[English] 日本語
Yorodumi
- PDB-6nn6: Structure of Dot1L-H2BK120ub nucleosome complex -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6nn6
TitleStructure of Dot1L-H2BK120ub nucleosome complex
Components
  • (DNA (145-MER)) x 2
  • Histone H2A type 1
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • Histone-lysine N-methyltransferase, H3 lysine-79 specificHistone methyltransferase
  • Ubiquitin
KeywordsGENE REGULATION / chromatin / structural biology / single particle / cryo-EM / histone methyltransferase / nucleosome / Dot1L
Function / homologyHistone H4, conserved site / Histone H2A/H2B/H3 / Histone H3/CENP-A / Histone H2B / Ubiquitin domain / Histone H4 / Histone H2A / TATA box binding protein associated factor (TAF) / Histone-fold / Histone H2A, C-terminal domain ...Histone H4, conserved site / Histone H2A/H2B/H3 / Histone H3/CENP-A / Histone H2B / Ubiquitin domain / Histone H4 / Histone H2A / TATA box binding protein associated factor (TAF) / Histone-fold / Histone H2A, C-terminal domain / Histone H2A conserved site / Ubiquitin conserved site / Ubiquitin / Histone H3-K79 methyltransferase, metazoa / Histone-lysine N-methyltransferase DOT1 domain / S-adenosyl-L-methionine-dependent methyltransferase / Ubiquitin-like domain superfamily / CENP-T/Histone H4, histone fold / Core histone H2A/H2B/H3/H4 / Ubiquitin family / Ubiquitin domain signature. / PKMTs methylate histone lysines / Histone-lysine N-methyltransferase DOT1 (EC 2.1.1.43) domain profile. / Ubiquitin domain profile. / Histone H3 signature 2. / Histone H2B signature. / Histone H3 signature 1. / Histone H4 signature. / Histone H2A signature. / C-terminus of histone H2A / Centromere kinetochore component CENP-T histone fold / Histone methylation protein DOT1 / Histone H3-K79 methyltransferase / histone methyltransferase activity (H3-K79 specific) / regulation of transcription regulatory region DNA binding / histone H3-K79 methylation / histone methyltransferase activity / regulation of receptor signaling pathway via JAK-STAT / chromatin silencing at telomere / histone-lysine N-methyltransferase / histone-lysine N-methyltransferase activity / telomere organization / DNA-templated transcription, initiation / DNA damage checkpoint / nucleosome / chromosome, telomeric region / nucleosome assembly / intracellular membrane-bounded organelle / transcription factor binding / positive regulation of cell population proliferation / protein heterodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / Polyubiquitin-C / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Histone-lysine N-methyltransferase, H3 lysine-79 specific
Function and homology information
Specimen sourceXenopus laevis (African clawed frog)
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsAnderson, C.J. / Baird, M.R. / Hsu, A. / Barbour, E.H. / Koyama, Y. / Borgnia, M.J. / McGinty, R.K.
CitationJournal: Cell Rep / Year: 2019
Title: Structural Basis for Recognition of Ubiquitylated Nucleosome by Dot1L Methyltransferase.
Authors: Cathy J Anderson / Matthew R Baird / Allen Hsu / Emily H Barbour / Yuka Koyama / Mario J Borgnia / Robert K McGinty
Abstract: Histone H3 lysine 79 (H3K79) methylation is enriched on actively transcribed genes, and its misregulation is a hallmark of leukemia. Methylation of H3K79, which resides on the structured disk face of ...Histone H3 lysine 79 (H3K79) methylation is enriched on actively transcribed genes, and its misregulation is a hallmark of leukemia. Methylation of H3K79, which resides on the structured disk face of the nucleosome, is mediated by the Dot1L methyltransferase. Dot1L activity is part of a trans-histone crosstalk pathway, requiring prior histone H2B ubiquitylation of lysine 120 (H2BK120ub) for optimal activity. However, the molecular details describing both how Dot1L binds to the nucleosome and why Dot1L is activated by H2BK120 ubiquitylation are unknown. Here, we present the cryoelectron microscopy (cryo-EM) structure of Dot1L bound to a nucleosome reconstituted with site-specifically ubiquitylated H2BK120. The structure reveals that Dot1L engages the nucleosome acidic patch using a variant arginine anchor and occupies a conformation poised for methylation. In this conformation, Dot1L and ubiquitin interact directly through complementary hydrophobic surfaces. This study establishes a path to better understand Dot1L function in normal and leukemia cells.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 14, 2019 / Release: Feb 13, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 13, 2019Structure modelrepositoryInitial release
1.1Feb 27, 2019Structure modelData collection / Database referencescitation / citation_author_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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-0458
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A type 1
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A type 1
H: Histone H2B 1.1
I: DNA (145-MER)
J: DNA (145-MER)
K: Histone-lysine N-methyltransferase, H3 lysine-79 specific
L: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)254,26212
Polyers254,26212
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

-
Components

-
Protein/peptide , 6 types, 10 molecules AEBFCGDHKL

#1: Protein/peptide Histone H3.2


Mass: 15303.930 Da / Num. of mol.: 2 / Mutation: G103A / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid name: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P84233
#2: Protein/peptide Histone H4 /


Mass: 11263.231 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid name: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P62799
#3: Protein/peptide Histone H2A type 1


Mass: 13978.241 Da / Num. of mol.: 2 / Mutation: G100R, A124S / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid name: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P06897
#4: Protein/peptide Histone H2B 1.1 / H2B1.1


Mass: 13642.846 Da / Num. of mol.: 2 / Mutation: S33T, K121C / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid name: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P02281
#7: Protein/peptide Histone-lysine N-methyltransferase, H3 lysine-79 specific / Histone methyltransferase / DOT1-like protein / Histone H3-K79 methyltransferase / H3-K79-HMTase / Lysine N-methyltransferase 4


Mass: 47462.039 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: DOT1L, KIAA1814, KMT4 / Plasmid name: pST50 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q8TEK3, histone-lysine N-methyltransferase
#8: Protein/peptide Ubiquitin /


Mass: 8911.180 Da / Num. of mol.: 1 / Mutation: G76S / Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid name: pST50 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: F5H388

-
DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (145-MER)


Mass: 44520.383 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others) / Details: Widom 601 nucleosome positioning sequence
#6: DNA chain DNA (145-MER)


Mass: 44991.660 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others) / Details: Widom 601 nucleosome positioning sequence

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Dot1L-H2BK120ub nucleosome complex (Class 2A) / Type: COMPLEX / Entity ID: 1,2,3,4,5,6,7,8 / Source: RECOMBINANT
Molecular weightValue: 0.27 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 0.93 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 kelvins

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 60 sec. / Electron dose: 48 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Number of grids imaged: 1 / Number of real images: 1000

-
Processing

EM software
IDNameVersionCategory
1RELION2.1particle selection
2EPUimage acquisition
4Gctf1.06CTF correction
7UCSF Chimera1.12model fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIX1.13model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 408526
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 39558 / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL
Atomic model building
IDPDB-IDPdb chain ID 3D fitting IDPdb chain residue range
11NW3A11-332
21UBQA11-74
33LZ0A1
43LZ0B1
53LZ0C1
63LZ0D1
73LZ0E1
83LZ0F1
93LZ0G1
103LZ0H1
113LZ0I1
123LZ0J1

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more