9BAQ

CryoEM structure of DIM2-HP1-H3K9me3-DNA complex

• PDB DOI: https://doi.org/10.2210/pdb9BAQ/pdb
• NAKB: 9BAQ
• EM Map EMD-44411: EMDB EMDataResource

• Classification: Transferase/DNA Binding Protein/DNA
• Organism(s): Neurospora crassa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-04-04 Released: 2024-07-24 
• Deposition Author(s): Song, J., Shao, Z.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.79 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

CryoEM structure of DIM2-HP1-H3K9me3-DNA complex

Song, J., Shao, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B1C1D1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 217.98 kDa 
• Atom Count: 9,733 
• Modelled Residue Count: 1,189 
• Deposited Residue Count: 1,866 
• Unique protein chains: 3
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA (cytosine-5-)-methyltransferase	A	1,244	Neurospora crassa	Mutation(s): 0  Gene Names: dim-2, GE21DRAFT_10473 EC: 2.1.1.37
UniProt
Find proteins for Q96W73 (Neurospora crassa) Explore Q96W73  Go to UniProtKB:  Q96W73

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heterochromatin protein one	B, C	268	Neurospora crassa	Mutation(s): 0  Gene Names: 49D12.150, hpo, GE21DRAFT_9232
UniProt
Find proteins for Q870N8 (Neurospora crassa) Explore Q870N8  Go to UniProtKB:  Q870N8

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	D, E [auth F]	25	Neurospora crassa	Mutation(s): 0
UniProt
Find proteins for Q5MYA4 (Cichorium intybus) Explore Q5MYA4  Go to UniProtKB:  Q5MYA4

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*TP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*TP*AP*GP*T)-3')	F [auth G]	18	Neurospora crassa

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*CP*TP*AP*CP*T)-R(P*(PYO))-D(P*CP*TP*CP*CP*TP*CP*CP*TP*AP*CP*T)-3')	G [auth H]	18	Neurospora crassa

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	H [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
ZN	I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L	D, E [auth F]	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.79 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-24 
Deposition Author(s): Song, J., Shao, Z.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2024-07-24
  Type: Initial release