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- PDB-9mvy: Crystal structure of ZMET2 in complex with unmethylated CTG DNA a... -

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Basic information

Entry
Database: PDB / ID: 9mvy
TitleCrystal structure of ZMET2 in complex with unmethylated CTG DNA and a histone H3Kc9me2 peptide
Components
  • C49 ssDNA
  • DNA (cytosine-5)-methyltransferase 1
  • Histone H3.2
  • ssDNA
KeywordsTRANSFERASE / methylation complex / epigenetics / and DNA methyltransferase
Function / homology
Function and homology information


chromocenter / 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 / negative regulation of gene expression via chromosomal CpG island methylation / structural constituent of chromatin / nucleosome / methylation / protein heterodimerization activity ...chromocenter / 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 / negative regulation of gene expression via chromosomal CpG island methylation / structural constituent of chromatin / nucleosome / methylation / protein heterodimerization activity / chromatin binding / DNA binding / nucleus
Similarity search - Function
: / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Bromo adjacent homology domain ...: / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / Histone H3.2 / DNA (cytosine-5)-methyltransferase 1
Similarity search - Component
Biological speciesZea mays (maize)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsHerle, G. / Fang, J. / Song, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM119721 United States
CitationJournal: J.Mol.Biol. / Year: 2025
Title: Structure of an Unfavorable de Novo DNA Methylation Complex of Plant Methyltransferase ZMET2.
Authors: Herle, G. / Fang, J. / Song, J.
History
DepositionJan 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (cytosine-5)-methyltransferase 1
B: ssDNA
C: C49 ssDNA
D: DNA (cytosine-5)-methyltransferase 1
E: ssDNA
F: C49 ssDNA
G: Histone H3.2
H: Histone H3.2
I: Histone H3.2
P: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,80212
Polymers206,03310
Non-polymers7692
Water12,016667
1
A: DNA (cytosine-5)-methyltransferase 1
B: ssDNA
C: C49 ssDNA
H: Histone H3.2
P: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4016
Polymers103,0165
Non-polymers3841
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: DNA (cytosine-5)-methyltransferase 1
E: ssDNA
F: C49 ssDNA
G: Histone H3.2
I: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4016
Polymers103,0165
Non-polymers3841
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.515, 277.296, 64.479
Angle α, β, γ (deg.)90.00, 97.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 2 types, 4 molecules BECF

#2: DNA chain ssDNA


Mass: 5562.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain C49 ssDNA


Mass: 5528.659 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / Protein/peptide , 2 types, 6 molecules ADGHIP

#1: Protein DNA (cytosine-5)-methyltransferase 1 / Chromomethylase 1 / DNA cytosine methyltransferase MET2a / Zea methyltransferase2 / Zmet2


Mass: 85139.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: MET2A / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9AXT8, DNA (cytosine-5-)-methyltransferase
#4: Protein/peptide
Histone H3.2


Mass: 3392.999 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: H3C2, H3C3, H3C4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P69246

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Non-polymers , 2 types, 669 molecules

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


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 667 / 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: 2.7 Å3/Da / Density % sol: 54.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M magnesium acetate, 0.1 M sodium cacodylate pH 6.5, 15% w/v polyethylene glycol 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Sep 8, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.71→48.4 Å / Num. obs: 59203 / % possible obs: 98.04 % / Redundancy: 2.8 % / CC1/2: 0.973 / Rmerge(I) obs: 0.147 / Net I/σ(I): 5.04
Reflection shellResolution: 2.71→2.78 Å / Redundancy: 2.8 % / Num. unique obs: 3959 / CC1/2: 0.199 / % possible all: 91.54

