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- PDB-8t1u: Crystal structure of the DRM2-CTA DNA complex -

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Basic information

Entry
Database: PDB / ID: 8t1u
TitleCrystal structure of the DRM2-CTA DNA complex
Components
  • DNA (5'-D(P*AP*TP*TP*AP*TP*TP*AP*AP*TP*(C49)P*TP*AP*AP*AP*TP*TP*TP*A)-3')
  • DNA (5'-D(P*TP*AP*AP*AP*TP*TP*TP*AP*GP*AP*TP*TP*AP*AP*TP*AP*AP*T)-3')
  • DNA (cytosine-5)-methyltransferase DRM2
KeywordsTRANSFERASE/DNA / plant DNA methyltransferase / TRANSFERASE / TRANSFERASE-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 / 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: 2.91 Å
AuthorsChen, J. / Lu, J. / Song, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: DNA conformational dynamics in the context-dependent non-CG CHH methylation by plant methyltransferase DRM2.
Authors: Chen, J. / Lu, J. / Liu, J. / Fang, J. / Zhong, X. / Song, J.
History
DepositionJun 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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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
E: DNA (5'-D(P*TP*AP*AP*AP*TP*TP*TP*AP*GP*AP*TP*TP*AP*AP*TP*AP*AP*T)-3')
G: DNA (5'-D(P*AP*TP*TP*AP*TP*TP*AP*AP*TP*(C49)P*TP*AP*AP*AP*TP*TP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6794
Polymers51,2943
Non-polymers3841
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-27 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.469, 232.853, 118.497
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-841-

HOH

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Components

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


Mass: 40206.113 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
#2: DNA chain DNA (5'-D(P*TP*AP*AP*AP*TP*TP*TP*AP*GP*AP*TP*TP*AP*AP*TP*AP*AP*T)-3')


Mass: 5536.652 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#3: DNA chain DNA (5'-D(P*AP*TP*TP*AP*TP*TP*AP*AP*TP*(C49)P*TP*AP*AP*AP*TP*TP*TP*A)-3')


Mass: 5551.696 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.66 Å3/Da / Density % sol: 66.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium citrate tribasic and 20% w/v polyethylene glycol 3350 (pH 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: 0.97741 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 16195 / % possible obs: 95.3 % / Redundancy: 3 % / CC1/2: 0.888 / CC star: 0.97 / Rmerge(I) obs: 0.26 / Rpim(I) all: 0.177 / Rrim(I) all: 0.316 / Χ2: 0.717 / Net I/σ(I): 2.7 / Num. measured all: 48468
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.9-32.60.80415100.5450.840.5680.990.6690.3
3-3.122.90.71415440.5070.820.4950.8740.66493.3
3.12-3.273.10.41516220.8580.9610.2770.5020.64797.5
3.27-3.443.20.38716550.8180.9490.2580.4680.67698.2
3.44-3.653.10.29116450.8640.9630.1950.3520.66497.8
3.65-3.9430.25416450.9080.9760.1720.3080.69197.2
3.94-4.332.80.17416180.9410.9850.1250.2150.7596.3
4.33-4.9630.15916340.9530.9880.1080.1940.7295.2
4.96-6.243.20.1816360.9530.9880.1190.2170.71695.2
6.24-502.90.116860.9840.9960.0680.1220.97792

