6O22

Structure of Asf1-H3:H4-Rtt109-Vps75 histone chaperone-lysine acetyltransferase complex with the histone substrate.

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 150 
  • Conformers Submitted: 1 
  • Selection Criteria: structures with the least restraint violations 
  • Method: SOLUTION SCATTERING

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Histone chaperone exploits intrinsic disorder to switch acetylation specificity.

Danilenko, N., Lercher, L., Kirkpatrick, J., Gabel, F., Codutti, L., Carlomagno, T.

(2019) Nat Commun 10: 3435-3435

  • DOI: 10.1038/s41467-019-11410-7
  • Primary Citation of Related Structures:  
    6O22

  • PubMed Abstract: 

    • Histones, the principal protein components of chromatin, contain long disordered sequences, which are extensively post-translationally modified. Although histone chaperones are known to control both the activity and specificity of histone-modifying e ...

    Histones, the principal protein components of chromatin, contain long disordered sequences, which are extensively post-translationally modified. Although histone chaperones are known to control both the activity and specificity of histone-modifying enzymes, the mechanisms promoting modification of highly disordered substrates, such as lysine-acetylation within the N-terminal tail of histone H3, are not understood. Here, to understand how histone chaperones Asf1 and Vps75 together promote H3 K9-acetylation, we establish the solution structural model of the acetyltransferase Rtt109 in complex with Asf1 and Vps75 and the histone dimer H3:H4. We show that Vps75 promotes K9-acetylation by engaging the H3 N-terminal tail in fuzzy electrostatic interactions with its disordered C-terminal domain, thereby confining the H3 tail to a wide central cavity faced by the Rtt109 active site. These fuzzy interactions between disordered domains achieve localization of lysine residues in the H3 tail to the catalytic site with minimal loss of entropy, and may represent a common mechanism of enzymatic reactions involving highly disordered substrates.

    Organizational Affiliation: 

    Helmholtz Centre for Infection Research, Group of Structural Chemistry, Inhoffenstrasse 7, D-38124, Braunschweig, Germany. teresa.carlomagno@oci.uni-hannover.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 75A, B264Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VPS75, YNL246W, N0890
Find proteins for P53853 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P53853
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone acetyltransferase RTT109C442Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RTT109, KIM2, REM50, YLL002W, L1377
EC: 2.3.1.48
Find proteins for Q07794 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone chaperone ASF1D279Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ASF1, CIA1, YJL115W, J0755
Find proteins for P32447 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2E136Xenopus laevisMutation(s): 0 
Find proteins for P84233 (Xenopus laevis)
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Go to UniProtKB:  P84233
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4F103Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 150 
  • Conformers Submitted: 1 
  • Selection Criteria: structures with the least restraint violations 
  • OLDERADO: 6O22 Olderado
  • Method: SOLUTION SCATTERING

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Data collection, Database references