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- PDB-8guj: Bre1-nucleosome complex (Model II) -

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Basic information

Entry
Database: PDB / ID: 8guj
TitleBre1-nucleosome complex (Model II)
Components
  • (DNA (147-mer)) x 2
  • (E3 ubiquitin-protein ligase ...) x 2
  • Histone H2A type 1
  • Histone H2B type 1-J
  • Histone H3.1
  • Histone H4
KeywordsGENE REGULATION/DNA / transcription / ubiquitin ligase / cancer / chromatin / GENE REGULATION / GENE REGULATION-DNA complex
Function / homology
Function and homology information


histone H2B C-terminal K residue ubiquitin ligase activity / HULC complex / RHOBTB1 GTPase cycle / ubiquitin ligase complex / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome ...histone H2B C-terminal K residue ubiquitin ligase activity / HULC complex / RHOBTB1 GTPase cycle / ubiquitin ligase complex / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / negative regulation of cell migration / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / mRNA 3'-UTR binding / innate immune response in mucosa / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / RING-type E3 ubiquitin transferase / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / protein polyubiquitination / HCMV Early Events / ubiquitin-protein transferase activity / antimicrobial humoral immune response mediated by antimicrobial peptide / p53 binding / ubiquitin protein ligase activity / structural constituent of chromatin / UCH proteinases / antibacterial humoral response / nucleosome / heterochromatin formation / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / histone binding / defense response to Gram-negative bacterium / gene expression / killing of cells of another organism / Estrogen-dependent gene expression / transcription coactivator activity / chromosome, telomeric region / defense response to Gram-positive bacterium / Ub-specific processing proteases / protein ubiquitination / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / ubiquitin protein ligase binding / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / nucleolus
Similarity search - Function
E3 ubiquitin ligase Bre1 / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. ...E3 ubiquitin ligase Bre1 / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / : / 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 / Zinc finger RING-type profile. / Zinc finger, RING-type / 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 / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / E3 ubiquitin-protein ligase BRE1B / Histone H2B type 1-J / Histone H2A type 1 / Histone H4 / Histone H3.1 / E3 ubiquitin-protein ligase BRE1A
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsOnishi, S. / Sato, K. / Hamada, K. / Nishizawa, T. / Nureki, O. / Ogata, K. / Sengoku, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nat Commun / Year: 2024
Title: Structure of the human Bre1 complex bound to the nucleosome.
Authors: Shuhei Onishi / Kotone Uchiyama / Ko Sato / Chikako Okada / Shunsuke Kobayashi / Keisuke Hamada / Tomohiro Nishizawa / Osamu Nureki / Kazuhiro Ogata / Toru Sengoku /
Abstract: Histone H2B monoubiquitination (at Lys120 in humans) regulates transcription elongation and DNA repair. In humans, H2B monoubiquitination is catalyzed by the heterodimeric Bre1 complex composed of ...Histone H2B monoubiquitination (at Lys120 in humans) regulates transcription elongation and DNA repair. In humans, H2B monoubiquitination is catalyzed by the heterodimeric Bre1 complex composed of Bre1A/RNF20 and Bre1B/RNF40. The Bre1 proteins generally function as tumor suppressors, while in certain cancers, they facilitate cancer cell proliferation. To obtain structural insights of H2BK120 ubiquitination and its regulation, we report the cryo-electron microscopy structure of the human Bre1 complex bound to the nucleosome. The two RING domains of Bre1A and Bre1B recognize the acidic patch and the nucleosomal DNA phosphates around SHL 6.0-6.5, which are ideally located to recruit the E2 enzyme and ubiquitin for H2BK120-specific ubiquitination. Mutational experiments suggest that the two RING domains bind in two orientations and that ubiquitination occurs when Bre1A binds to the acidic patch. Our results provide insights into the H2BK120-specific ubiquitination by the Bre1 proteins and suggest that H2B monoubiquitination can be regulated by nuclesomal DNA flexibility.
History
DepositionSep 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 2.0Feb 7, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / ndb_struct_na_base_pair ...atom_site / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_contact_author / pdbx_database_related / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conf / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.hbond_type_28 / _ndb_struct_na_base_pair.opening / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair.shear / _ndb_struct_na_base_pair.stagger / _ndb_struct_na_base_pair.stretch / _ndb_struct_na_base_pair_step.helical_rise / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.rise / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.shift / _ndb_struct_na_base_pair_step.slide / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _ndb_struct_na_base_pair_step.twist / _ndb_struct_na_base_pair_step.x_displacement / _ndb_struct_na_base_pair_step.y_displacement / _pdbx_struct_conn_angle.value / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value
Description: Atomic clashes / Provider: author / Type: Coordinate replacement
Revision 2.1Apr 3, 2024Group: 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
Revision 2.2Jun 18, 2025Group: Data collection / Structure summary / Category: em_software / pdbx_entry_details
Item: _em_software.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.1
B: Histone H4
C: Histone H2A type 1
D: Histone H2B type 1-J
E: Histone H3.1
F: Histone H4
G: Histone H2A type 1
H: Histone H2B type 1-J
I: DNA (147-mer)
J: DNA (147-mer)
K: E3 ubiquitin-protein ligase BRE1A
L: E3 ubiquitin-protein ligase BRE1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)428,55416
Polymers428,29212
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H3.1


Mass: 15437.167 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P68431
#2: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Protein Histone H2A type 1 / H2A.1 / Histone H2A/ptl


Mass: 13990.342 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H2AC11, H2AFP, HIST1H2AG, H2AC13, H2AFC, HIST1H2AI, H2AC15, H2AFD, HIST1H2AK, H2AC16, H2AFI, HIST1H2AL, H2AC17, H2AFN, HIST1H2AM
Production host: Escherichia coli (E. coli) / References: UniProt: P0C0S8
#4: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 14217.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2BC11, H2BFR, HIST1H2BJ / Production host: Escherichia coli (E. coli) / References: UniProt: P06899

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (147-mer)


Mass: 45145.754 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (147-mer)


Mass: 45604.047 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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E3 ubiquitin-protein ligase ... , 2 types, 2 molecules KL

#7: Protein E3 ubiquitin-protein ligase BRE1A / BRE1-A / hBRE1 / RING finger protein 20 / RING-type E3 ubiquitin transferase BRE1A


Mass: 113861.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF20, BRE1A / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q5VTR2, RING-type E3 ubiquitin transferase
#8: Protein E3 ubiquitin-protein ligase BRE1B / BRE1-B / 95 kDa retinoblastoma-associated protein / RBP95 / RING finger protein 40 / RING-type E3 ...BRE1-B / 95 kDa retinoblastoma-associated protein / RBP95 / RING finger protein 40 / RING-type E3 ubiquitin transferase BRE1B


Mass: 113863.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF40, BRE1B, KIAA0661 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: O75150, RING-type E3 ubiquitin transferase

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Non-polymers , 1 types, 4 molecules

#9: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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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
1Bre1-nucleosome complexCOMPLEX#1-#80MULTIPLE SOURCES
2HistoneCOMPLEX#1-#41RECOMBINANT
3DNACOMPLEX#5-#61SYNTHETIC
4Bre1COMPLEX#7-#81RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
42Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
42Trichoplusia ni (cabbage looper)7111
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 / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83000 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 67.85 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003814180
ELECTRON MICROSCOPYf_angle_d0.57420386
ELECTRON MICROSCOPYf_chiral_restr0.03572305
ELECTRON MICROSCOPYf_plane_restr0.00521563
ELECTRON MICROSCOPYf_dihedral_angle_d31.64213979

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