Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 113.03 kDa 
• Atom Count: 5,534 
• Modelled Residue Count: 688 
• Deposited Residue Count: 971 
• Unique protein chains: 4

 5ZBA

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

• PDB DOI: 10.2210/pdb5ZBA/pdb

• Classification: TRANSFERASE/STRUCTURAL PROTEIN
• Organism(s): Aspergillus fumigatus Af293, Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2018-02-10 Released: 2018-07-25 
• Deposition Author(s): Zhang, L., Serra-Cardona, A., Zhou, H., Wang, M., Yang, N., Zhang, Z., Xu, R.M.
• Funding Organization(s): NSFC, Ministry of Science and Technology of China, Chinese Academy of Sciences, Beijing Municipal Science and Technology Project, NIH

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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 

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

• PubMed: 30057113 
• 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. 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.

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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: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage response protein Rtt109, putative	A	544	Aspergillus fumigatus Af293	Mutation(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)) Explore Q4WUS9  Go to UniProtKB:  Q4WUS9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone chaperone asf1	B	188	Aspergillus fumigatus Af293	Mutation(s): 0  Gene Names: asf1, AFUA_3G11030
UniProt
Find proteins for Q4WXX5 (Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)) Explore Q4WXX5  Go to UniProtKB:  Q4WXX5

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	C	136	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749
UniProt
Find proteins for P61830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P61830  Go to UniProtKB:  P61830

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	D	103	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752
UniProt
Find proteins for P02309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P02309  Go to UniProtKB:  P02309

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	E [auth A]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
IOD	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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	A	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

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 = 111.903	α = 90
b = 111.903	β = 90
c = 332.715	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-07-25 
Deposition Author(s): Zhang, L., Serra-Cardona, A., Zhou, H., Wang, M., Yang, N., Zhang, Z., Xu, R.M.

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Funding Organization	Location	Grant Number
NSFC	China	31210103914
NSFC	China	31521002
NSFC	China	31430018
Ministry of Science and Technology of China	China	2015CB856200
Chinese Academy of Sciences	China	XDB08010100
Beijing Municipal Science and Technology Project	China	Z171100000417001
NIH	United States	GM118015

Revision History  

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