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- PDB-5ww0: Crystal structure of Set7, a novel histone methyltransferase in S... -

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Basic information

Entry
Database: PDB / ID: 5ww0
TitleCrystal structure of Set7, a novel histone methyltransferase in Schizossacharomyces pombe
ComponentsSET domain-containing protein 7
KeywordsTRANSCRIPTION / Histone / methytransferase / Schizosaccharomyces pombe SET7 / Epigenetic
Function / homology
Function and homology information


histone H3K37 methyltransferase activity / sporulation resulting in formation of a cellular spore / Transferases; Transferring one-carbon groups; Methyltransferases / chromatin organization / methylation / chromatin / nucleus / cytosol / cytoplasm
Similarity search - Function
Histone-lysine N-methyltransferase, H3 lysine-37 specific / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain
Similarity search - Domain/homology
Histone-lysine N-methyltransferase, H3 lysine-37 specific
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMevius, D.E.H.F. / Shen, Y. / Morishita, M. / Carrozzini, B. / Caliandro, R. / di Luccio, E.
Funding support Korea, Republic Of, Italy, 4items
OrganizationGrant numberCountry
BK21 Plus KNU Creative BioResearch Group, Kyungpook National University Korea, Republic Of
National Research Foundation of Korea (NRF)NRF-2013R1A1A2012486 Korea, Republic Of
NRFCNR-NRF joint projects 2016 Korea, Republic Of
National Research Council (Italy)CNR-NRF joint projects 2016 Italy
CitationJournal: Structure / Year: 2019
Title: Set7 Is a H3K37 Methyltransferase in Schizosaccharomyces pombe and Is Required for Proper Gametogenesis.
Authors: Shen, Y. / Mevius, D.E.H.F. / Caliandro, R. / Carrozzini, B. / Roh, Y. / Kim, J. / Kim, S. / Ha, S.C. / Morishita, M. / di Luccio, E.
History
DepositionDec 30, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2May 15, 2019Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 14, 2022Group: Database references / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_src_gen / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.details / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref_seq_dif.details
Revision 1.4Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SET domain-containing protein 7
B: SET domain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3884
Polymers39,1962
Non-polymers1922
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-41 kcal/mol
Surface area12370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.119, 66.119, 259.073
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein SET domain-containing protein 7


Mass: 19597.812 Da / Num. of mol.: 2 / Fragment: UNP residues 1-145
Source method: isolated from a genetically manipulated source
Details: Authors state that YPYDVPDYAAPG at the C-terminal are detection tags
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Strain: 972 / ATCC 24843 / Gene: set7, SPCC297.04c / Plasmid: pTYB12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9Y7Q6, histone-lysine N-methyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.09 Å3/Da / Density % sol: 41.11 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% ethylene glycol (cryoprotectant for 101)250mM Ammonium Sulfate, 14% PEG 3.350, 1(protein):1(buffer):0.4 ratio of 0.3M Glycyl-glycyl-glycine (~48mM final conc), Protein ...Details: 30% ethylene glycol (cryoprotectant for 101)250mM Ammonium Sulfate, 14% PEG 3.350, 1(protein):1(buffer):0.4 ratio of 0.3M Glycyl-glycyl-glycine (~48mM final conc), Protein concentration(4mg/mL), Protein buffer(10mM Tris pH 7.5) Temperature(13), Well volume(500ul), 5uL of HCL (12.1M) was added to the reservoir drop prior to drop setup
Temp details: 13

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 16, 2016
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 19879 / % possible obs: 95 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.824 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-20002.3.9data reduction
HKL-20002.3.9data scaling
Sir201416.1phasing
PHENIX1.10.1-2155model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KMA

3kma


Resolution: 2.1→45 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.811 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.185
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/ F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 960 5.1 %RANDOM
Rwork0.176 ---
obs0.179 18019 92.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 10 199 2222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192073
X-RAY DIFFRACTIONr_bond_other_d0.0020.021907
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.9522807
X-RAY DIFFRACTIONr_angle_other_deg1.01134392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0375241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05723.67109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49815359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4541516
X-RAY DIFFRACTIONr_chiral_restr0.1090.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212330
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02502
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_it2.7492.618970
X-RAY DIFFRACTIONr_mcbond_other2.7382.616969
X-RAY DIFFRACTIONr_mcangle_it4.1393.9061209
X-RAY DIFFRACTIONr_mcangle_other4.1373.9081210
X-RAY DIFFRACTIONr_scbond_it3.8333.1871103
X-RAY DIFFRACTIONr_scbond_other3.7193.1751095
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0394.5611586
X-RAY DIFFRACTIONr_long_range_B_refined8.54722.3122442
X-RAY DIFFRACTIONr_long_range_B_other8.42221.7812369
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 57 -
Rwork0.226 1059 -
obs--75.97 %

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