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- PDB-7ubu: Crystal structure of ZMET2 in complex with hemimethylated CAG DNA... -

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Basic information

Entry
Database: PDB / ID: 7ubu
TitleCrystal structure of ZMET2 in complex with hemimethylated CAG DNA and a histone H3Kc9me2 peptide
Components
  • 5MC SSDNA
  • C49 SSDNA
  • DNA (cytosine-5)-methyltransferase 1
  • Histone H3.2
KeywordsTRANSFERASE/DNA / DNA methyltransferase / complex / DNA BINDING PROTEIN / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


chromocenter / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / 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 domain / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 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: Nat Commun / Year: 2022
Title: Mechanistic basis for maintenance of CHG DNA methylation in plants.
Authors: Fang, J. / Jiang, J. / Leichter, S.M. / Liu, J. / Biswal, M. / Khudaverdyan, N. / Zhong, X. / Song, J.
History
DepositionMar 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 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

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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
P: Histone H3.2
B: 5MC SSDNA
C: C49 SSDNA
Q: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,9716
Polymers105,5865
Non-polymers3841
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10170 Å2
ΔGint-37 kcal/mol
Surface area35870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.574, 121.392, 160.446
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules BC

#3: DNA chain 5MC SSDNA


Mass: 5583.666 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Zea mays (maize)
#4: DNA chain C49 SSDNA


Mass: 5537.673 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Zea mays (maize)

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Protein / Protein/peptide , 2 types, 3 molecules APQ

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


Mass: 87504.750 Da / Num. of mol.: 1
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
#2: Protein/peptide Histone H3.2


Mass: 3480.077 Da / Num. of mol.: 2
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, 121 molecules

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


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium citrate pH 5.5, 15% w/v polyethylene glycol 6,000
PH range: 5.0-7.0

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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: AGILENT ATLAS CCD / Detector: CCD / Date: Nov 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.39→160.45 Å / Num. obs: 50383 / % possible obs: 99.3 % / Redundancy: 5.7 % / Biso Wilson estimate: 62.9 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.062 / Rrim(I) all: 0.143 / Net I/σ(I): 10.1 / Num. measured all: 286070
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
2.39-2.4761.8732754246040.380.842.0580.899.9
9.56-160.4550.03645499050.9970.0180.0432.798.9

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Processing

Software
NameVersionClassification
HKL-30000.5.32data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
Cootmodel building
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FT2

