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- PDB-6px3: Set2 bound to nucleosome -

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Basic information

Entry
Database: PDB / ID: 6px3
TitleSet2 bound to nucleosome
Components
  • (DNA (145-MER)) x 2
  • Histone H2B 1.1
  • Histone H3
  • Histone H4
  • Histone-lysine N-methyltransferase
  • Ubiquitin-60S ribosomal protein L40,Histone H2A
KeywordsGENE REGULATION / Set2 / nucleosome / chromatin / KMT
Function / homology
Function and homology information


[histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / ribosomal large subunit export from nucleus / modification-dependent protein catabolic process / protein tag activity / structural constituent of chromatin / nucleosome / heterochromatin formation / ribosome biogenesis / nucleosome assembly ...[histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / ribosomal large subunit export from nucleus / modification-dependent protein catabolic process / protein tag activity / structural constituent of chromatin / nucleosome / heterochromatin formation / ribosome biogenesis / nucleosome assembly / chromosome / ribosomal large subunit assembly / methylation / cytosolic large ribosomal subunit / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / protein heterodimerization activity / ubiquitin protein ligase binding / regulation of DNA-templated transcription / mitochondrion / DNA binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Histone-lysine N-methyltransferase, Set2, fungi / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Set2 Rpb1 interacting domain superfamily / SETD2/Set2, SET domain / : / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / AWS domain / AWS domain / AWS domain profile. ...Histone-lysine N-methyltransferase, Set2, fungi / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Set2 Rpb1 interacting domain superfamily / SETD2/Set2, SET domain / : / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / TFIIS/LEDGF domain superfamily / WW domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / WW domain superfamily / SET domain / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / SET domain superfamily / SET domain profile. / WW domain / SET domain / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Histone-lysine N-methyltransferase, H3 lysine-36 specific / Histone H2B 1.1 / Histone H3.3C / Ubiquitin-ribosomal protein eL40B fusion protein / Histone H4 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Saccharomyces cerevisiae (brewer's yeast)
Chaetomium thermophilum (fungus)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsHalic, M. / Bilokapic, S.
CitationJournal: Nat Commun / Year: 2019
Title: Nucleosome and ubiquitin position Set2 to methylate H3K36.
Authors: Silvija Bilokapic / Mario Halic /
Abstract: Histone H3 lysine 36 methylation (H3K36me) is a conserved histone modification deposited by the Set2 methyltransferases. Recent findings show that over-expression or mutation of Set2 enzymes promotes ...Histone H3 lysine 36 methylation (H3K36me) is a conserved histone modification deposited by the Set2 methyltransferases. Recent findings show that over-expression or mutation of Set2 enzymes promotes cancer progression, however, mechanisms of H3K36me are poorly understood. Set2 enzymes show spurious activity on histones and histone tails, and it is unknown how they obtain specificity to methylate H3K36 on the nucleosome. In this study, we present 3.8 Å cryo-EM structure of Set2 bound to the mimic of H2B ubiquitinated nucleosome. Our structure shows that Set2 makes extensive interactions with the H3 αN, the H3 tail, the H2A C-terminal tail and stabilizes DNA in the unwrapped conformation, which positions Set2 to specifically methylate H3K36. Moreover, we show that ubiquitin contributes to Set2 positioning on the nucleosome and stimulates the methyltransferase activity. Notably, our structure uncovers interfaces that can be targeted by small molecules for development of future cancer therapies.
History
DepositionJul 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.0Aug 28, 2019Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 28, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 28, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Aug 28, 2019Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 28, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 28, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Aug 28, 2019Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 28, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 28, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.3May 28, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

Deposited unit
A: Histone H3
B: Histone H4
C: Ubiquitin-60S ribosomal protein L40,Histone H2A
D: Histone H2B 1.1
E: Histone H3
F: Histone H4
G: Ubiquitin-60S ribosomal protein L40,Histone H2A
H: Histone H2B 1.1
I: DNA (145-MER)
J: DNA (145-MER)
S: Histone-lysine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)326,67514
Polymers326,47811
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area59550 Å2
ΔGint-418 kcal/mol
Surface area87030 Å2

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Components

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Protein , 5 types, 9 molecules AEBFCGDHS

#1: Protein Histone H3


Mass: 15437.144 Da / Num. of mol.: 2 / Mutation: K36M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: XELAEV_18002543mg / Production host: Escherichia coli (E. coli) / References: UniProt: A0A310TTQ1, UniProt: P02302*PLUS
#2: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein Ubiquitin-60S ribosomal protein L40,Histone H2A


Mass: 24045.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Xenopus laevis (African clawed frog)
Strain: ATCC 204508 / S288c
Gene: RPL40B, UBI2, YKR094C, hist1h2aj, LOC494591, XELAEV_18003602mg
Production host: Escherichia coli (E. coli) / References: UniProt: P0CH09, UniProt: Q6AZJ8
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13655.948 Da / Num. of mol.: 2 / Mutation: S29T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281
#7: Protein Histone-lysine N-methyltransferase


Mass: 105425.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0025760 / Production host: Escherichia coli (E. coli)
References: UniProt: G0S676, histone-lysine N-methyltransferase

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (145-MER)


Mass: 45764.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (145-MER)


Mass: 46222.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 1 types, 3 molecules

#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Set2 bound to ubiquitinated nucleosomeCOMPLEX#1-#70MULTIPLE SOURCES
2Histone-lysine N-methyltransferaseCOMPLEX#71RECOMBINANT
3DNACOMPLEX#5-#61RECOMBINANT
4Histone H3, Histone H4, Ubiquitin-60S ribosomal protein L40,Histone H2A, Histone H2B 1.1COMPLEX#1-#41RECOMBINANT
Molecular weightValue: 0.26 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
34Xenopus laevis (African clawed frog)8355
12Chaetomium thermophilum (fungus)759272
23synthetic construct (others)32630
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli (E. coli)562
34Escherichia coli (E. coli)562
23synthetic construct (others)32630
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recording
IDImaging-IDElectron dose (e/Å2)Detector modeFilm or detector model
1175COUNTINGGATAN K2 SUMMIT (4k x 4k)
2175GATAN K2 BASE (4k x 4k)
3175GATAN K2 BASE (4k x 4k)
4175GATAN K2 BASE (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.16_3546: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00815161
ELECTRON MICROSCOPYf_angle_d0.9321702
ELECTRON MICROSCOPYf_dihedral_angle_d24.0588125
ELECTRON MICROSCOPYf_chiral_restr0.0562447
ELECTRON MICROSCOPYf_plane_restr0.0071760

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