8SKZ | pdb_00008skz

Cryo-EM structure of DDM1-HELLS chimera bound to the nucleosome

• PDB DOI: https://doi.org/10.2210/pdb8SKZ/pdb
• NAKB: 8SKZ
• EM Map EMD-40569: EMDB EMDataResource

• Classification: TRANSLOCASE
• Organism(s): Arabidopsis thaliana, Homo sapiens, Xenopus laevis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-04-20 Released: 2024-11-20 
• Deposition Author(s): Nartey, W., Williams, G.J.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM complex of DDM1-HELLS chimera bound to the nucleosome

Nartey, W., Williams, G.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A2B2C2D2E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A6B2C1 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: gel filtration

Macromolecule Content 

• Total Structure Weight: 323.87 kDa 
• Atom Count: 17,251 
• Modeled Residue Count: 1,661 
• Deposited Residue Count: 2,209 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent DNA helicase DDM1,Lymphoid-specific helicase chimera	A	821	Arabidopsis thaliana, Homo sapiens	Mutation(s): 0  Gene Names: DDM1, HELLS EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRZ9 (Homo sapiens) Explore Q9NRZ9  Go to UniProtKB:  Q9NRZ9
PHAROS:  Q9NRZ9 GTEx:  ENSG00000119969
Find proteins for Q9XFH4 (Arabidopsis thaliana) Explore Q9XFH4  Go to UniProtKB:  Q9XFH4
UniProt Groups	Q9NRZ9Q9XFH4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	B, E	136	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P84233 (Xenopus laevis) Explore P84233  Go to UniProtKB:  P84233

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	C, G	133	Xenopus laevis	Mutation(s): 0  Gene Names: h2ac14.L
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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	F, I	110	Xenopus laevis	Mutation(s): 0  Gene Names: LOC121398084
UniProt
Find proteins for A0A8J1LTD2 (Xenopus laevis) Explore A0A8J1LTD2  Go to UniProtKB:  A0A8J1LTD2

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (192-MER)	J	192	Homo sapiens

Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA (192-MER)	K	192	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	L [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF (Subject of Investigation/LOI)	M [auth A]	BERYLLIUM TRIFLUORIDE ION Be F3 OGIAHMCCNXDTIE-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3.2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-20 
Deposition Author(s): Nartey, W., Williams, G.J.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-2018-04327

Revision History  

• Version 1.0: 2024-11-20
  Type: Initial release