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- PDB-4ft4: crystal structure of Zea mays ZMET2 in complex H3(1-32)K9me2 pept... -

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Basic information

Entry
Database: PDB / ID: 4ft4
Titlecrystal structure of Zea mays ZMET2 in complex H3(1-32)K9me2 peptide and SAH
Components
  • DNA (cytosine-5)-methyltransferase 1
  • H3(1-32)K9me2 peptide
KeywordsTRANSFERASE / chromodomain / BAH domain / DNA methyltransferase domain / H3K9me2 binding / methylation
Function / homology
Function and homology information


chromocenter / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / plastid / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication ...chromocenter / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / plastid / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Senescence-Associated Secretory Phenotype (SASP) / methylation / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / chromatin binding / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
Bromo adjacent homology (BAH) domain / DNA Methylase, subunit A, domain 2 / DNA Methylase; Chain A, domain 2 / 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 ...Bromo adjacent homology (BAH) domain / DNA Methylase, subunit A, domain 2 / DNA Methylase; Chain A, domain 2 / 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 (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Vaccinia Virus protein VP39 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / SH3 type barrels. / Histone-fold / Roll / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone H3.1 / Histone H3.1 / DNA (cytosine-5)-methyltransferase 1
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDu, J. / Patel, D.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Dual Binding of Chromomethylase Domains to H3K9me2-Containing Nucleosomes Directs DNA Methylation in Plants.
Authors: Du, J. / Zhong, X. / Bernatavichute, Y.V. / Stroud, H. / Feng, S. / Caro, E. / Vashisht, A.A. / Terragni, J. / Chin, H.G. / Tu, A. / Hetzel, J. / Wohlschlegel, J.A. / Pradhan, S. / Patel, D.J. / Jacobsen, S.E.
History
DepositionJun 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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 1
A: DNA (cytosine-5)-methyltransferase 1
P: H3(1-32)K9me2 peptide
Q: H3(1-32)K9me2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,7026
Polymers181,9344
Non-polymers7692
Water2,882160
1
B: DNA (cytosine-5)-methyltransferase 1
Q: H3(1-32)K9me2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3513
Polymers90,9672
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-5 kcal/mol
Surface area31430 Å2
MethodPISA
2
A: DNA (cytosine-5)-methyltransferase 1
P: H3(1-32)K9me2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3513
Polymers90,9672
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-5 kcal/mol
Surface area31510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.645, 111.558, 151.480
Angle α, β, γ (deg.)90.00, 101.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 87591.828 Da / Num. of mol.: 2 / Fragment: UNP residues 130-912
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: MET2A, ZMET2 / Plasmid: pET-Sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL
References: UniProt: Q9AXT8, DNA (cytosine-5-)-methyltransferase
#2: Protein/peptide H3(1-32)K9me2 peptide


Mass: 3374.961 Da / Num. of mol.: 2 / Fragment: histone H3 peptide, UNP residues 33-64 / Source method: obtained synthetically / Details: H3(1-32)K9me2 peptide was synthesized / References: UniProt: P68431, UniProt: P59226*PLUS
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

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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: 2.94 Å3/Da / Density % sol: 58.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M sodium citrate, 0.1 M bis-tris propane, pH 6.5 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 58033 / Num. obs: 57221 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 65 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 21.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.507 / % possible all: 98.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FSX

