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- PDB-4ft2: crystal structure of Zea mays ZMET2 in complex H3(1-15)K9me2 pept... -

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Basic information

Entry
Database: PDB / ID: 4ft2
Titlecrystal structure of Zea mays ZMET2 in complex H3(1-15)K9me2 peptide and SAH
Components
  • DNA (cytosine-5)-methyltransferase 1
  • H3 peptide
KeywordsTRANSFERASE / chromodomain / BAH domain / DNA methyltransferase domain / DNA methyltransferase / H3K9me2 binding / methylation
Function / homology
Function and homology information


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 / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication ...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 / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / methylation / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane
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 ...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 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 / Vaccinia Virus protein VP39 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / SH3 type barrels. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / 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 / DNA (cytosine-5)-methyltransferase 1
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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
A: DNA (cytosine-5)-methyltransferase 1
B: DNA (cytosine-5)-methyltransferase 1
P: H3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,5455
Polymers176,7763
Non-polymers7692
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.861, 88.858, 113.501
Angle α, β, γ (deg.)93.15, 95.72, 110.70
Int Tables number1
Space group name H-MP1

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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 peptide


Mass: 1592.843 Da / Num. of mol.: 1 / Fragment: histone H3 peptide, UNP residues 16-30 / Source method: obtained synthetically / Details: H3 peptide was synthesized / References: UniProt: P68431
#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

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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: 3.43 Å3/Da / Density % sol: 64.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M calcium acetate, 0.1 M imidazole pH 8.0, and 10% PEG8000, 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: 3.2→50 Å / Num. all: 39197 / Num. obs: 38805 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 12.6
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.503 / % possible all: 98.8

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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: PDB ENTRY 4FSX

4fsx


Resolution: 3.2→40.099 Å / SU ML: 1.04 / σ(F): 1.98 / Phase error: 28.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2773 1928 5.04 %
Rwork0.2352 --
obs0.2373 38283 98.92 %
all-40211 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.828 Å2 / ksol: 0.281 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.9959 Å2-2.1425 Å2-4.6629 Å2
2--2.0362 Å2-4.3368 Å2
3---0.9597 Å2
Refinement stepCycle: LAST / Resolution: 3.2→40.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10605 0 52 0 10657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910918
X-RAY DIFFRACTIONf_angle_d1.57514804
X-RAY DIFFRACTIONf_dihedral_angle_d19.1814034
X-RAY DIFFRACTIONf_chiral_restr0.1031580
X-RAY DIFFRACTIONf_plane_restr0.0121924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.280.35141390.32222568X-RAY DIFFRACTION99
3.28-3.36870.33141260.29982618X-RAY DIFFRACTION99
3.3687-3.46770.35521590.28552572X-RAY DIFFRACTION99
3.4677-3.57960.32431470.28262615X-RAY DIFFRACTION99
3.5796-3.70740.31871310.26722574X-RAY DIFFRACTION99
3.7074-3.85580.25481200.24182627X-RAY DIFFRACTION99
3.8558-4.03110.27691410.22832623X-RAY DIFFRACTION99
4.0311-4.24340.30141350.20032606X-RAY DIFFRACTION99
4.2434-4.50890.21261440.19532586X-RAY DIFFRACTION99
4.5089-4.85650.22121330.17832591X-RAY DIFFRACTION99
4.8565-5.34420.22051440.20522618X-RAY DIFFRACTION99
5.3442-6.11520.28551460.24942584X-RAY DIFFRACTION99
6.1152-7.69560.2721220.24382616X-RAY DIFFRACTION99
7.6956-40.10210.2941410.23842557X-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)
12.9740.48721.1681.02540.44311.20750.06390.4835-0.1621-0.0523-0.14050.16730.1629-0.29460.09770.383-0.0520.01790.6017-0.07570.3775-58.774734.9625-67.4074
21.9066-0.10980.33122.1830.80771.5196-0.1712-0.21510.83620.4019-0.05920.0146-0.5089-0.04640.10880.5263-0.0229-0.19840.3689-0.01360.6991-35.553563.7902-45.3377
32.2347-0.59090.88650.5527-0.20381.4449-0.09270.1553-0.08230.17030.1142-0.0890.14140.1216-0.04390.40820.0072-0.03220.2946-0.01320.3182-21.899136.9575-45.8552
41.6242-1.0558-0.6471.60210.94051.4359-0.121-0.0808-0.20260.0017-0.08240.26740.142-0.22110.12790.2952-0.04090.03820.41020.01510.3315-46.188372.55230.7823
52.64870.3528-0.95031.07820.0740.849-0.09370.08250.102-0.14840.2094-0.1658-0.06940.1895-0.09370.3957-0.00370.02460.3926-0.0330.2602-23.564781.5327-5.6491
61.66411.1694-0.48511.07510.28031.4252-0.31230.20420.21-0.42310.52910.0472-0.3540.1555-0.05760.5206-0.11440.05480.37210.05540.3216-18.160886.5583-16.681
7-0.0080.01070.005-0.0198-0.0039-0.00360.08030.4787-0.1729-0.12960.19980.1706-0.03080.018400.73560.031-0.08770.5359-0.10060.5651-33.365836.5231-21.2486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 132:364)
2X-RAY DIFFRACTION2chain 'A' and (resseq 365:566)
3X-RAY DIFFRACTION3chain 'A' and (resseq 567:886)
4X-RAY DIFFRACTION4chain 'B' and (resseq 134:551)
5X-RAY DIFFRACTION5chain 'B' and (resseq 552:732)
6X-RAY DIFFRACTION6chain 'B' and (resseq 733:885)
7X-RAY DIFFRACTION7chain 'P'

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