6K1P

The complex of ISWI-nucleosome in the ADP.BeF-bound state

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.87 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

Structures of the ISWI-nucleosome complex reveal a conserved mechanism of chromatin remodeling.

Yan, L., Wu, H., Li, X., Gao, N., Chen, Z.

(2019) Nat Struct Mol Biol 26: 258-266

  • DOI: 10.1038/s41594-019-0199-9
  • Primary Citation of Related Structures:  
    6IRO, 6JYL, 6K1P

  • PubMed Abstract: 

    • Chromatin remodelers are diverse enzymes, and different models have been proposed to explain how these proteins work. Here we report the 3.3 Å-resolution cryogenic electron microscopy (cryo-EM) structures of Saccharomyces cerevisiae ISWI (ISW1) in complex with the nucleosome in adenosine diphosphate (ADP)-bound and ADP-BeF x -bound states ...

    Chromatin remodelers are diverse enzymes, and different models have been proposed to explain how these proteins work. Here we report the 3.3 Å-resolution cryogenic electron microscopy (cryo-EM) structures of Saccharomyces cerevisiae ISWI (ISW1) in complex with the nucleosome in adenosine diphosphate (ADP)-bound and ADP-BeF x -bound states. The data show that after nucleosome binding, ISW1 is activated by substantial rearrangement of the catalytic domains, with the regulatory AutoN domain packing the first RecA-like core and the NegC domain being disordered. The high-resolution structure reveals local DNA distortion and translocation induced by ISW1 in the ADP-bound state, which is essentially identical to that induced by the Snf2 chromatin remodeler, suggesting a common mechanism of DNA translocation. The histone core remains largely unperturbed, and prevention of histone distortion by crosslinking did not inhibit the activity of yeast ISW1 or its human homolog. Together, our findings suggest a general mechanism of chromatin remodeling involving local DNA distortion without notable histone deformation.

    Organizational Affiliation: 

    Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing, China. zhucheng_chen@tsinghua.edu.cn.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3A, E135Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18002543mg, LOC121398065, LOC108703785, LOC121398067
UniProt
Find proteins for A0A310TTQ1 (Xenopus laevis)
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Go to UniProtKB:  A0A310TTQ1
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UniProt GroupA0A310TTQ1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F102Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AC, G129Xenopus laevisMutation(s): 0 
Gene Names: hist1h2aj, LOC494591, XELAEV_18003602mg, h2ac14.L, h2ac14, hist1h2aj.L
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis)
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UniProt GroupQ6AZJ8
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1D, H122Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
ISWI chromatin-remodeling complex ATPase ISW1K1,061Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ISW1, YBR245C, YBR1633
EC: 3.6.4
UniProt
Find proteins for P38144 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (167-MER)I167Escherichia coli K-12
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (167-MER)J167Escherichia coli K-12
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP
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N [auth K]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
BEF (Subject of Investigation/LOI)
Query on BEF
Download Ideal Coordinates CCD File 
L [auth K]BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K		 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG
Download Ideal Coordinates CCD File 
M [auth K]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Other