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- PDB-9it4: Structure of Clr4 catalyzing histone H3 K9 methylation -

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Basic information

Entry
Database: PDB / ID: 9it4
TitleStructure of Clr4 catalyzing histone H3 K9 methylation
Components
  • Histone H3.1/H3.2
  • Histone-lysine N-methyltransferase, H3 lysine-9 specific
KeywordsGENE REGULATION / Epigenetics / Methylation / Crosstalk / Histone
Function / homology
Function and homology information


Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / CLRC complex / Oxidative Stress Induced Senescence / Factors involved in megakaryocyte development and platelet production / co-transcriptional gene silencing by RNA interference machinery / Estrogen-dependent gene expression / RNA Polymerase I Promoter Escape ...Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / CLRC complex / Oxidative Stress Induced Senescence / Factors involved in megakaryocyte development and platelet production / co-transcriptional gene silencing by RNA interference machinery / Estrogen-dependent gene expression / RNA Polymerase I Promoter Escape / siRNA-independent facultative heterochromatin formation / [histone H3]-lysine9 N-trimethyltransferase / nucleolar peripheral inclusion body / subtelomeric heterochromatin / Transcriptional regulation by small RNAs / mating-type region heterochromatin / [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / heterochromatin boundary formation / histone H3K9 trimethyltransferase activity / mitotic sister chromatid biorientation / histone H3K9 monomethyltransferase activity / [histone H3]-lysine9 N-methyltransferase / siRNA-mediated pericentric heterochromatin formation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / ubiquitin-modified histone reader activity / pericentric heterochromatin formation / chromatin-protein adaptor activity / spindle pole body / protein-lysine N-methyltransferase activity / silent mating-type cassette heterochromatin formation / histone methyltransferase activity / histone reader activity / subtelomeric heterochromatin formation / pericentric heterochromatin / heterochromatin / ubiquitin binding / methyltransferase activity / structural constituent of chromatin / heterochromatin formation / nucleosome / single-stranded DNA binding / double-stranded DNA binding / methylation / single-stranded RNA binding / protein heterodimerization activity / DNA damage response / DNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Histone H3-K9 methyltransferase / : / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain ...Histone H3-K9 methyltransferase / : / Pre-SET motif / Pre-SET domain / 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. / 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 / SET domain profile. / SET domain superfamily / 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 domain / Histone-fold
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase, H3 lysine-9 specific / Histone H3.1/H3.2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsDu, Y.X. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22137005 China
CitationJournal: Sci Adv / Year: 2025
Title: Mechanistic insights into the stimulation of the histone H3K9 methyltransferase Clr4 by proximal H3K14 ubiquitination.
Authors: Du, Y. / Sun, M. / Li, Z. / Wu, X. / Qu, Q. / Ai, H. / Liu, L.
History
DepositionJul 19, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Database references / Category: citation / citation_author
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

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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
F: Histone H3.1/H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5457
Polymers35,8852
Non-polymers6605
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-8 kcal/mol
Surface area14320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.130, 70.384, 110.466
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-681-

HOH

21B-714-

HOH

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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 / HKMT / Lysine N- ...Cryptic loci regulator 4 / Histone H3-K9 methyltransferase / H3-K9-HMTase / HKMT / Lysine N-methyltransferase 1 / Protein lysine methyltransferase clr4 / PKMT


Mass: 34078.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Strain: 972 / Gene: clr4, kmt1, SPBC428.08c / Variant: 972 / ATCC 24843 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli)
References: UniProt: O60016, [histone H3]-lysine9 N-trimethyltransferase, [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase, [histone H3]-lysine9 N-methyltransferase
#2: Protein/peptide Histone H3.1/H3.2


Mass: 1807.084 Da / Num. of mol.: 1 / Mutation: K9L, K14C / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: P09988
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Magnesium chloride hexahydrate, 0.1 M MES, pH 6.0, 8 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979176 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979176 Å / Relative weight: 1
ReflectionResolution: 2.29→36.88 Å / Num. obs: 14058 / % possible obs: 97.9 % / Redundancy: 10 % / Biso Wilson estimate: 30.07 Å2 / CC1/2: 0.925 / CC star: 0.98 / Rpim(I) all: 0.053 / Rrim(I) all: 0.169 / Χ2: 0.922 / Net I/σ(I): 15.56
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
2.29-2.345650.9551
2.34-2.386170.9541
2.38-2.436440.9651
2.43-2.486820.9791
2.48-2.536970.9741
2.53-2.597040.9761
2.59-2.666950.981
2.66-2.737040.9851
2.73-2.817190.991
2.81-2.96950.9911
2.9-37200.9911
3-3.127070.9921
3.12-3.267310.9951
3.26-3.446900.9951
3.44-3.657320.9931
3.65-3.937320.9911
3.93-4.337120.9961
4.33-4.957420.9941
4.95-6.247560.9941
6.24-36.888140.9941

