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- PDB-6qxz: Solution structure of the ASHH2 CW domain with the N-terminal his... -

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Basic information

Entry
Database: PDB / ID: 6qxz
TitleSolution structure of the ASHH2 CW domain with the N-terminal histone H3 tail mimicking peptide monomethylated on lysine 4
Components
  • ALA-ARG-THR-MLZ-GLN-THR-ALA-ARG-TYR
  • Histone-lysine N-methyltransferase ASHH2
KeywordsTRANSFERASE / The CW domain of the methyltransferase from Arabidopsis (ASHH2). ASHH2 binds mono- di- and tri-methylated on K4 N-terminal histone tail H3 via CW domain. / PLANT PROTEIN
Function / homology
Function and homology information


carotenoid metabolic process / response to nitrate starvation / anther development / regulation of plant-type hypersensitive response / negative regulation of flower development / plant ovule development / embryo sac development / secondary shoot formation / pollen development / regulation of programmed cell death ...carotenoid metabolic process / response to nitrate starvation / anther development / regulation of plant-type hypersensitive response / negative regulation of flower development / plant ovule development / embryo sac development / secondary shoot formation / pollen development / regulation of programmed cell death / SUMO binding / histone H3K4 methyltransferase activity / chromosome, centromeric region / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Transferases; Transferring one-carbon groups; Methyltransferases / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / epigenetic regulation of gene expression / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDMs demethylate histones / 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 / 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 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nucleosome assembly / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Oxidative Stress Induced Senescence / methylation / gene expression / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / protein-containing complex / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane
Similarity search - Function
SETD2/Set2, SET domain / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / : / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Cysteine-rich motif following a subset of SET domains ...SETD2/Set2, SET domain / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / : / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / 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
Similarity search - Domain/homology
Histone H3.1 / Histone-lysine N-methyltransferase ASHH2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Homo sapiens (human)
MethodSOLUTION NMR / distance geometry
AuthorsDobrovolska, O. / Madeleine, N. / Teigen, K. / Halskau, O. / Bril'kov, M.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway226244/F50 Norway
Citation
Journal: Febs J. / Year: 2020
Title: The Arabidopsis (ASHH2) CW domain binds monomethylated K4 of the histone H3 tail through conformational selection.
Authors: Dobrovolska, O. / Brilkov, M. / Madeleine, N. / Odegard-Fougner, O. / Stromland, O. / Martin, S.R. / De Marco, V. / Christodoulou, E. / Teigen, K. / Isaksson, J. / Underhaug, J. / Reuter, N. ...Authors: Dobrovolska, O. / Brilkov, M. / Madeleine, N. / Odegard-Fougner, O. / Stromland, O. / Martin, S.R. / De Marco, V. / Christodoulou, E. / Teigen, K. / Isaksson, J. / Underhaug, J. / Reuter, N. / Aalen, R.B. / Aasland, R. / Halskau, O.
#1: Journal: Biomol NMR Assign / Year: 2018
Title: 1H, 13C, and 15N resonance assignments of CW domain of the N-methyltransferase ASHH2 free and bound to the mono-, di- and tri-methylated histone H3 tail peptides.
Authors: Dobrovolska, O. / Bril'kov, M. / Odegard-Fougner, O. / Aasland, R. / Halskau, O.
History
DepositionMar 8, 2019Deposition site: PDBE / Processing site: PDBE
SupersessionDec 4, 2019ID: 6HBO
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_conn_type
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.2Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.database_code / _database_2.pdbx_DOI ..._database_2.database_code / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase ASHH2
B: ALA-ARG-THR-MLZ-GLN-THR-ALA-ARG-TYR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0673
Polymers10,0022
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1600 Å2
ΔGint-4 kcal/mol
Surface area5750 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein Histone-lysine N-methyltransferase ASHH2 / ASH1 homolog 2 / H3-K4-HMTase / Histone H3-K36 methyltransferase 8 / H3-K36-HMTase 8 / Protein ...ASH1 homolog 2 / H3-K4-HMTase / Histone H3-K36 methyltransferase 8 / H3-K36-HMTase 8 / Protein EARLY FLOWERING IN SHORT DAYS / Protein LAZARUS 2 / Protein SET DOMAIN GROUP 8


Mass: 8891.677 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ASHH2, EFS, LAZ2, SDG8, SET8, At1g77300, T14N5.15 / Production host: Escherichia coli
References: UniProt: Q2LAE1, histone-lysine N-methyltransferase
#2: Protein/peptide ALA-ARG-THR-MLZ-GLN-THR-ALA-ARG-TYR


Mass: 1110.267 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D 1H-15N NOESY
151isotropic13D 1H-13C NOESY aliphatic
1151isotropic13D 1H-13C NOESY aromatic
161isotropic13D 1H-13C NOESY aromatic filtered-edited
171isotropic13D 1H-13C NOESY filtered-edited
181isotropic13D 1H-15N NOESY filtered-edited
192isotropic12D 1H-15N HSQC
1102isotropic13D 1H-15N NOESY
1112isotropic12D 1H-13C HSQC aliphatic
1122isotropic13D 1H-13C NOESY aliphatic
1131isotropic12D 1H-1H NOESY filtered
1141isotropic12D 1H-1H TOCSY filtered

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11 mM [U-99% 13C; U-99% 15N] CW domain of methyltransferase from Arabidopsis (ASHH2), 1 mM H3K4me1 (ART(MLZ)QTARY), 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O15N, 13C-labeled CW domain in complex With unlabeled H3K4me115N13C_CW_H3K4me190% H2O/10% D2O
solution21 mM CW domain of methyltransferase from Arabidopsis (ASHH2), 1 mM [U-99% 13C; U-99% 15N] H3K4me1 (ART(MLZ)QTARY), 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2OUnlabeled CW domain in complex with selectively 13C15N-labeled H3K4me1 (A*R*T(MLZ)QTA*R*Y)CW_15N13C_H3K4me190% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCW domain of methyltransferase from Arabidopsis (ASHH2)[U-99% 13C; U-99% 15N]1
1 mMH3K4me1 (ART(MLZ)QTARY)natural abundance1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
1 mMDTTnatural abundance1
1 mMCW domain of methyltransferase from Arabidopsis (ASHH2)natural abundance2
1 mMH3K4me1 (ART(MLZ)QTARY)[U-99% 13C; U-99% 15N]2
20 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
1 mMDTTnatural abundance2
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 6.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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