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- PDB-6bp4: Structure of the S. pombe Clr4 catalytic domain bound to SAM -

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Basic information

Entry
Database: PDB / ID: 6bp4
TitleStructure of the S. pombe Clr4 catalytic domain bound to SAM
ComponentsHistone-lysine N-methyltransferase, H3 lysine-9 specific
KeywordsTRANSFERASE / Methyltransferase / SET domain
Function / homology
Function and homology information


CLRC complex / positive regulation of pericentric heterochromatin formation / [histone H3]-lysine9 N-trimethyltransferase / mating-type region heterochromatin / [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / nuclear polyadenylation-dependent antisense transcript catabolic process / histone H3K9 monomethyltransferase activity / siRNA-mediated pericentric heterochromatin formation / [histone H3]-lysine9 N-methyltransferase ...CLRC complex / positive regulation of pericentric heterochromatin formation / [histone H3]-lysine9 N-trimethyltransferase / mating-type region heterochromatin / [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / nuclear polyadenylation-dependent antisense transcript catabolic process / histone H3K9 monomethyltransferase activity / siRNA-mediated pericentric heterochromatin formation / [histone H3]-lysine9 N-methyltransferase / ubiquitin-modified histone reader activity / chromosome, subtelomeric region / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / pericentric heterochromatin formation / protein-lysine N-methyltransferase activity / spindle pole body / silent mating-type cassette heterochromatin formation / histone methyltransferase activity / pericentric heterochromatin / histone reader activity / ubiquitin binding / methyltransferase activity / single-stranded DNA binding / methylation / double-stranded DNA binding / single-stranded RNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Histone H3-K9 methyltransferase / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. ...Histone H3-K9 methyltransferase / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Beta-clip-like / SET domain / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase, H3 lysine-9 specific
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7701 Å
AuthorsCurrie, M.A. / Moazed, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1 GM072805 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2018
Title: Automethylation-induced conformational switch in Clr4 (Suv39h) maintains epigenetic stability.
Authors: Iglesias, N. / Currie, M.A. / Jih, G. / Paulo, J.A. / Siuti, N. / Kalocsay, M. / Gygi, S.P. / Moazed, D.
History
DepositionNov 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 22, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Sep 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 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 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_high / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Histone-lysine N-methyltransferase, H3 lysine-9 specific
A: Histone-lysine N-methyltransferase, H3 lysine-9 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,81712
Polymers68,4972
Non-polymers1,32010
Water79344
1
B: Histone-lysine N-methyltransferase, H3 lysine-9 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9086
Polymers34,2481
Non-polymers6605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Histone-lysine N-methyltransferase, H3 lysine-9 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9086
Polymers34,2481
Non-polymers6605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)131.919, 71.040, 96.674
Angle α, β, γ (deg.)90.00, 125.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Histone-lysine N-methyltransferase, H3 lysine-9 specific / Cryptic loci regulator 4 / Histone H3-K9 methyltransferase / H3-K9-HMTase / Lysine N-methyltransferase 1


Mass: 34248.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: clr4, kmt1, SPBC428.08c / Production host: Escherichia coli (E. coli)
References: UniProt: O60016, histone-lysine N-methyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.76 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M magnesium formate dihydrate and 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.7701→79.14 Å / Num. obs: 14482 / % possible obs: 77.15 % / Redundancy: 2.94 % / CC1/2: 0.995 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.084 / Net I/σ(I): 6.5
Reflection shellResolution: 2.7701→2.9839 Å / Rmerge(I) obs: 0.712 / Num. unique obs: 1958 / CC1/2: 0.328 / Rpim(I) all: 0.48

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MVH

1mvh


Resolution: 2.7701→59.349 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2644 704 4.86 %
Rwork0.2228 --
obs0.2248 14482 77.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7701→59.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4386 0 62 44 4492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064574
X-RAY DIFFRACTIONf_angle_d0.5856143
X-RAY DIFFRACTIONf_dihedral_angle_d14.871653
X-RAY DIFFRACTIONf_chiral_restr0.041649
X-RAY DIFFRACTIONf_plane_restr0.003811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7701-2.98390.33421090.27791849X-RAY DIFFRACTION52
2.9839-3.28420.3461110.25542230X-RAY DIFFRACTION63
3.2842-3.75940.32451470.26042834X-RAY DIFFRACTION79
3.7594-4.73610.24521730.20433395X-RAY DIFFRACTION95
4.7361-59.36260.21051640.19823470X-RAY DIFFRACTION95

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