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
Aimlessdata scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→48.4 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2714 2011 3.4 %
Rwork0.2267 --
obs0.2282 59203 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.71→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11257 1375 0 667 13299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.619
X-RAY DIFFRACTIONf_dihedral_angle_d21.2675004
X-RAY DIFFRACTIONf_chiral_restr0.0441941
X-RAY DIFFRACTIONf_plane_restr0.0052085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.780.34331400.30663819X-RAY DIFFRACTION92
2.78-2.860.32791440.28584098X-RAY DIFFRACTION99
2.86-2.940.31241390.2674165X-RAY DIFFRACTION99
2.94-3.040.32821440.26844091X-RAY DIFFRACTION99
3.04-3.140.28171440.25294086X-RAY DIFFRACTION99
3.14-3.270.28491460.24194124X-RAY DIFFRACTION99
3.27-3.420.27951430.22434156X-RAY DIFFRACTION99
3.42-3.60.29071440.22354134X-RAY DIFFRACTION99
3.6-3.830.30461450.21974064X-RAY DIFFRACTION99
3.83-4.120.26891440.20734090X-RAY DIFFRACTION99
4.12-4.530.23361440.19264120X-RAY DIFFRACTION99
4.53-5.190.22571420.1944081X-RAY DIFFRACTION98
5.19-6.540.2281460.22844110X-RAY DIFFRACTION98
6.54-48.40.25661460.22214054X-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)
13.79-2.8743-0.33595.79080.79461.32730.05880.0337-0.3981-0.1904-0.11640.04670.15260.06750.09980.24160.02590.07520.39540.07750.324932.481-15.391913.147
21.60050.0562-0.18271.1262-0.09571.5955-0.0342-0.59720.47170.43430.0366-0.0948-0.40730.01560.02090.49260.06080.01160.4905-0.15630.34112.914720.34529.1376
31.4201-0.47230.23190.7089-0.3161.50790.051-0.001-0.04040.0065-0.03670.0709-0.1151-0.0923-0.02060.23440.05220.03980.265-0.0510.1984-5.36687.47095.0136
42.5809-1.0875-1.68686.53640.84864.10430.0661-0.71441.35990.8952-0.2047-0.5776-0.5365-0.41120.09631.0810.296-0.01610.3972-0.18170.734-5.645234.6859-0.2058
55.6899-1.54020.2574.93270.1643.85250.43260.1443-0.3248-0.3802-0.4607-0.67810.8342-0.2280.18640.7714-0.00230.11640.3617-0.01220.32125.215710.4484-10.524
63.0664-1.065-1.00914.8717-3.36583.43921.3488-0.0551-0.283-0.427-1.2386-0.30881.37330.0595-0.11861.7780.423-0.37031.8616-0.34441.21612.5507-8.888-22.1974
71.05850.67110.66342.1529-2.28035.05980.87881.4756-0.6234-0.8241-1.0074-0.83880.03620.40280.07051.33690.4260.1360.8056-0.03370.75768.2479-1.3145-20.3245
84.02730.8571-0.11331.47-1.32721.91970.054-0.00820.554-0.1833-0.1973-0.1047-0.7025-0.53130.1640.79160.1330.04240.39-0.12370.314-0.475222.4232-5.1182
91.7377-1.1321-0.72445.8131.92263.53480.1248-0.15620.29390.0265-0.05290.0307-0.5344-0.0756-0.00180.3212-0.0740.06830.3688-0.09130.3195.570399.301536.6283
101.54630.09240.44010.91550.26981.36670.00460.0914-0.22530.02780.0119-0.09770.10630.20430.00160.1630.02330.04980.3123-0.05330.26539.953472.57161.9316
112.56431.8315-0.11021.80681.37754.2498-0.0699-0.264-0.34010.9878-0.1080.12260.82450.07670.28940.39980.0779-0.01820.24860.14260.5129-9.419758.81321.438
