941.6135-20.1426
52.65540.6297-1.73220.7906-0.09131.6524-0.14650.1648-0.1024-0.16350.0464-0.08720.11640.06420.01980.3880.068-0.00050.3751-0.03120.403118.003739.785-8.7055
63.64791.1602-0.03751.35550.04711.21810.02340.11660.4429-0.16860.0550.1449-0.1645-0.1138-0.0440.35780.03740.01610.32260.04380.308310.856748.1643-3.1146
73.5296-1.00011.05872.4303-0.15063.8346-0.0267-0.21750.13380.25590.02870.038-0.55640.09030.09460.3669-0.0644-0.01240.3518-0.01450.340612.890552.77897.6673
82.7082-1.4599-0.2171.98470.9910.9814-0.0914-0.5401-0.11890.33110.0596-0.04470.10750.09880.06230.4477-0.0003-0.04160.42250.07260.348621.133538.74998.3359
94.44981.94662.16474.22440.45653.52710.3676-0.39590.14660.546-0.2306-0.7289-0.63160.5509-0.14540.4966-0.15240.05570.55210.0310.646939.007152.8592-12.6061
102.8155-2.0054-0.25183.21040.07872.36540.17360.2561-0.863-1.5507-0.58940.06461.14170.00030.45320.96950.1886-0.01680.6107-0.00810.918536.833420.1271-7.0064
114.6704-0.5228-0.02754.52270.16150.99390.2799-0.6604-0.52740.3757-0.75970.12230.69091.21460.41871.36150.1148-0.04230.79890.33591.641639.24857.8706-2.9443
122.17771.72350.7765.07730.31743.3009-0.4764-0.0604-0.4498-0.11720.4513-0.01620.45870.69790.03350.57130.1370.05620.43980.13860.536431.733926.312-9.2778
130.42460.5485-0.36794.931-4.7654.67530.2934-0.3450.08430.5088-1.3149-0.99020.17351.45091.04740.5401-0.0721-0.02630.65570.20560.704144.54247.4498-10.4419
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 275 through 294 )A275 - 294
2X-RAY DIFFRACTION2chain 'A' and (resid 295 through 400 )A295 - 400
3X-RAY DIFFRACTION3chain 'A' and (resid 401 through 435 )A401 - 435
4X-RAY DIFFRACTION4chain 'A' and (resid 436 through 470 )A436 - 470
5X-RAY DIFFRACTION5chain 'A' and (resid 471 through 494 )A471 - 494
6X-RAY DIFFRACTION6chain 'A' and (resid 495 through 547 )A495 - 547
7X-RAY DIFFRACTION7chain 'A' and (resid 548 through 575 )A548 - 575
8X-RAY DIFFRACTION8chain 'A' and (resid 576 through 626 )A576 - 626
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 5 )B1 - 5
10X-RAY DIFFRACTION10chain 'B' and (resid 6 through 18 )B6 - 18
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 5 )C1 - 5
12X-RAY DIFFRACTION12chain 'C' and (resid 6 through 11 )C6 - 11
13X-RAY DIFFRACTION13chain 'C' and (resid 12 through 18 )C12 - 18

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