6NE3

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 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

  • 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 unk ...

    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

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.,Tetrad Graduate Program, University of California, San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, E
136Xenopus laevisMutation(s): 1 
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
103Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1
C, G
130Xenopus laevisMutation(s): 1 
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B
D
99Xenopus laevisMutation(s): 0 
Find proteins for A0A1L8FQ56 (Xenopus laevis)
Go to UniProtKB:  A0A1L8FQ56
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Histone H2B
H
93Xenopus laevisMutation(s): 0 
Find proteins for A0A1L8FQ56 (Xenopus laevis)
Go to UniProtKB:  A0A1L8FQ56
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5
W
467Homo sapiensMutation(s): 0 
Gene Names: SMARCA5 (SNF2H, WCRF135)
EC: 3.6.4.-
Find proteins for O60264 (Homo sapiens)
Go to Gene View: SMARCA5
Go to UniProtKB:  O60264
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (156-MER)J156Xenopus laevis
Entity ID: 7
MoleculeChainsLengthOrganism
DNA (156-MER)I156Xenopus laevis
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
W
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesGM073767
National Institutes of Health/National Human Genome Research InstituteUnited StatesGM108455
National Institutes of Health/National Human Genome Research InstituteUnited StatesR01GM082893
National Institutes of Health/National Human Genome Research InstituteUnited States1S10OD020054
Other governmentUnited StatesUCSF Program for Breakthrough Biomedical Research - New Technology Award

Revision History 

  • Version 1.0: 2019-07-17
    Type: Initial release