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- PDB-7l4c: Crystal structure of the DRM2-CTT DNA complex -

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Basic information

Entry
Database: PDB / ID: 7l4c
TitleCrystal structure of the DRM2-CTT DNA complex
Components
  • DNA (5'-D(*AP*TP*TP*AP*TP*TP*AP*AP*TP*(C49)P*TP*TP*AP*AP*TP*TP*TP*A)-3')
  • DNA (5'-D(*TP*AP*AP*AP*TP*TP*AP*AP*GP*AP*TP*TP*AP*AP*TP*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 activity / DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates / DNA (cytosine-5-)-methyltransferase / 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: 2.11 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 18, 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 1.2Nov 6, 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*AP*AP*GP*AP*TP*TP*AP*AP*TP*AP*AP*T)-3')
C: DNA (5'-D(*AP*TP*TP*AP*TP*TP*AP*AP*TP*(C49)P*TP*TP*AP*AP*TP*TP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7715
Polymers51,2943
Non-polymers4772
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-33 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.376, 232.512, 117.789
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1092-

HOH

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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: 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

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DNA chain , 2 types, 2 molecules BC

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


Mass: 5545.667 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#3: DNA chain DNA (5'-D(*AP*TP*TP*AP*TP*TP*AP*AP*TP*(C49)P*TP*TP*AP*AP*TP*TP*TP*A)-3')


Mass: 5542.683 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)

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Non-polymers , 3 types, 381 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 3.6 Å3/Da / Density % sol: 65.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2% v/v Tacsimate TM (pH 6.0), 0.1 M BIS-TRIS (pH 6.5) and 20% w/v Polyethylene glycol 3,350.
PH range: 6.2 - 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9792 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Nov 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. obs: 43203 / % possible obs: 99.2 % / Redundancy: 5.8 % / Biso Wilson estimate: 38.44 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.059 / Rrim(I) all: 0.145 / Net I/σ(I): 10.7
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
2.11-2.175.32.0041826534790.3370.9392.2210.998.1
8.95-48.2950.02132596460.9990.010.02446.899

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
Cootmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ONJ

4onj


Resolution: 2.11→48.29 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2149 1999 4.63 %
Rwork0.1854 41159 -
obs0.1867 43158 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.18 Å2 / Biso mean: 46.5694 Å2 / Biso min: 22.16 Å2
Refinement stepCycle: final / Resolution: 2.11→48.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2809 733 32 379 3953
Biso mean--34.08 47.99 -
Num. residues----389
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.11-2.160.34381400.33682896303698
2.16-2.220.28321400.29752865300599
2.22-2.290.32351390.28852856299598
2.29-2.360.27851400.25972915305599
2.36-2.440.2851420.253529113053100
2.44-2.540.2751410.24792900304199
2.54-2.660.22471410.22552901304299
2.66-2.80.2681420.2122933307599
2.8-2.970.27781430.20312936307999
2.97-3.20.22441430.1952940308399
3.2-3.530.21581440.168429663110100
3.53-4.040.19721440.1529763120100
4.04-5.080.1351470.131530183165100
5.08-48.290.18041530.15593146329999
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)
17.29360.70660.93736.58161.30932.2761-0.0950.12630.664-0.2889-0.1033-0.3979-0.5937-0.17110.33070.36460.0050.00380.29140.05710.5007-19.1135-21.1143-16.3775
26.4631-0.293-0.64912.18970.50212.03930.14980.17710.4474-0.052-0.0201-0.2664-0.24510.2127-0.09760.2261-0.0226-0.01260.20470.01420.2659-10.8805-29.4961-13.82
35.46870.377-2.57810.67120.13492.76550.12540.30640.333-0.0853-0.03560.1853-0.1643-0.5092-0.07790.29770.0157-0.02170.2912-0.00260.3201-33.3647-31.3231-10.3371
49.3015-2.8963-1.81138.5392-1.21398.2071-0.0139-1.15240.3931.0667-0.1530.2819-0.8867-0.22030.20460.5358-0.08820.00250.6033-0.11910.3859-41.1609-27.65169.9886
52.4283-0.6409-1.32770.53680.27362.3846-0.09920.037-0.26830.04120.04850.2340.1844-0.48270.05910.2456-0.0285-0.01330.3006-0.00410.2999-28.988-41.2058-7.3814
62.21240.0512-0.35982.6519-2.90688.0713-0.11640.14-0.3366-0.26290.13530.22020.5515-0.35210.00620.2061-0.01580.00480.2093-0.04220.3165-16.6858-48.4774-18.5785
75.7450.77870.86173.32231.20534.9849-0.05750.0141-0.4248-0.20120.0305-0.37180.26530.3187-0.00230.26690.04020.03340.18990.02260.3344-5.9188-53.0832-16.582
80.3561-0.1546-0.60520.99711.29263.87970.0158-0.1369-0.01510.120.0458-0.06070.1960.3452-0.03770.2717-0.0211-0.02310.31280.04520.3003-9.9956-37.7189-3.2001
98.3275-2.7711-8.55765.41744.78129.5370.2491-0.39110.2422-0.29370.138-0.6085-0.35030.7867-0.39310.219-0.0221-0.00810.2820.00790.38570.2537-40.6651-14.6072
107.78278.7372-0.73152.0905-1.4521.93160.2787-0.65360.45650.873-0.55421.02330.0707-0.00660.26920.4589-0.03780.01240.34730.02910.416-24.8067-43.207811.4513
115.3457-1.5782-0.28782.7157-4.37632.03310.16160.39340.58510.6228-0.22990.3003-1.18150.146-0.11130.5415-0.0123-0.00330.3098-0.06730.464-17.9129-18.86791.3725
127.3034-0.62260.06384.5549-5.81751.980.5206-0.44511.84460.8066-1.44820.2607-1.9632-0.69190.86671.39210.13630.38060.4236-0.09461.2777-25.0948-5.40412.6337
137.1562.5555-0.14876.8467-6.81457.82890.42810.13992.26350.79710.0228-2.5229-0.93281.1402-0.26121.773-0.10890.1360.4331-0.0791.5886-17.836-6.62044.0979
144.55055.2526-0.80847.3294-3.07332.76750.4592-0.4644-0.26871.2835-0.70640.0744-0.47940.25180.25730.4671-0.0260.08880.3405-0.02910.2742-23.4914-37.99629.0234
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 353 )A295 - 353
3X-RAY DIFFRACTION3chain 'A' and (resid 354 through 400 )A354 - 400
4X-RAY DIFFRACTION4chain 'A' and (resid 401 through 435 )A401 - 435
5X-RAY DIFFRACTION5chain 'A' and (resid 436 through 494 )A436 - 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 605 )A576 - 605
9X-RAY DIFFRACTION9chain 'A' and (resid 606 through 626 )A606 - 626
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 10 )B1 - 10
11X-RAY DIFFRACTION11chain 'B' and (resid 11 through 15 )B11 - 15
12X-RAY DIFFRACTION12chain 'B' and (resid 16 through 18 )B16 - 18
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 5 )C1 - 5
14X-RAY DIFFRACTION14chain 'C' and (resid 6 through 18 )C6 - 18

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