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
Aimless0.7.4data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BP4

6bp4


Resolution: 2.39→36.88 Å / SU ML: 0.2617 / Cross valid method: FREE R-VALUE / σ(F): 0.42 / Phase error: 25.2182
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2653 1142 10.01 %
Rwork0.221 10266 -
obs0.2254 11408 90.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.6 Å2
Refinement stepCycle: LAST / Resolution: 2.39→36.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2262 0 31 142 2435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052339
X-RAY DIFFRACTIONf_angle_d0.88453161
X-RAY DIFFRACTIONf_chiral_restr0.052333
X-RAY DIFFRACTIONf_plane_restr0.0044419
X-RAY DIFFRACTIONf_dihedral_angle_d16.7538862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.50.33691080.2622980X-RAY DIFFRACTION70.51
2.5-2.630.33961160.2671075X-RAY DIFFRACTION76.2
2.63-2.790.33941320.25391186X-RAY DIFFRACTION84.76
2.8-3.010.27831530.24341343X-RAY DIFFRACTION96.52
3.01-3.310.29471560.231394X-RAY DIFFRACTION98.98
3.31-3.790.2871490.22061351X-RAY DIFFRACTION95.3
3.79-4.780.19361600.18711430X-RAY DIFFRACTION98.82
4.78-36.880.24221680.21021507X-RAY DIFFRACTION98.13
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)
14.256036289992.066883814362.514558562283.27175540425-2.891925564379.060971716670.164501179520.30117306722-0.141438413618-0.189090629219-0.398140666247-0.0569020309743-0.1583183708040.04123981381590.1201904854240.5540645025270.1069236382090.07025986253220.260347291818-0.03794367578690.35411108683222.907254882818.48136875574.07866056676
20.924273155578-0.5009816029140.3487805332543.40140446612-0.4926541852652.86156727645-0.07493201977170.00352263170737-0.02581825439120.160862750837-0.117969963216-0.2253397461020.03683866528890.208065556640.1717904834150.138226908635-0.02070839981040.02913006994860.167432830318-0.002253062894370.21073267319821.33951749065.3667964529829.0779692932
31.25223335249-1.12104322749-0.3618777993716.908439927640.8199711458712.55225952887-0.0555784485891-0.0963868189386-0.06584333708090.0139763937047-0.1145084493070.765101747055-0.0173449740966-0.4478632644990.07454650476580.126814894158-0.0268107334139-0.01823885800070.213685359416-0.02277812006920.2659982530619.086616665789.2859336579125.7285869603
45.65179659586-1.32808004866-2.392906839924.87108250144-0.0809640108893.59100660281-0.4940632288010.328651909319-0.692323713911-0.690884294826-0.05755443525010.5226967775920.486181111279-0.2145906237910.2105100679490.413079285562-0.1389336362150.001205036172910.127542471594-0.09005956504850.27770097457814.464677328-3.7417209379417.4796107347
54.0675169519-1.173000301533.110463981386.55974497191-1.256395041515.341520583150.132047108109-0.713686092265-0.0741759959799-0.2225923436290.4959905415451.645541838980.314892467716-0.882406161863-0.442540883280.351073342789-0.11106703496-0.1518888152750.440298914280.00943462662130.6945516152912.44377454527-4.570856598513.4059857923
67.29368285668-9.91421766264.902799684242.00072796735-5.293609642034.488634294210.110852557725-0.662428628614-1.114994725512.10360906524-0.1666635673682.497590284181.2826466697-2.699103081160.04097365818910.470600449859-0.235500441250.278286291210.891600647817-0.1318883481570.527947098986-1.572746321887.3303103740423.2361469678
71.69982163171-2.40904155391-0.6453612587117.4728217776.185036178897.11584161624-0.0462643791159-0.395722733561-2.280989069311.39655631686-0.28612594219-0.07092995746652.956696452121.342725226390.162352494780.7886502646010.1704258698160.004496036321410.4878703638720.1245287043530.9642961645326.77771635454-4.2542813644732.884563147
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 195 through 214 )BA195 - 2141 - 20
22chain 'B' and (resid 215 through 359 )BA215 - 35921 - 162
33chain 'B' and (resid 360 through 437 )BA360 - 437163 - 238
44chain 'B' and (resid 438 through 475 )BA438 - 475239 - 257
55chain 'B' and (resid 476 through 490 )BA476 - 490258 - 272
66chain 'F' and (resid 5 through 8 )FH5 - 81 - 4
77chain 'F' and (resid 10 through 18 )FH10 - 186 - 14

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