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- PDB-7l4h: Crystal structure of the DRM2-CTG DNA complex -

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Basic information

Entry
Database: PDB / ID: 7l4h
TitleCrystal structure of the DRM2-CTG DNA complex
Components
  • DNA (5'-D(*AP*TP*TP*CP*CP*TP*AP*AP*TP*(C49)P*TP*GP*AP*AP*TP*TP*TP*A)-3')
  • DNA (5'-D(*TP*AP*AP*AP*TP*TP*CP*AP*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 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
IODIDE ION / 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: 2.56 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 1.2Nov 20, 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*AP*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*TP*GP*AP*AP*TP*TP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,55613
Polymers51,1683
Non-polymers1,38710
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-38 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.888, 230.379, 54.244
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 40077.000 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*AP*GP*AP*TP*TP*AP*GP*GP*AP*AP*T)-3')


Mass: 5562.654 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*TP*GP*AP*AP*TP*TP*TP*A)-3')


Mass: 5528.659 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)

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Non-polymers , 4 types, 108 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 3.53 Å3/Da / Density % sol: 65.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Potassium iodide,20% w/v Polyethylene glycol 3,350, pH 7.0.
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Jul 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.56→115.19 Å / Num. obs: 23715 / % possible obs: 98.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 50.78 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.089 / Rrim(I) all: 0.188 / Net I/σ(I): 7.3 / Num. measured all: 103577
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
2.56-2.684.41.3731205127290.5920.7231.561.294.3
8.88-115.193.80.05923676240.9960.0360.0721.896.1

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
Cootmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ONJ

