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- PDB-6jma: cryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome -

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Entry
Database: PDB / ID: 6jma
Titlecryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome
Components
  • DNA I&J
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • Histone-lysine N-methyltransferase, H3 lysine-79 specificHistone methyltransferase
  • Ubiquitin
KeywordsGENE REGULATION / histone / nucleosome / methylation
Function / homology
Function and homology information


histone methyltransferase activity (H3-K79 specific) / [histone H3]-lysine79 N-trimethyltransferase / regulation of transcription regulatory region DNA binding / histone H3-K79 methylation / hypothalamus gonadotrophin-releasing hormone neuron development / mitochondrion transport along microtubule / regulation of receptor signaling pathway via JAK-STAT / fat pad development / histone methyltransferase activity / female meiosis I ...histone methyltransferase activity (H3-K79 specific) / [histone H3]-lysine79 N-trimethyltransferase / regulation of transcription regulatory region DNA binding / histone H3-K79 methylation / hypothalamus gonadotrophin-releasing hormone neuron development / mitochondrion transport along microtubule / regulation of receptor signaling pathway via JAK-STAT / fat pad development / histone methyltransferase activity / female meiosis I / positive regulation of protein monoubiquitination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / male meiosis I / histone-lysine N-methyltransferase activity / chromatin silencing at telomere / female gonad development / seminiferous tubule development / regulation of neuron death / energy homeostasis / telomere organization / MyD88-independent toll-like receptor signaling pathway / nucleotide-excision repair, DNA gap filling / regulation of proteasomal protein catabolic process / nucleotide-binding oligomerization domain containing signaling pathway / nucleotide-excision repair, DNA damage recognition / regulation of mitochondrial membrane potential / nucleotide-excision repair, DNA duplex unwinding / TRIF-dependent toll-like receptor signaling pathway / DNA-templated transcription, initiation / positive regulation of protein ubiquitination / global genome nucleotide-excision repair / DNA damage checkpoint / nucleotide-excision repair, preincision complex assembly / neuron projection morphogenesis / endosomal transport / intracellular transport of virus / DNA damage response, detection of DNA damage / MyD88-dependent toll-like receptor signaling pathway / nucleotide-excision repair, DNA incision, 5'-to lesion / host cell / error-free translesion synthesis / modification-dependent protein catabolic process / nucleotide-excision repair, DNA incision / JNK cascade / protein targeting to peroxisome / chromosome, telomeric region / nucleosome / protein tag / stress-activated MAPK cascade / interstrand cross-link repair / endocytic vesicle membrane / error-prone translesion synthesis / interleukin-1-mediated signaling pathway / regulation of transcription from RNA polymerase II promoter in response to hypoxia / I-kappaB kinase/NF-kappaB signaling / viral life cycle / transcription-coupled nucleotide-excision repair / negative regulation of transforming growth factor beta receptor signaling pathway / translesion synthesis / transforming growth factor beta receptor signaling pathway / virion assembly / anaphase-promoting complex-dependent catabolic process / transmembrane transport / regulation of mRNA stability / membrane organization / protein polyubiquitination / Wnt signaling pathway / mitochondrial outer membrane / vesicle / activation of MAPK activity / endosome membrane / positive regulation of NF-kappaB transcription factor activity / protein ubiquitination / protein deubiquitination / protein heterodimerization activity / neuron projection / positive regulation of apoptotic process / intracellular membrane-bounded organelle / DNA repair / cytokine-mediated signaling pathway / transcription factor binding / neuronal cell body / endoplasmic reticulum membrane / cellular protein metabolic process / ubiquitin protein ligase binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / plasma membrane / nucleus / cytosol / cytoplasm
Ubiquitin family / Ubiquitin domain / Histone H2B / Ubiquitin-like domain / Histone H4 / Histone H2A / TATA box binding protein associated factor (TAF) / Histone H2A/H2B/H3 / Histone-fold / Histone H4, conserved site ...Ubiquitin family / Ubiquitin domain / Histone H2B / Ubiquitin-like domain / Histone H4 / Histone H2A / TATA box binding protein associated factor (TAF) / Histone H2A/H2B/H3 / Histone-fold / Histone H4, conserved site / Ubiquitin conserved site / Histone H3-K79 methyltransferase, metazoa / Histone-lysine N-methyltransferase DOT1 domain / S-adenosyl-L-methionine-dependent methyltransferase / Ubiquitin-like domain superfamily / Histone H3-K79 methyltransferase / Histone H2A, C-terminal domain / Histone H2A conserved site / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / C-terminus of histone H2A / Histone methylation protein DOT1 / Histone H3/CENP-A
Histone H2B 1.1 / Polyubiquitin-B / Histone H4 / Histone H3.2 / Histone H2A / Histone-lysine N-methyltransferase, H3 lysine-79 specific
Biological speciessynthetic construct (others)
Xenopus laevis (African clawed frog)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsJang, S. / Song, J.J.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2016R1A2B3006293 Korea, Republic Of
National Research Foundation (Korea)NRF-2016K1A1A2912057 Korea, Republic Of
National Research Foundation (Korea)NRF- 2016H1A2A1908806 Korea, Republic Of
CitationJournal: Genes Dev. / Year: 2019
Title: Structural basis of recognition and destabilization of the histone H2B ubiquitinated nucleosome by the DOT1L histone H3 Lys79 methyltransferase.
Authors: Seongmin Jang / Chanshin Kang / Han-Sol Yang / Taeyang Jung / Hans Hebert / Ka Young Chung / Seung Joong Kim / Sungchul Hohng / Ji-Joon Song /
Abstract: DOT1L is a histone H3 Lys79 methyltransferase whose activity is stimulated by histone H2B Lys120 ubiquitination, suggesting cross-talk between histone H3 methylation and H2B ubiquitination. Here, we ...DOT1L is a histone H3 Lys79 methyltransferase whose activity is stimulated by histone H2B Lys120 ubiquitination, suggesting cross-talk between histone H3 methylation and H2B ubiquitination. Here, we present cryo-EM structures of DOT1L complexes with unmodified or H2B ubiquitinated nucleosomes, showing that DOT1L recognizes H2B ubiquitin and the H2A/H2B acidic patch through a C-terminal hydrophobic helix and an arginine anchor in DOT1L, respectively. Furthermore, the structures combined with single-molecule FRET experiments show that H2B ubiquitination enhances a noncatalytic function of the DOT1L-destabilizing nucleosome. These results establish the molecular basis of the cross-talk between H2B ubiquitination and H3 Lys79 methylation as well as nucleosome destabilization by DOT1L.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 19, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 6, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB

