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- PDB-6z2a: Structure of Clr4 mutant - F256A/F310A/F427A bound to SAH -

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Basic information

Entry
Database: PDB / ID: 6z2a
TitleStructure of Clr4 mutant - F256A/F310A/F427A bound to SAH
Components(Histone-lysine N-methyltransferase, H3 lysine-9 ...) x 2
KeywordsTRANSFERASE / H3K9 methyltransferase / Heterochromatin
Function / homology
Function and homology information


CLRC complex / positive regulation of pericentric heterochromatin formation / co-transcriptional gene silencing by RNA interference machinery / siRNA-independent facultative heterochromatin formation / [histone H3]-lysine9 N-trimethyltransferase / subtelomeric heterochromatin / mating-type region heterochromatin / [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / nuclear polyadenylation-dependent antisense transcript catabolic process / histone H3K9 trimethyltransferase activity ...CLRC complex / positive regulation of pericentric heterochromatin formation / co-transcriptional gene silencing by RNA interference machinery / siRNA-independent facultative heterochromatin formation / [histone H3]-lysine9 N-trimethyltransferase / subtelomeric heterochromatin / mating-type region heterochromatin / [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / nuclear polyadenylation-dependent antisense transcript catabolic process / histone H3K9 trimethyltransferase activity / 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 / protein-lysine N-methyltransferase activity / spindle pole body / silent mating-type cassette heterochromatin formation / histone methyltransferase activity / subtelomeric heterochromatin formation / pericentric heterochromatin / ubiquitin binding / histone reader activity / methyltransferase activity / single-stranded DNA binding / double-stranded DNA binding / methylation / single-stranded RNA 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 superfamily / SET domain profile. / SET domain
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone-lysine N-methyltransferase, H3 lysine-9 specific
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.456 Å
AuthorsStirpe, A. / Schalch, T.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science FoundationPP00P3_139137 Switzerland
Swiss National Science FoundationPP00P3_163760_1 Switzerland
Swiss National Science FoundationPP00P3_172904 Switzerland
CitationJournal: Elife / Year: 2021
Title: SUV39 SET domains mediate crosstalk of heterochromatic histone marks.
Authors: Stirpe, A. / Guidotti, N. / Northall, S.J. / Kilic, S. / Hainard, A. / Vadas, O. / Fierz, B. / Schalch, T.
History
DepositionMay 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,90114
Polymers66,5602
Non-polymers1,34112
Water39622
1
A: Histone-lysine N-methyltransferase, H3 lysine-9 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0377
Polymers33,3661
Non-polymers6706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone-lysine N-methyltransferase, H3 lysine-9 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8647
Polymers33,1941
Non-polymers6706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.444, 110.288, 70.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 196 - 489

Dom-IDAuth asym-IDLabel asym-IDLabel seq-ID
1AA2 - 295
2BB1 - 294

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Components

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Histone-lysine N-methyltransferase, H3 lysine-9 ... , 2 types, 2 molecules AB

#1: Protein Histone-lysine N-methyltransferase, H3 lysine-9 specific / Cryptic loci regulator 4 / Histone H3-K9 methyltransferase / HKMT / Lysine N-methyltransferase 1 / ...Cryptic loci regulator 4 / Histone H3-K9 methyltransferase / HKMT / Lysine N-methyltransferase 1 / Protein lysine methyltransferase clr4 / PKMT


Mass: 33366.195 Da / Num. of mol.: 1 / Mutation: F256A, F310A, F427A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Gene: clr4, kmt1, SPBC428.08c / Cell line (production host): RosettaII / Production host: Escherichia coli (E. coli)
References: UniProt: O60016, [histone H3]-lysine9 N-trimethyltransferase
#2: Protein Histone-lysine N-methyltransferase, H3 lysine-9 specific / Cryptic loci regulator 4 / Histone H3-K9 methyltransferase / HKMT / Lysine N-methyltransferase 1 / ...Cryptic loci regulator 4 / Histone H3-K9 methyltransferase / HKMT / Lysine N-methyltransferase 1 / Protein lysine methyltransferase clr4 / PKMT


Mass: 33194.059 Da / Num. of mol.: 1 / Mutation: F256A, F310A, F427A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Gene: clr4, kmt1, SPBC428.08c / Cell line (production host): RosettaII / Production host: Escherichia coli (E. coli)
References: UniProt: O60016, [histone H3]-lysine9 N-trimethyltransferase

