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  (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: gel filtration

Macromolecule Content

• Total Structure Weight: 254.76 kDa 
• Atom Count: 16,336 
• Modelled Residue Count: 1,557 
• Deposited Residue Count: 1,709 
• Unique protein chains: 6
• Unique nucleic acid chains: 2

 6NE3

Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h bound at SHL-2

• PDB DOI: 10.2210/pdb6NE3/pdb
• EM Map EMD-9356: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Xenopus laevis, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-12-16 Released: 2019-07-17 
• Deposition Author(s): Armache, J.-P., Gamarra, N., Johnson, S.L., Leonard, J.D., Wu, S., Narlikar, G.N., Cheng, Y.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI), Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome.

Armache, J.P., Gamarra, N., Johnson, S.L., Leonard, J.D., Wu, S., Narlikar, G.J., Cheng, Y.

(2019) Elife 8

• PubMed: 31210637 
• DOI: 10.7554/eLife.46057
• Primary Citation of Related Structures:  
  6NE3


• PubMed Abstract: 
  

The SNF2h remodeler slides nucleosomes most efficiently as a dimer, yet how the two protomers avoid a tug-of-war is unclear. Furthermore, SNF2h couples histone octamer deformation to nucleosome sliding, but the underlying structural basis remains unknown. Here we present cryo-EM structures of SNF2h-nucleosome complexes with ADP-BeF _x that capture two potential reaction intermediates. In one structure, histone residues near the dyad and in the H2A-H2B acidic patch, distal to the active SNF2h protomer, appear disordered. The disordered acidic patch is expected to inhibit the second SNF2h protomer, while disorder near the dyad is expected to promote DNA translocation. The other structure doesn't show octamer deformation, but surprisingly shows a 2 bp translocation. FRET studies indicate that ADP-BeF _x predisposes SNF2h-nucleosome complexes for an elemental translocation step. We propose a model for allosteric control through the nucleosome, where one SNF2h protomer promotes asymmetric octamer deformation to inhibit the second protomer, while stimulating directional DNA translocation.

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Organizational Affiliation: 

Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	A, E	136	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
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	130	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	D	99	Xenopus laevis	Mutation(s): 0  Gene Names: XELAEV_18032686mg
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281  Go to UniProtKB:  P02281

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	H	93	Xenopus laevis	Mutation(s): 0  Gene Names: XELAEV_18032686mg
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281  Go to UniProtKB:  P02281

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5	K [auth W]	467	Homo sapiens	Mutation(s): 0  Gene Names: SMARCA5, SNF2H, WCRF135 EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for O60264 (Homo sapiens) Explore O60264  Go to UniProtKB:  O60264
PHAROS:  O60264

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (156-MER)	I [auth J]	156	Xenopus laevis

Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA (156-MER)	J [auth I]	156	Xenopus laevis

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	L [auth W]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-17 
Deposition Author(s): Armache, J.-P., Gamarra, N., Johnson, S.L., Leonard, J.D., Wu, S., Narlikar, G.N., Cheng, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	GM073767
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	GM108455
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R01GM082893
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	1S10OD020054
Other government	United States	UCSF Program for Breakthrough Biomedical Research - New Technology Award

Revision History  

• Version 1.0: 2019-07-17
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence, Other