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Structure visualization

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Assembly

Deposited unit
I: DNA I&J
J: DNA I&J
A: Histone H3.2
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
X: Histone-lysine N-methyltransferase, H3 lysine-79 specific
Y: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,47813
Polymers206,08012
Non-polymers3981
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area54510 Å2
ΔGint-367 kcal/mol
Surface area81990 Å2

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Components

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Protein , 6 types, 10 molecules AEBFCGDHXY

#2: Protein Histone H3.2


Mass: 11488.410 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 BL21 (bacteria) / Variant (production host): BL21 / References: UniProt: P84233
#3: Protein Histone H4 /


Mass: 9990.770 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 BL21 (bacteria) / Variant (production host): BL21 / References: UniProt: P62799
#4: Protein Histone H2A /


Mass: 12660.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): BL21 / References: UniProt: Q6AZJ8
#5: Protein Histone H2B 1.1 / H2B1.1


Mass: 10478.032 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 BL21 (bacteria) / Variant (production host): BL21 / References: UniProt: P02281
#6: Protein Histone-lysine N-methyltransferase, H3 lysine-79 specific / Histone methyltransferase / DOT1-like protein


Mass: 37930.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DOT1L / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): BL21
References: UniProt: Q8TEK3, histone-lysine N-methyltransferase
#7: Protein Ubiquitin /


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): BL21 / References: UniProt: P0CG47

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DNA chain / Non-polymers , 2 types, 3 molecules IJ

#1: DNA chain DNA I&J


Mass: 35168.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli DH5[alpha] (bacteria)
#8: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S

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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

ComponentName: DOT1L bound to H2B ubiquitinated nucleosome / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.29 MDa / Experimental value: NO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Source (recombinant)Organism: Escherichia coli BL21 (bacteria)
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

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 37.28 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 122242 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT

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