4ft2


Resolution: 2.39→96.81 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2563 2000 3.98 %
Rwork0.2114 48221 -
obs0.2132 50221 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.33 Å2 / Biso mean: 77.662 Å2 / Biso min: 40.09 Å2
Refinement stepCycle: final / Resolution: 2.39→96.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5803 733 26 120 6682
Biso mean--64.89 67.98 -
Num. residues----776
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 (%)
2.39-2.450.38921390.3873342348198
2.45-2.520.41411420.37253423356599
2.52-2.590.38191420.34723436357899
2.59-2.670.3761410.327533983539100
2.67-2.770.35221420.311434203562100
2.77-2.880.32191430.296934363579100
2.88-3.010.31591410.28993414355599
3.01-3.170.31081420.26443429357199
3.17-3.370.32721430.23573441358499
3.37-3.630.23981420.22043430357299
3.63-3.990.24381430.19933425356898
3.99-4.570.20821430.15323468361198
4.57-5.760.20041450.15863495364098
5.76-96.810.2091520.173664381698
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)
13.07111.9350.05368.8844-0.70161.3376-0.041-0.01050.0250.15190.0478-0.3473-0.15810.1267-0.00850.35890.00970.00270.53990.03740.5552-2.258923.078412.5213
21.61320.5305-0.06812.63740.66210.8926-0.070.1808-0.4855-0.14110.00170.04040.19720.00730.07160.40220.02540.00320.40470.02540.5743-28.619-15.10150.4167
31.37340.3924-0.48561.5016-0.33461.09110.0508-0.2069-0.11060.2739-0.0550.14040.0368-0.035-0.00150.4673-0.0099-0.00440.48160.05880.6211-40.8051-0.554222.4789
44.2003-1.5836-3.94734.41630.72753.9726-0.1477-0.2848-0.53110.5793-0.48680.347-0.05370.39850.3690.9598-0.0168-0.18171.1705-0.13291.17156.68521.488324.2743
56.0315-5.1442-5.53524.38314.71875.07180.797-0.65381.84030.3947-1.11441.3851-1.0859-1.07320.19640.67030.02340.07110.7414-0.04621.1527-8.346621.108221.748
67.3862-6.0372-7.01955.77265.69756.6738-0.7371-0.05351.13410.63031.3731-2.3053-0.39281.1295-0.06421.0152-0.1445-0.04140.9661-0.14791.497-29.209821.201323.0136
71.94652.64161.90427.2273.66292.17810.77370.95332.42150.6744-0.97550.6194-1.86260.02920.12410.90090.08660.15910.96760.1321.1669-39.632520.361525.8805
82.95590.74711.3275.6094-0.78160.8463-0.1712-0.1442-0.8626-0.2796-0.1114-0.34170.93950.026-0.01651.2853-0.03580.16030.99530.13841.0057-41.1558-26.404333.9634
93.71911.3593-2.72133.8698-1.4282.03820.3218-1.378-0.43030.7476-0.6562-0.57140.00310.37430.27830.8703-0.054-0.10720.90040.16450.7413-32.1061-8.443440.4112
106.25343.87990.07177.19960.36518.98850.2258-0.11922.70721.335-0.6231-0.2729-1.1603-0.85540.340.95030.02330.00150.8008-0.1381.1429-29.335612.24337.0108
115.13374.0816-5.42925.4534-3.97595.7914-2.1622-0.3376-0.7460.06780.6655-0.46961.1212-1.09951.83961.37330.0193-0.25891.3708-0.78131.8683-31.363720.906447.8104
126.74042.3181.56543.88273.7593.54710.8031-0.45170.63730.7608-0.0379-1.4623-0.251-0.1524-0.81690.9255-0.0787-0.08070.6967-0.02571.0045-30.12897.452638.5416
135.45594.8055-4.48668.0438-6.40627.3872-0.2323-0.5047-0.87450.6442-0.0971-0.01480.91040.03570.29191.0666-0.0295-0.00420.81730.27291.0139-36.7565-22.598638.7578
142.3561-0.446-3.55390.15570.81425.77570.65230.337-0.0481-0.0641-0.1141-0.07860.18910.4414-0.52230.9565-0.0020.02440.8987-0.17411.1948-32.1549-41.6378-8.574
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 133 through 268 )A133 - 268
2X-RAY DIFFRACTION2chain 'A' and (resid 269 through 518 )A269 - 518
3X-RAY DIFFRACTION3chain 'A' and (resid 519 through 889 )A519 - 889
4X-RAY DIFFRACTION4chain 'P' and (resid 2 through 6 )P2 - 6
5X-RAY DIFFRACTION5chain 'P' and (resid 7 through 14 )P7 - 14
6X-RAY DIFFRACTION6chain 'P' and (resid 15 through 19 )P15 - 19
7X-RAY DIFFRACTION7chain 'P' and (resid 20 through 24 )P20 - 24
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 5 )B1 - 5
9X-RAY DIFFRACTION9chain 'B' and (resid 6 through 11 )B6 - 11
10X-RAY DIFFRACTION10chain 'B' and (resid 12 through 16 )B12 - 16
11X-RAY DIFFRACTION11chain 'B' and (resid 17 through 18 )B17 - 18
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 11 )C1 - 11
13X-RAY DIFFRACTION13chain 'C' and (resid 12 through 18 )C12 - 18
14X-RAY DIFFRACTION14chain 'Q' and (resid 0 through 11 )Q0 - 11

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