4onj


Resolution: 2.56→115.19 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 1996 8.45 %
Rwork0.2086 --
obs0.2119 23629 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.56→115.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2816 733 55 98 3702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093773
X-RAY DIFFRACTIONf_angle_d0.7025269
X-RAY DIFFRACTIONf_dihedral_angle_d22.795753
X-RAY DIFFRACTIONf_chiral_restr0.169567
X-RAY DIFFRACTIONf_plane_restr0.005554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.630.40061240.36791366X-RAY DIFFRACTION88
2.63-2.70.35411420.35231523X-RAY DIFFRACTION99
2.7-2.780.40451410.32821528X-RAY DIFFRACTION99
2.78-2.870.41211430.3171568X-RAY DIFFRACTION100
2.87-2.970.34261430.31161530X-RAY DIFFRACTION99
2.97-3.090.37241400.2891523X-RAY DIFFRACTION99
3.09-3.230.28211430.25531544X-RAY DIFFRACTION98
3.23-3.40.25571450.21961563X-RAY DIFFRACTION99
3.4-3.610.2471430.22321554X-RAY DIFFRACTION99
3.61-3.890.23021450.1971570X-RAY DIFFRACTION99
3.89-4.280.21381400.1621523X-RAY DIFFRACTION97
4.28-4.90.17581460.15091587X-RAY DIFFRACTION99
4.9-6.170.19951470.16271594X-RAY DIFFRACTION98
6.18-115.190.2081540.16251660X-RAY DIFFRACTION97
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)
18.26283.27914.08551.4481.11737.57840.96120.0485-0.67190.7089-0.19670.20210.75140.3547-0.87020.8270.0668-0.00070.28340.01530.503813.299620.3191-5.5354
21.5659-1.36220.11372.82210.16114.0318-0.13370.0893-0.20490.369-0.04410.17150.5638-0.26520.19630.5049-0.00640.00810.34020.04290.324112.782529.54496.1485
33.18780.2617-0.18792.24250.32512.30740.1414-0.399-0.28810.2597-0.1301-0.10780.1131-0.16060.03420.5170.0147-0.02930.36840.03460.35417.947528.10880.2003
41.8034-0.5301-0.79160.50540.07142.7328-0.04310.3036-0.1558-0.059-0.08740.03580.34850.07660.16130.54610.05860.02610.3873-0.00490.363919.199130.5717-19.7685
56.12681.5967-1.13523.56582.10934.3812-0.0361-0.2528-0.8689-0.2366-0.0864-0.49860.64170.94320.22730.63610.27850.00110.85210.13720.56339.5726.8019-27.6557
63.53280.4042-1.81630.0822-0.3692.01840.15990.6280.3464-0.1562-0.1569-0.0308-0.1687-0.3009-0.04140.61730.0348-0.00870.53570.06770.410925.00141.2943-20.1599
77.68013.1207-3.41071.7493-1.1662.47650.18380.2665-0.1051-0.0715-0.0762-0.0255-0.18750.0004-0.17530.45810.08850.01270.37650.00010.389518.441339.8453-8.761
88.73212.19140.95861.97731.07971.6417-0.02880.11850.3388-0.27490.1167-0.0358-0.0743-0.1751-0.09350.49620.0511-0.01360.30570.04360.27510.71147.7816-3.1329
98.7536-2.34123.57153.70060.48166.0665-0.2242-0.62130.46180.5350.02060.072-0.6787-0.16480.29680.604-0.0678-0.00280.3369-0.01580.36212.72452.46497.6333
107.0815-3.1167-0.89442.18260.71510.79980.2171-0.29050.0563-0.0121-0.1406-0.1661-0.09460.1954-0.08760.5217-0.003-0.04470.41920.05620.361426.291837.15723.5896
112.979-3.9457-2.60075.67232.28953.7476-0.4172-1.1867-0.27781.00350.38570.35470.2220.44970.20420.61350.0236-00.55910.05510.32914.860440.034313.8458
125.5259-0.6010.92823.87425.51588.39380.3541-0.22870.120.0602-0.043-0.46350.2107-0.058-0.33060.7383-0.04160.09760.48760.07970.5938.755452.6059-12.7489
135.2543-3.36574.5672.0205-7.74559.69611.27210.38940.0497-2.4604-1.58540.08080.61031.33830.34630.85020.2570.09330.60520.14660.862642.965433.3239-9.8561
142.7307-0.5305-2.10813.30813.24414.08250.2493-0.1572-2.0722-0.6349-1.0915-02.1323-0.47380.55841.06650.0795-0.03790.51630.02280.980931.988316.9177-3.3669
159.5574-3.999-5.82222.84913.36082.0034-0.32290.8346-2.232-1.1539-0.76923.8123-0.22840.29531.07531.60060.1427-0.29740.635-0.08832.107834.78682.5121-8.1923
165.2761-2.9032.17353.80931.3375.36290.4445-0.6304-0.1466-0.6592-0.30680.83133.09890.9442-0.11821.53630.1525-0.01720.75310.39591.744839.37377.7641-2.9509
173.7814.2922-1.10198.1286-5.38445.44410.239-0.1944-0.2842-0.0919-0.4873-0.5999-0.14460.44890.27660.40060.14920.12880.36290.01430.449838.493537.5748-9.9449
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 320 )
3X-RAY DIFFRACTION3chain 'A' and (resid 321 through 353 )
4X-RAY DIFFRACTION4chain 'A' and (resid 354 through 400 )
5X-RAY DIFFRACTION5chain 'A' and (resid 401 through 435 )
6X-RAY DIFFRACTION6chain 'A' and (resid 436 through 470 )
7X-RAY DIFFRACTION7chain 'A' and (resid 471 through 494 )
8X-RAY DIFFRACTION8chain 'A' and (resid 495 through 547 )
9X-RAY DIFFRACTION9chain 'A' and (resid 548 through 575 )
10X-RAY DIFFRACTION10chain 'A' and (resid 576 through 605 )
11X-RAY DIFFRACTION11chain 'A' and (resid 606 through 626 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 5 )
13X-RAY DIFFRACTION13chain 'B' and (resid 6 through 10 )
14X-RAY DIFFRACTION14chain 'B' and (resid 11 through 15 )
15X-RAY DIFFRACTION15chain 'B' and (resid 16 through 18 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 5 )
17X-RAY DIFFRACTION17chain 'C' and (resid 6 through 18 )

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