Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A6B2C1D1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis, microscopy

Macromolecule Content

• Total Structure Weight: 233.8 kDa 
• Atom Count: 15,578 
• Modelled Residue Count: 1,521 
• Deposited Residue Count: 1,554 
• Unique protein chains: 6
• Unique nucleic acid chains: 2

 7K6Q

Active state Dot1 bound to the H4K16ac nucleosome

• PDB DOI: 10.2210/pdb7K6Q/pdb
• EM Map EMD-22692: EMDB EMDataResource

• Classification: Structural Protein/DNA/Transferase
• Organism(s): Xenopus laevis, synthetic construct, Saccharomyces cerevisiae, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-09-21 Released: 2021-02-10 
• Deposition Author(s): Valencia-Sanchez, M.I., De Ioannes, P.E., Miao, W., Truong, D.M., Lee, R., Armache, J.-P., Boeke, J.D., Armache, K.-J.
• Funding Organization(s): David and Lucile Packard Foundation, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Regulation of the Dot1 histone H3K79 methyltransferase by histone H4K16 acetylation.

Valencia-Sanchez, M.I., De Ioannes, P., Wang, M., Truong, D.M., Lee, R., Armache, J.P., Boeke, J.D., Armache, K.J.

(2021) Science 371

• PubMed: 33479126 
• DOI: 10.1126/science.abc6663
• Primary Citation of Related Structures:  
  7K6P, 7K6Q


• PubMed Abstract: 
  

Dot1 (disruptor of telomeric silencing-1), the histone H3 lysine 79 (H3K79) methyltransferase, is conserved throughout evolution, and its deregulation is found in human leukemias. Here, we provide evidence that acetylation of histone H4 allosterically stimulates yeast Dot1 in a manner distinct from but coordinating with histone H2B ubiquitination (H2BUb). We further demonstrate that this stimulatory effect is specific to acetylation of lysine 16 (H4K16ac), a modification central to chromatin structure. We provide a mechanism of this histone cross-talk and show that H4K16ac and H2BUb play crucial roles in H3K79 di- and trimethylation in vitro and in vivo. These data reveal mechanisms that control H3K79 methylation and demonstrate how H4K16ac, H3K79me, and H2BUb function together to regulate gene transcription and gene silencing to ensure optimal maintenance and propagation of an epigenetic state.

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Organizational Affiliation: 

Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	A, E	98	Xenopus laevis	Mutation(s): 2
UniProt
Find proteins for P84233 (Xenopus laevis) Explore P84233  Go to UniProtKB:  P84233

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	92	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799  Go to UniProtKB:  P62799

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1	C, G	107	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P06897 (Xenopus laevis) Explore P06897  Go to UniProtKB:  P06897

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	D, H	93	Xenopus laevis	Mutation(s): 2
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281  Go to UniProtKB:  P02281

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase, H3 lysine-79 specific	K	406	Saccharomyces cerevisiae	Mutation(s): 0  EC: 2.1.1.360
UniProt
Find proteins for Q04089 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04089  Go to UniProtKB:  Q04089

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	L	76	Homo sapiens	Mutation(s): 1  Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (146-MER)	I	146	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (146-MER)	J	146	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM (Subject of Investigation/LOI)	M [auth K]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	B, F	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cisTEM	1.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-02-10 
Deposition Author(s): Valencia-Sanchez, M.I., De Ioannes, P.E., Miao, W., Truong, D.M., Lee, R., Armache, J.-P., Boeke, J.D., Armache, K.-J.

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Funding Organization	Location	Grant Number
David and Lucile Packard Foundation	United States	na
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R01GM115882-03

Revision History  

• Version 1.0: 2021-02-10
  Type: Initial release