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- PDB-7l4m: Crystal structure of the DRM2-CCT DNA complex -

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Basic information

Entry
Database: PDB / ID: 7l4m
TitleCrystal structure of the DRM2-CCT DNA complex
Components
  • DNA (5'-D(*TP*AP*AP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*AP*T)-3')
  • DNA (5'-D(P*AP*TP*TP*CP*CP*TP*CP*CP*TP*(C49)P*CP*TP*CP*CP*TP*TP*TP*A)-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 / THYMIDINE-5'-PHOSPHATE / DNA / DNA (> 10) / DNA (cytosine-5)-methyltransferase DRM2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.805 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 23, 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
Revision 2.0Feb 12, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)104,5279
Polymers103,4366
Non-polymers1,0913
Water21612
1
B: DNA (cytosine-5)-methyltransferase DRM2
C: DNA (5'-D(*TP*AP*AP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*AP*T)-3')
D: DNA (5'-D(P*AP*TP*TP*CP*CP*TP*CP*CP*TP*(C49)P*CP*TP*CP*CP*TP*TP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1024
Polymers51,7183
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-40 kcal/mol
Surface area20130 Å2
MethodPISA
2
A: DNA (cytosine-5)-methyltransferase DRM2
E: DNA (5'-D(*TP*AP*AP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*AP*T)-3')
G: DNA (5'-D(P*AP*TP*TP*CP*CP*TP*CP*CP*TP*(C49)P*CP*TP*CP*CP*TP*TP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4245
Polymers51,7183
Non-polymers7072
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-34 kcal/mol
Surface area20220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.924, 70.981, 104.087
Angle α, β, γ (deg.)90.000, 97.900, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules BA

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


Mass: 40622.496 Da / Num. of mol.: 2
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, 4 molecules CEDG

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


Mass: 5702.729 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#3: DNA chain DNA (5'-D(P*AP*TP*TP*CP*CP*TP*CP*CP*TP*(C49)P*CP*TP*CP*CP*TP*TP*TP*A)-3')


Mass: 5392.535 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)

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Non-polymers , 3 types, 15 molecules

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


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.04 Å3/Da / Density % sol: 59.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Sodium formate pH 7.0, 12% w/v Polyethylene glycol 3,350.
PH range: 6.5-7.5

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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: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 30526 / % possible obs: 99.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 67.78 Å2 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.058 / Rrim(I) all: 0.114 / Χ2: 0.638 / Net I/σ(I): 7.1 / Num. measured all: 108188
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.93.30.99829430.5540.6111.1740.47696.5
2.9-3.023.40.7230070.7020.440.8460.46799.1
3.02-3.153.30.43930260.9050.2760.5210.4999.8
3.15-3.323.50.22230690.9910.1370.2610.57799.6
3.32-3.533.80.17830230.990.1040.2060.61799.9
3.53-3.83.70.13130710.9870.0770.1520.71199.9
3.8-4.183.60.09230640.9910.0560.1080.73499.9
4.18-4.793.70.07130650.9940.0420.0830.826100
4.79-6.033.60.06530860.9950.0380.0760.769100
6.03-503.60.04931720.9950.0290.0570.63399.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ONJ

