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- PDB-6mm1: Structure of the cysteine-rich region from human EHMT2 -

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Basic information

Entry
Database: PDB / ID: 6mm1
TitleStructure of the cysteine-rich region from human EHMT2
ComponentsHistone-lysine N-methyltransferase EHMT2
KeywordsTRANSFERASE / cysteine-rich region / RING-like / zinc-binding
Function / homology
Function and homology information


regulation of protein modification process / histone H3K56 methyltransferase activity / : / phenotypic switching / neuron fate specification / : / [histone H3]-lysine9 N-methyltransferase / histone H3K27 methyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity ...regulation of protein modification process / histone H3K56 methyltransferase activity / : / phenotypic switching / neuron fate specification / : / [histone H3]-lysine9 N-methyltransferase / histone H3K27 methyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / peptidyl-lysine dimethylation / synaptonemal complex assembly / negative regulation of autophagosome assembly / oocyte development / protein-lysine N-methyltransferase activity / C2H2 zinc finger domain binding / fertilization / : / cellular response to cocaine / : / organ growth / Transcriptional Regulation by E2F6 / spermatid development / behavioral response to cocaine / regulation of DNA replication / RNA Polymerase I Transcription Initiation / Transcriptional Regulation by VENTX / long-term memory / response to fungicide / Transferases; Transferring one-carbon groups; Methyltransferases / cellular response to starvation / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / cellular response to xenobiotic stimulus / p53 binding / Senescence-Associated Secretory Phenotype (SASP) / response to ethanol / nuclear speck / chromatin / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
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 domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily ...Histone-lysine N-methyltransferase EHMT2 / Histone-lysine N-methyltransferase EHMT1/EHMT2 / : / Histone-lysine N-methyltransferase EHMT1/EHMT2, Cys-rich region / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Histone-lysine N-methyltransferase EHMT2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsKerchner, K.M. / Mou, T.C. / Sprang, S.R. / Briknarova, K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103546 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM114657 United States
CitationJournal: J Struct Biol X / Year: 2021
Title: The structure of the cysteine-rich region from human histone-lysine N-methyltransferase EHMT2 (G9a).
Authors: Kerchner, K.M. / Mou, T.C. / Sun, Y. / Rusnac, D.V. / Sprang, S.R. / Briknarova, K.
History
DepositionSep 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Feb 17, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_site.details / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1May 17, 2023Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase EHMT2
B: Histone-lysine N-methyltransferase EHMT2
C: Histone-lysine N-methyltransferase EHMT2
D: Histone-lysine N-methyltransferase EHMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,98020
Polymers59,9334
Non-polymers1,04716
Water9,458525
1
A: Histone-lysine N-methyltransferase EHMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2455
Polymers14,9831
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone-lysine N-methyltransferase EHMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2455
Polymers14,9831
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Histone-lysine N-methyltransferase EHMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2455
Polymers14,9831
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Histone-lysine N-methyltransferase EHMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2455
Polymers14,9831
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.996, 54.358, 59.317
Angle α, β, γ (deg.)91.68, 100.92, 96.89
Int Tables number1
Space group name H-MP1

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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: 14983.312 Da / Num. of mol.: 4 / Fragment: residues 419-552
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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M potassium sodium tartrate 18% PEG 3350 0.1M HEPES, pH 8.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
31001N
41001N
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL12-231.28
SYNCHROTRONAPS 19-BM40.98
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M3PIXELFeb 8, 2017
MARMOSAIC 325 mm CCD4CCDNov 16, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
3SINGLE WAVELENGTHMx-ray1
4SINGLE WAVELENGTHMx-ray2
2x-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
11.281
20.981
31
ReflectionResolution: 1.897→24.507 Å / Num. obs: 43917 / % possible obs: 95.4 % / Redundancy: 2.2 % / Biso Wilson estimate: 16.7 Å2 / Rsym value: 0.12 / Net I/σ(I): 7.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4011 / Rsym value: 0.73 / % possible all: 89.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→24.51 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.27
RfactorNum. reflection% reflection
Rfree0.223 1999 4.55 %
Rwork0.174 --
obs0.176 43917 95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→24.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4080 0 16 525 4621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064173
X-RAY DIFFRACTIONf_angle_d0.7465609
X-RAY DIFFRACTIONf_dihedral_angle_d8.0672813
X-RAY DIFFRACTIONf_chiral_restr0.049601
X-RAY DIFFRACTIONf_plane_restr0.004746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8966-1.9440.35651300.31072717X-RAY DIFFRACTION85
1.944-1.99660.33091410.28882952X-RAY DIFFRACTION94
1.9966-2.05530.30691390.25172915X-RAY DIFFRACTION94
2.0553-2.12160.26571410.23672958X-RAY DIFFRACTION93
2.1216-2.19740.27531450.21443036X-RAY DIFFRACTION95
2.1974-2.28530.27251410.20912933X-RAY DIFFRACTION93
2.2853-2.38920.22681440.18713042X-RAY DIFFRACTION96
2.3892-2.51510.24941440.18233006X-RAY DIFFRACTION96
2.5151-2.67250.2161450.17513049X-RAY DIFFRACTION96
2.6725-2.87850.2341450.18333041X-RAY DIFFRACTION97
2.8785-3.16760.24181460.16793084X-RAY DIFFRACTION98
3.1676-3.62470.19871470.14213077X-RAY DIFFRACTION97
3.6247-4.5620.16081460.12373084X-RAY DIFFRACTION98
4.562-24.50810.16661450.13253024X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 46.914 Å / Origin y: 36.1146 Å / Origin z: 47.9702 Å
111213212223313233
T0.1804 Å20.0033 Å2-0.0034 Å2-0.165 Å20.0098 Å2--0.1778 Å2
L0.2341 °20.1158 °2-0.006 °2-0.3372 °20.0209 °2--0.1876 °2
S-0.0121 Å °0.0069 Å °0.0167 Å °-0.0025 Å °0.0086 Å °0.0098 Å °-0.0291 Å °-0.0037 Å °0.0033 Å °
Refinement TLS groupSelection details: ALL

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