8T9H

Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1

• PDB DOI: https://doi.org/10.2210/pdb8T9H/pdb
• EM Map EMD-41111: EMDB EMDataResource
• NAKB: 8T9H

• Classification: GENE REGULATION
• Organism(s): Xenopus laevis, Escherichia coli 'BL21-Gold(DE3)pLysS AG, Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2023-06-24 Released: 2023-09-13 
• Deposition Author(s): Abini-Agbomson, S., Armache, K.-J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), The Mark Foundation, National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.37 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1

Abini-Agbomson, S., Armache, K.-J.

(2023) Mol Cell 83: 2872-2883

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A2B2C2D2E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A8B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 243.76 kDa 
• Atom Count: 12,039 
• Modelled Residue Count: 1,204 
• Deposited Residue Count: 1,668 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	A, E	135	Xenopus laevis	Mutation(s): 1
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	103	Xenopus laevis	Mutation(s): 0  Gene Names: LOC121398084
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	C, G	130	Xenopus laevis	Mutation(s): 0  Gene Names: hist1h2aj, LOC494591, XELAEV_18003602mg
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	123	Xenopus laevis	Mutation(s): 1
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 KMT5B	K	394	Homo sapiens	Mutation(s): 0  Gene Names: KMT5B
UniProt & NIH Common Fund Data Resources
Find proteins for Q4FZB7 (Homo sapiens) Explore Q4FZB7  Go to UniProtKB:  Q4FZB7
PHAROS:  Q4FZB7 GTEx:  ENSG00000110066

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (146-MER)	I	146	Escherichia coli 'BL21-Gold(DE3)pLysS AG

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (146-MER)	J	146	Escherichia coli 'BL21-Gold(DE3)pLysS AG

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.37 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-13 
Deposition Author(s): Abini-Agbomson, S., Armache, K.-J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM115882
The Mark Foundation	United States	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5T32GM088118
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA266978

Revision History  

• Version 1.0: 2023-09-13
  Type: Initial release