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→48.41 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2533 1616 10 %
Rwork0.2061 --
obs0.2109 16153 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.91→48.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2799 740 26 88 3653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043830
X-RAY DIFFRACTIONf_angle_d0.7375380
X-RAY DIFFRACTIONf_dihedral_angle_d28.096792
X-RAY DIFFRACTIONf_chiral_restr0.045586
X-RAY DIFFRACTIONf_plane_restr0.005552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-30.38661210.32221094X-RAY DIFFRACTION88
3-3.10.36611270.28741143X-RAY DIFFRACTION91
3.1-3.210.3031350.28581213X-RAY DIFFRACTION96
3.21-3.330.28251360.22631218X-RAY DIFFRACTION99
3.33-3.490.25221370.22371228X-RAY DIFFRACTION98
3.49-3.670.2521380.20451240X-RAY DIFFRACTION98
3.67-3.90.26891370.211241X-RAY DIFFRACTION98
3.9-4.20.241370.17731222X-RAY DIFFRACTION96
4.2-4.620.23361330.1661206X-RAY DIFFRACTION95
4.62-5.290.20231370.16641229X-RAY DIFFRACTION96
5.29-6.660.2211370.18581238X-RAY DIFFRACTION95
6.66-48.410.19061410.16521265X-RAY DIFFRACTION92
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)
11.7105-1.4255-0.16222.8861.02232.5939-0.1984-0.32610.18860.25690.4695-0.7940.50870.09980.04220.1985-0.0032-0.07230.1406-0.04270.28718.278721.141416.4262
21.9375-0.11710.21030.76080.06451.53640.2094-0.1773-0.46850.053-0.0416-0.12140.00750.0719-0.04280.15030.08560.06650.09730.02110.269111.53930.386515.6465
33.6151-1.12811.06181.7890.61262.1868-0.30090.19280.13870.3530.11350.3866-0.0088-0.13680.15320.14620.0197-0.04820.1965-0.01970.2199-11.074630.96422.1062
45.2623-0.7725-0.39791.5113-1.712.26090.0990.8908-0.8922-0.9446-0.43530.31020.70150.0336-0.02080.53650.1464-0.13220.788-0.16130.2406-13.653127.6859-9.8084
51.78850.75090.67192.35041.19012.8174-0.06130.05970.4639-0.1399-0.06150.2718-0.2164-0.45710.14110.1871-0.0170.07150.3001-0.02020.2785-6.697341.93024.3156
61.31970.28450.49321.6169-0.5492.4154-0.0433-0.03710.2250.12910.02740.2618-0.3821-0.29680.03850.15690.0355-0.00810.1374-0.02570.13878.680145.929716.5657
70.9618-0.0010.57112.27550.82912.31540.02410.0318-0.00490.00860.0956-0.2213-0.03520.5421-0.06370.1035-0.00520.04430.2106-0.00040.17221.662444.500211.6299
84.0521-1.7907-0.3183.66180.9488.76370.0270.12121.01620.0376-0.2955-0.3674-0.60710.48550.14670.5010.0122-0.18690.24090.01020.65181.229953.6028-9.5381
91.76181.46110.64262.28911.07642.4811-0.1840.11030.4151-0.3809-0.45190.77060.0016-0.31230.10020.59950.1013-0.18150.3908-0.18150.39342.962735.7884-13.8905
102.5625-0.0349-1.64850.03120.28412.78710.396-0.188-1.341-0.4532-0.17190.40491.0327-0.098-0.02470.572-0.003-0.19780.2598-0.03190.58866.563313.8808-1.5747
113.15240.6902-0.62848.6663-2.78531.50390.05450.106-1.36860.1087-0.0427-1.01341.32730.29610.05791.4107-0.1085-0.10860.2347-0.33561.41959.73456.6247-3.7594
122.0667-1.1538-0.07333.6491-1.5872.4830.29110.2262-0.0777-0.7352-0.26050.0450.22160.21430.06360.34240.0789-0.04420.26750.00860.28314.204838.2507-8.9126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 275 through 294 )
2X-RAY DIFFRACTION2chain 'A' and (resid 295 through 375 )
3X-RAY DIFFRACTION3chain 'A' and (resid 376 through 400 )
4X-RAY DIFFRACTION4chain 'A' and (resid 401 through 435 )
5X-RAY DIFFRACTION5chain 'A' and (resid 436 through 470 )
6X-RAY DIFFRACTION6chain 'A' and (resid 471 through 547 )
7X-RAY DIFFRACTION7chain 'A' and (resid 548 through 626 )
8X-RAY DIFFRACTION8chain 'E' and (resid 1 through 5 )
9X-RAY DIFFRACTION9chain 'E' and (resid 6 through 10 )
10X-RAY DIFFRACTION10chain 'E' and (resid 11 through 18 )
11X-RAY DIFFRACTION11chain 'G' and (resid 1 through 5 )
12X-RAY DIFFRACTION12chain 'G' and (resid 6 through 18 )

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