123.17874.7817-3.88278.3732-4.59616.05830.22290.69621.5627-0.5336-0.27121.2761-1.1182-0.8317-0.02010.52630.2015-0.08090.7160.30311.1634-15.423885.90016.896
130.30620.00090.81670.33730.27432.39780.03210.19380.01330.0160.1437-0.1173-0.02170.0485-0.16491.4895-0.06260.35421.40210.1863.044-25.772591.88431.5979
143.9136-1.0180.46921.9634-1.9383.07840.0013-0.30580.0035-0.0669-0.43381.01430.32-0.44930.25480.24910.06070.01350.427-0.20980.5634-11.746166.13632.6685
159.44634.3367.06592.05473.4295.81980.5046-1.35450.210.0146-0.4540.745-0.9085-2.7114-0.04830.46790.19840.15120.91670.00180.9932-7.88998.76639.6767
164.03881.46672.54462.2923-0.49562.86950.8649-1.21181.19910.8091-0.728-0.4898-0.3211-2.6598-0.13960.7312-0.11870.24141.414-0.30170.7704-4.37698.04419.6072
176.3765-0.3861-0.35652.40590.42430.91710.38910.62020.9154-0.5235-0.1148-0.2483-0.5969-1.3585-0.350.56560.15590.40640.91190.03750.787-3.711695.98921.4519
184.25660.24631.84724.5422-6.91512-0.0218-0.95190.0280.81530.3135-0.8484-0.28232.1558-0.37651.1142-0.01420.0760.8116-0.42230.97832.972942.363137.5085
192-4.40266.62965.3423-3.94424.25141.0084-1.4708-0.64131.08750.22440.40280.4629-0.7797-1.25590.97450.0896-0.36910.6268-0.05280.954833.259941.202210.09
204.2919-4.2614.72954.237-4.83067.66930.49892.1647-1.0436-0.8208-0.27860.0889-0.13340.3551-0.22510.55950.15290.010.5747-0.2050.4637.6115-15.1855-0.1533
210.225-0.4386-0.74923.21410.61272.79890.23230.8453-0.60710.117-0.49040.16690.64170.92140.34370.53160.08850.25150.6019-0.00130.460711.8124-13.85941.3524
220.07-0.5145-0.70399.34843.69337.44780.3591.6053-1.277-0.3022-0.69651.740.8146-0.73230.38450.6354-0.0734-0.13140.5045-0.25910.6538-2.7328-12.2167-1.2241
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 133 through 300 )
2X-RAY DIFFRACTION2chain 'A' and (resid 301 through 518 )
3X-RAY DIFFRACTION3chain 'A' and (resid 519 through 885 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 5 )
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 15 )
6X-RAY DIFFRACTION6chain 'B' and (resid 16 through 18 )
7X-RAY DIFFRACTION7chain 'C' and (resid 2 through 6 )
8X-RAY DIFFRACTION8chain 'C' and (resid 7 through 18 )
9X-RAY DIFFRACTION9chain 'D' and (resid 134 through 289 )
10X-RAY DIFFRACTION10chain 'D' and (resid 290 through 887 )
11X-RAY DIFFRACTION11chain 'E' and (resid 2 through 11 )
12X-RAY DIFFRACTION12chain 'E' and (resid 12 through 16 )
13X-RAY DIFFRACTION13chain 'E' and (resid 17 through 17 )
14X-RAY DIFFRACTION14chain 'F' and (resid 3 through 18 )
15X-RAY DIFFRACTION15chain 'G' and (resid 4 through 8 )
16X-RAY DIFFRACTION16chain 'G' and (resid 10 through 16 )
17X-RAY DIFFRACTION17chain 'G' and (resid 17 through 24 )
18X-RAY DIFFRACTION18chain 'H' and (resid 5 through 10 )
19X-RAY DIFFRACTION19chain 'I' and (resid 5 through 11 )
20X-RAY DIFFRACTION20chain 'P' and (resid 4 through 8 )
21X-RAY DIFFRACTION21chain 'P' and (resid 10 through 18 )
22X-RAY DIFFRACTION22chain 'P' and (resid 19 through 24 )

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