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- PDB-5t0k: Structure of G9a SET-domain with H3K9M mutant peptide and SAM -

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Basic information

Entry
Database: PDB / ID: 5t0k
TitleStructure of G9a SET-domain with H3K9M mutant peptide and SAM
Components
  • H3K9 mutant peptide
  • Histone-lysine N-methyltransferase EHMT2
KeywordsTRANSFERASE / histone methyltransferase / SET domain
Function / homology
Function and homology information


regulation of protein modification process / phenotypic switching / neuron fate specification / [histone H3]-lysine9 N-methyltransferase / peptidyl-lysine dimethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K27 methyltransferase activity / synaptonemal complex assembly / negative regulation of autophagosome assembly ...regulation of protein modification process / phenotypic switching / neuron fate specification / [histone H3]-lysine9 N-methyltransferase / peptidyl-lysine dimethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K27 methyltransferase activity / synaptonemal complex assembly / negative regulation of autophagosome assembly / histone H3K56 methyltransferase activity / protein-lysine N-methyltransferase activity / oocyte development / C2H2 zinc finger domain binding / fertilization / cellular response to cocaine / organ growth / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / spermatid development / Transcriptional Regulation by E2F6 / behavioral response to cocaine / regulation of DNA replication / RNA Polymerase I Transcription Initiation / Transcriptional Regulation by VENTX / long-term memory / Chromatin modifying enzymes / response to fungicide / 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 / Transferases; Transferring one-carbon groups; Methyltransferases / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / cellular response to starvation / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / transcription corepressor binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / promoter-specific chromatin binding / 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 / Regulation of TP53 Activity through Methylation / 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 / p53 binding / nucleosome / cellular response to xenobiotic stimulus / 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 / Estrogen-dependent gene expression / response to ethanol / nuclear speck / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane
Similarity search - Function
Histone-lysine N-methyltransferase EHMT2 / Histone-lysine N-methyltransferase EHMT1/EHMT2 / : / Histone-lysine N-methyltransferase EHMT1/EHMT2, Cys-rich region / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Beta-clip-like / SET domain ...Histone-lysine N-methyltransferase EHMT2 / Histone-lysine N-methyltransferase EHMT1/EHMT2 / : / Histone-lysine N-methyltransferase EHMT1/EHMT2, Cys-rich region / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Ankyrin repeat / Beta Complex / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing 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 / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Histone H3.1 / Histone-lysine N-methyltransferase EHMT2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsXu, K. / Tong, L.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM085145 United States
National Institutes of Health/Office of the DirectorS10-OD012018 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)P41-RR011823 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41-GM103533 United States
CitationJournal: Elife / Year: 2016
Title: A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading.
Authors: Shan, C.M. / Wang, J. / Xu, K. / Chen, H. / Yue, J.X. / Andrews, S. / Moresco, J.J. / Yates, J.R. / Nagy, P.L. / Tong, L. / Jia, S.
History
DepositionAug 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase EHMT2
B: Histone-lysine N-methyltransferase EHMT2
P: H3K9 mutant peptide
Q: H3K9 mutant peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,37714
Polymers68,0574
Non-polymers1,32010
Water12,394688
1
A: Histone-lysine N-methyltransferase EHMT2
P: H3K9 mutant peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6897
Polymers34,0292
Non-polymers6605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-6 kcal/mol
Surface area13640 Å2
MethodPISA
2
B: Histone-lysine N-methyltransferase EHMT2
Q: H3K9 mutant peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6897
Polymers34,0292
Non-polymers6605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-6 kcal/mol
Surface area13540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.101, 92.307, 93.143
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histone-lysine N-methyltransferase EHMT2 / Euchromatic histone-lysine N-methyltransferase 2 / HLA-B-associated transcript 8 / Histone H3-K9 ...Euchromatic histone-lysine N-methyltransferase 2 / HLA-B-associated transcript 8 / Histone H3-K9 methyltransferase 3 / H3-K9-HMTase 3 / Lysine N-methyltransferase 1C / Protein G9a


Mass: 32460.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EHMT2, BAT8, C6orf30, G9A, KMT1C, NG36 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96KQ7, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase
#2: Protein/peptide H3K9 mutant peptide


Mass: 1567.813 Da / Num. of mol.: 2 / 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.: 8
Source method: isolated from a genetically manipulated source
Formula: Zn
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C15H22N6O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Bis-Tris propane (pH 7.5), 18% (w/v) PEG3350, 0.2 M NaF, and 5% (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 71263 / % possible obs: 98.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 17.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2.8 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000704udata reduction
HKL-2000704udata scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O8J

2o8j


Resolution: 1.7→50 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.94
RfactorNum. reflection% reflection
Rfree0.1928 1996 2.8 %
Rwork0.165 --
obs0.1658 71258 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4459 0 0 688 5147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074584
X-RAY DIFFRACTIONf_angle_d1.0376198
X-RAY DIFFRACTIONf_dihedral_angle_d14.461724
X-RAY DIFFRACTIONf_chiral_restr0.045662
X-RAY DIFFRACTIONf_plane_restr0.004810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6984-1.74090.22761360.20524588X-RAY DIFFRACTION93
1.7409-1.7880.23251350.19384921X-RAY DIFFRACTION100
1.788-1.84060.22771460.18724951X-RAY DIFFRACTION100
1.8406-1.90.20441430.18484962X-RAY DIFFRACTION100
1.9-1.96790.20291440.17294903X-RAY DIFFRACTION100
1.9679-2.04670.20841390.17044952X-RAY DIFFRACTION100
2.0467-2.13980.21361410.17274922X-RAY DIFFRACTION99
2.1398-2.25260.18681440.16674947X-RAY DIFFRACTION99
2.2526-2.39380.21911430.16654980X-RAY DIFFRACTION100
2.3938-2.57860.18361440.16664947X-RAY DIFFRACTION99
2.5786-2.83810.16951430.17064993X-RAY DIFFRACTION99
2.8381-3.24870.19381470.16925014X-RAY DIFFRACTION100
3.2487-4.09270.18771440.14775022X-RAY DIFFRACTION99
4.0927-49.41170.17321470.1515160X-RAY DIFFRACTION98

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