4onj


Resolution: 2.805→47.056 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.263 1997 6.56 %
Rwork0.2135 28437 -
obs0.2168 30434 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 330.86 Å2 / Biso mean: 105.8656 Å2 / Biso min: 32.69 Å2
Refinement stepCycle: final / Resolution: 2.805→47.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5399 1429 72 12 6912
Biso mean--102.42 61.17 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047232
X-RAY DIFFRACTIONf_angle_d0.62910148
X-RAY DIFFRACTIONf_chiral_restr0.0271122
X-RAY DIFFRACTIONf_plane_restr0.0031067
X-RAY DIFFRACTIONf_dihedral_angle_d20.3752699
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.805-2.8750.33751330.3247189493
2.875-2.95270.33741400.3213200498
2.9527-3.03960.37211420.3235202399
3.0396-3.13770.35771430.30172025100
3.1377-3.24980.32481410.2633200198
3.2498-3.37990.30821430.2473202299
3.3799-3.53360.29131410.2447200599
3.5336-3.71990.29661450.22892078100
3.7199-3.95280.24221420.21612017100
3.9528-4.25780.25461440.19842042100
4.2578-4.6860.25321440.17282060100
4.686-5.36320.26231430.1772055100
5.3632-6.75390.25091480.20542086100
6.7539-47.0560.1921480.1748212599
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)
13.67320.6749-0.76725.8081-2.25514.46110.1521-0.3518-0.05091.1811-0.19651.0348-0.5734-0.40610.11370.6846-0.07250.20450.4923-0.08660.5221196.7164.19531.413
21.20021.02560.77136.02671.46641.72930.0921-0.0105-0.02380.122-0.14360.91330.3003-0.19890.09390.4181-0.07940.09850.3958-0.00530.5248195.06-9.26420.722
31.49470.06630.77275.10431.56042.27380.21610.0891-0.31260.1208-0.08450.39640.41910.0575-0.15790.4849-0.04210.04150.32480.03160.5599196.989-15.62812.853
42.877-0.99840.66824.4995-0.09382.701-0.14330.28940.4797-0.2913-0.00920.1465-0.70260.46420.18440.6344-0.17530.06950.41550.05270.4153204.14210.7213.981
54.74090.9878-1.23070.978-0.29935.40751.0751-0.10890.35660.06021.18490.6803-0.0394-0.1325-1.81771.76850.19720.3580.87620.01120.6824214.575-18.4398.244
67.69610.7167-3.09945.1854-2.93014.84450.0227-1.97020.26162.99590.47040.62051.7308-0.2127-0.38621.8189-0.19940.63091.01660.1130.7057203.112-17.95138.37
75.0272-1.178-0.90356.2632-0.63326.16160.2597-1.5575-0.05220.90540.14960.42732.18721.4282-0.48851.3742-0.09750.26181.14390.02920.5499204.441-20.48638.44
85.4443-1.1091-0.63752.09085.78343.34850.21730.0919-0.1048-0.93981.19740.21560.48321.6765-1.22821.05610.08370.09790.7335-0.1440.5214217.426-17.8037.482
93.40771.34060.45491.44770.74620.6253-0.63480.54960.7534-0.82110.3541-0.2169-1.93411.94240.05921.2407-0.8961-0.03871.65070.11690.7271232.30621.93824.464
104.17160.42010.66831.20882.02032.2945-0.74730.1713-0.1777-0.21810.7537-0.4554-0.21872.2361-0.09520.8482-0.30220.14122.7477-0.13180.8115253.21712.49836.944
115.1537-0.18970.58193.2218-0.82984.7013-0.6327-0.24740.43810.41970.2434-0.1592-0.83611.12120.32770.8462-0.3384-0.06461.0252-0.09710.4712225.94318.96740.52
122.03930.78412.26716.4348-0.05572.66510.4622-1.3254-1.06920.3820.33740.87610.15890.34930.26021.0270.30130.16832.45090.06921.3378241.337-5.05443.606
134.2063-1.70580.04144.16361.61293.33720.46012.38460.5319-4.5916-0.1036-0.9806-0.72441.5442-0.29642.60060.21750.57453.4896-0.35951.3979248.8276.26114.716
143.7981-1.6573-2.72470.80511.51322.85240.25750.95360.5579-3.41640.1202-1.55772.21861.01460.17573.1409-0.64040.90394.42930.06630.9515251.5825.56913.563
157.07094.0201-0.5339.17382.17812.25770.3171.478-1.66390.6717-0.0316-1.1891.13712.9661-0.15351.16660.2454-0.00221.2813-0.06220.9755238.774-7.10638.64
161.19540.70640.4885.4442.93063.1019-0.14930.0370.20290.1576-0.1047-0.00290.2155-0.17180.22871.5647-0.0124-0.21161.8146-0.30381.9364243.042-12.4651.349
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 275:320 )B275 - 320
2X-RAY DIFFRACTION2( CHAIN B AND RESID 321:411 )B321 - 411
3X-RAY DIFFRACTION3( CHAIN B AND RESID 412:494 )B412 - 494
4X-RAY DIFFRACTION4( CHAIN B AND RESID 495:624 )B495 - 624
5X-RAY DIFFRACTION5( CHAIN C AND RESID 1:9 )C1 - 9
6X-RAY DIFFRACTION6( CHAIN C AND RESID 10:18 )C10 - 18
7X-RAY DIFFRACTION7( CHAIN D AND RESID 1:9 )D1 - 9
8X-RAY DIFFRACTION8( CHAIN D AND RESID 11:18 )D11 - 18
9X-RAY DIFFRACTION9( CHAIN A AND RESID 275:353 )A275 - 353
10X-RAY DIFFRACTION10( CHAIN A AND RESID 354:471 )A354 - 471
11X-RAY DIFFRACTION11( CHAIN A AND RESID 472:624 )A472 - 624
12X-RAY DIFFRACTION12( CHAIN E AND RESID 2:8 )E2 - 8
13X-RAY DIFFRACTION13( CHAIN E AND RESID 9:18 )E9 - 18
14X-RAY DIFFRACTION14( CHAIN G AND RESID 1:9 )G1 - 9
15X-RAY DIFFRACTION15( CHAIN G AND RESID 11:16 )G11 - 16
16X-RAY DIFFRACTION16( CHAIN E AND RESID 101:101 )E101

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