5ZBA

Crystal structure of Rtt109-Asf1-H3-H4-CoA complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 

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Literature

Multisite Substrate Recognition in Asf1-Dependent Acetylation of Histone H3 K56 by Rtt109.

Zhang, L., Serra-Cardona, A., Zhou, H., Wang, M., Yang, N., Zhang, Z., Xu, R.M.

(2018) Cell 174: 818-830.e11

  • DOI: 10.1016/j.cell.2018.07.005
  • Primary Citation of Related Structures:  
    5ZB9, 5ZBA, 5ZBB

  • PubMed Abstract: 

    • Rtt109 is a unique histone acetyltransferase acetylating histone H3 lysine 56 (H3K56), a modification critical for DNA replication-coupled nucleosome assembly and genome stability. In cells, histone chaperone Asf1 is essential for H3K56 acetylation, yet the mechanisms for H3K56 specificity and Asf1 requirement remain unknown ...

    Rtt109 is a unique histone acetyltransferase acetylating histone H3 lysine 56 (H3K56), a modification critical for DNA replication-coupled nucleosome assembly and genome stability. In cells, histone chaperone Asf1 is essential for H3K56 acetylation, yet the mechanisms for H3K56 specificity and Asf1 requirement remain unknown. We have determined the crystal structure of the Rtt109-Asf1-H3-H4 complex and found that unwinding of histone H3 α N , where K56 is normally located, and stabilization of the very C-terminal β strand of histone H4 by Asf1 are prerequisites for H3K56 acetylation. Unexpectedly, an interaction between Rtt109 and the central helix of histone H3 is also required. The observed multiprotein, multisite substrate recognition mechanism among histone modification enzymes provides mechanistic understandings of Rtt109 and Asf1 in H3K56 acetylation, as well as valuable insights into substrate recognition by histone modification enzymes in general.

    Organizational Affiliation: 

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, 100049 Beijing, China. Electronic address: rmxu@ibp.ac.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA damage response protein Rtt109, putativeA544Aspergillus fumigatus Af293Mutation(s): 0 
Gene Names: AFUA_5G09540
EC: 2.3.1.48
UniProt
Find proteins for Q4WUS9 (Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100))
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Go to UniProtKB:  Q4WUS9
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone chaperone asf1B188Aspergillus fumigatus Af293Mutation(s): 0 
Gene Names: asf1, AFUA_3G11030
UniProt
Find proteins for Q4WXX5 (Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100))
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3C136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749
UniProt
Find proteins for P61830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4D103Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752
UniProt
Find proteins for P02309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA (Subject of Investigation/LOI)
Query on COA
Download Ideal Coordinates CCD File 
 E [auth A]COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N		 Ligand Interaction
IOD
Query on IOD
Download Ideal Coordinates CCD File 
AA [auth C] , BA [auth C] , CA [auth C] , DA [auth C] , EA [auth C] , F [auth A] , FA [auth C] , G [auth A] , 
AA [auth C],  BA [auth C],  CA [auth C],  DA [auth C],  EA [auth C],  F [auth A],  FA [auth C],  G [auth A],  GA [auth C],  H [auth A],  HA [auth C],  I [auth A],  IA [auth C],  J [auth A],  JA [auth C],  K [auth A],  KA [auth D],  L [auth A],  LA [auth D],  M [auth A],  MA [auth D],  N [auth A],  NA [auth D],  O [auth A],  OA [auth D],  P [auth A],  PA [auth D],  Q [auth A],  R [auth A],  S [auth A],  T [auth A],  U [auth A],  V [auth A],  W [auth B],  X [auth C],  Y [auth C],  Z [auth C]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY		AL-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.903α = 90
b = 111.903β = 90
c = 332.715γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
NSFCChina31210103914
NSFCChina31521002
NSFCChina31430018
Ministry of Science and Technology of ChinaChina2015CB856200
Chinese Academy of SciencesChinaXDB08010100
Beijing Municipal Science and Technology ProjectChinaZ171100000417001
NIHUnited StatesGM118015

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-08-22
    Changes: Data collection, Database references