4fsx


Resolution: 2.7→43.82 Å / SU ML: 0.69 / σ(F): 1.35 / Phase error: 27.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 2878 5.06 %
Rwork0.206 --
obs0.208 56933 98.4 %
all-59811 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.38 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.2113 Å20 Å2-1.4813 Å2
2--6.5354 Å2-0 Å2
3----9.7467 Å2
Refinement stepCycle: LAST / Resolution: 2.7→43.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11053 0 52 160 11265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911376
X-RAY DIFFRACTIONf_angle_d1.27515407
X-RAY DIFFRACTIONf_dihedral_angle_d17.9664252
X-RAY DIFFRACTIONf_chiral_restr0.1191637
X-RAY DIFFRACTIONf_plane_restr0.0091999
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.74430.36951150.31672539X-RAY DIFFRACTION98
2.7443-2.79160.3181300.30022562X-RAY DIFFRACTION98
2.7916-2.84230.39681250.29452555X-RAY DIFFRACTION98
2.8423-2.8970.3221380.2672583X-RAY DIFFRACTION98
2.897-2.95610.30461290.25552545X-RAY DIFFRACTION98
2.9561-3.02040.31061320.24542574X-RAY DIFFRACTION99
3.0204-3.09060.32111570.24162556X-RAY DIFFRACTION98
3.0906-3.16790.29281300.2442579X-RAY DIFFRACTION99
3.1679-3.25350.28891440.23132541X-RAY DIFFRACTION98
3.2535-3.34920.26711320.22392577X-RAY DIFFRACTION99
3.3492-3.45730.26131340.21872565X-RAY DIFFRACTION98
3.4573-3.58080.25381450.20892582X-RAY DIFFRACTION98
3.5808-3.72410.26781220.20482594X-RAY DIFFRACTION99
3.7241-3.89350.27221370.19252579X-RAY DIFFRACTION98
3.8935-4.09860.22221500.17852565X-RAY DIFFRACTION98
4.0986-4.35520.20621310.16332587X-RAY DIFFRACTION98
4.3552-4.69110.18061400.15352571X-RAY DIFFRACTION99
4.6911-5.16250.17941580.1632582X-RAY DIFFRACTION99
5.1625-5.9080.23821510.20672606X-RAY DIFFRACTION99
5.908-7.43750.27831360.20852621X-RAY DIFFRACTION99
7.4375-43.82360.20871420.19682592X-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)
12.26080.041.59670.85440.09122.3075-0.0362-0.39190.18020.1710.0232-0.00930.0103-0.35440.03960.24740.01810.07620.2687-0.05260.2814-20.5867-0.964-62.7745
21.3946-0.75180.39711.5524-0.14690.91520.04110.01810.09030.1372-0.0413-0.02490.08170.1398-0.00470.2296-0.03060.03010.2722-0.03460.18566.2065-16.1526-61.6773
30.4422-0.0635-0.85220.37330.42696.4992-0.12380.0474-0.046-0.1018-0.0770.15370.1573-0.82580.19720.8787-0.0171-0.03240.8028-0.06440.4303-10.3783-11.042412.3371
41.6157-0.077-0.44090.72161.41034.3466-0.13990.0839-0.2188-0.2841-0.11820.04770.7129-0.69070.40361.3312-0.19620.04780.8373-0.10410.444-8.163-20.3227-28.2305
51.72390.2643-0.78050.583-0.23293.09360.0051-0.39370.09060.1383-0.126-0.14580.04540.72990.1150.92330.0695-0.13420.857-0.10810.468514.87-4.5289-17.7728
65.64570.6744-0.2482.49120.3332.62070.1829-0.63921.0762-0.10110.3027-0.303-0.20590.4544-0.40591.24280.3619-0.03151.4124-0.12850.6112-11.07283.549517.3265
74.12984.35953.79774.89793.1965.7146-0.44741.1893-1.5058-0.8660.01661.26430.7198-0.70110.35910.8422-0.3551-0.17951.5562-0.06011.3911-34.3971-17.6469-81.9934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resseq 133:582)
2X-RAY DIFFRACTION2chain 'B' and (resseq 583:889)
3X-RAY DIFFRACTION3chain 'A' and (resseq 133:375)
4X-RAY DIFFRACTION4chain 'A' and (resseq 376:554)
5X-RAY DIFFRACTION5chain 'A' and (resseq 555:885)
6X-RAY DIFFRACTION6chain 'P'
7X-RAY DIFFRACTION7chain 'Q'

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