6NE3

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


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2A, E136Xenopus laevisMutation(s): 1 
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Find proteins for P84233 (Xenopus laevis)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F103Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1C, G130Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P06897 (Xenopus laevis)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2BD99Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18032686mg
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Find proteins for P02281 (Xenopus laevis)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2BH93Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18032686mg
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5K [auth W]467Homo sapiensMutation(s): 0 
Gene Names: SMARCA5SNF2HWCRF135
EC: 3.6.4
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Find proteins for O60264 (Homo sapiens)
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PHAROS:  O60264
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (156-MER)I [auth J]156Xenopus laevis
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (156-MER)J [auth I]156Xenopus laevis
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
L [auth W]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM073767
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM108455
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR01GM082893
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United States1S10OD020054
Other governmentUnited StatesUCSF Program for Breakthrough Biomedical Research - New Technology Award

Revision History  (Full details and data files)

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