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Non-polymers , 4 types, 34 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 71.4 mM MES, 28.6 mM Imidazole, 20% PEG 10000, 30mM Magnesium Acetate, 6.6% v/v MPD, 6.6% v/v PEG 1000, 6.6% v/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 8, 2018
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.456→70.68 Å / Num. obs: 19571 / % possible obs: 72.2 % / Redundancy: 6.1 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.093 / Rrim(I) all: 0.233 / Net I/σ(I): 6.6
Reflection shellResolution: 2.456→2.68 Å / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 979 / CC1/2: 0.627 / CC star: 0.878 / Rpim(I) all: 0.525 / Rrim(I) all: 1.046

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BOX

6box


Resolution: 2.456→70.68 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.91 / SU B: 24.391 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R: 1.848 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2498 973 5 %RANDOM
Rwork0.23851 ---
obs0.23909 18561 72.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.086 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2--0.54 Å2-0 Å2
3----0.3 Å2
Refinement stepCycle: 1 / Resolution: 2.456→70.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4411 0 62 22 4495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134595
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174005
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.6766258
X-RAY DIFFRACTIONr_angle_other_deg1.2271.5829313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7155554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61321.898274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.70415727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3631538
X-RAY DIFFRACTIONr_chiral_restr0.0560.2586
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025214
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021026
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7321.8762237
X-RAY DIFFRACTIONr_mcbond_other0.7321.8762237
X-RAY DIFFRACTIONr_mcangle_it1.3732.8022784
X-RAY DIFFRACTIONr_mcangle_other1.3732.8022785
X-RAY DIFFRACTIONr_scbond_it0.491.9142358
X-RAY DIFFRACTIONr_scbond_other0.491.9142358
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8542.8533475
X-RAY DIFFRACTIONr_long_range_B_refined3.96332.15814617
X-RAY DIFFRACTIONr_long_range_B_other3.96232.15614614
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8152 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.456→2.52 Å
RfactorNum. reflection% reflection
Rfree0.736 1 -
Rwork0.396 41 -
obs--2.1 %
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)
10.65060.91970.06044.47780.63152.4630.0317-0.06840.12040.19670.17630.0278-0.30170.2551-0.2080.1474-0.01690.01210.0524-0.03930.0534-21.989-5.5746-1.7889
20.9339-0.733-0.83653.44140.38674.6575-0.1696-0.0409-0.186-0.06260.1565-0.24730.56760.29210.01310.16030.03480.02290.0265-0.02410.1047-19.3178-35.2017-15.2761
30.95840.1001-0.79553.21680.21543.5353-0.01660.0556-0.0338-0.02640.0890.2305-0.0317-0.19-0.07250.03880.0029-0.02870.01360.00890.0463-30.6729-17.1929-11.5964
42.5824-1.9444-1.3882.17860.36157.2625-0.068-0.0866-0.10860.04430.08810.2312-0.1107-0.3366-0.02010.07470.0146-0.02730.13620.03560.1816-42.532-7.3138-19.1401
51.2379-0.9161-0.16053.65220.54242.69540.11120.0615-0.1074-0.18290.1709-0.00880.3450.3011-0.28210.12260.0208-0.02820.0537-0.04780.0491-21.803715.529-33.4415
61.41590.45530.6762.9780.48674.005-0.1714-0.00020.23390.04550.1614-0.1867-0.630.27150.00990.163-0.0445-0.01840.0327-0.03250.1007-19.404545.0687-20.0797
70.9724-0.13380.58632.87390.03783.3419-0.0085-0.04450.02680.06530.03110.18310.0483-0.1241-0.02260.0216-0.00110.02690.00550.00150.0429-30.17127.0346-23.6435
83.2925-1.9334-0.10434.19661.13598.24140.26520.06070.1739-0.138-0.160.5001-0.1195-0.5938-0.10520.0788-0.04540.03970.15840.050.2308-42.829519.1517-17.2015
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A192 - 248
2X-RAY DIFFRACTION2A249 - 329
3X-RAY DIFFRACTION3A330 - 462
4X-RAY DIFFRACTION4A463 - 490
5X-RAY DIFFRACTION5B192 - 248
6X-RAY DIFFRACTION6B249 - 329
7X-RAY DIFFRACTION7B330 - 462
8X-RAY DIFFRACTION8B463 - 490

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