5YPS

The structural basis of histone chaperoneVps75

• PDB DOI:  https://doi.org/10.2210/pdb5YPS/pdb

• Classification: CHAPERONE
• Organism(s): Pneumocystis carinii B80
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-11-03 Released: 2018-11-07 
• Deposition Author(s): Chen, Y., Zhang, Y., Dou, Y., Wang, M., Xu, S., Jiang, H., Limper, A., Su, D.
• Funding Organization(s): National Key Research and Development Program of China, The General Program of National Natural Science Foundation of China, The Province Science and Technology Support Program,

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.236 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

Structural basis for the acetylation of histone H3K9 and H3K27 mediated by the histone chaperone Vps75 inPneumocystis carinii.

Chen, Y., Zhang, Y., Ye, H., Dou, Y., Lu, D., Li, X., Limper, A.H., Hua, J., Su, D.

(2019) Signal Transduct Target Ther 4: 14-14

• PubMed: 31098304 
• DOI: https://doi.org/10.1038/s41392-019-0047-8
• Primary Citation of Related Structures:  
  5YPS, 5ZB5


• PubMed Abstract: 
  

Rtt109 is a histone acetyltransferase (HAT) that is a potential therapeutic target in conditioned pathogenic fungi Pneumocystis carinii (P. carinii) . The histone chaperone Vps75 can stimulate the Rtt109-dependent acetylation of several histone H3 lysines and preferentially acetylates H3K9 and H3K27 within canonical histone (H3-H4) ₂ tetramers. Vps75 shows two protein conformations assembled into dimeric and tetrameric forms, but the roles played by multimeric forms of Vps75 in Rtt109-mediated histone acetylation remain elusive. In P. carinii , we identified that Vps75 (PcVps75) dimers regulate H3K9 and H3K27 acetylation by directly interacting with histone (H3-H4) ₂ tetramers, rather than by forming a Vps75-Rtt109 complex. For PcVps75 tetramers, the major histone-binding surface is buried within a walnut-like structure in the absence of a histone cargo. Based on crystal structures of dimeric and tetrameric forms of PcVps75, as well as HAT assay data, we confirmed that residues 192E, 193D, 194E, 195E, and 196E and the disordered C-terminal tail (residues 224-250) of PcVps75 mediate interactions with histones and are important for the Rtt109 in P. carinii (PcRtt109)-mediated acetylation of H3K9 and H3K27, both in vitro and in yeast cells. Furthermore, expressing PcRtt109 alone or in combination with PcVps75 variants that cannot effectively bind histones could not fully restore cellular growth in the presence of genotoxic agents that block DNA replication owing to the absence of H3K9 and H3K27 acetylation. Together, these data indicate that the interaction between PcVps75 and histone (H3-H4) ₂ tetramers is a critical regulator of the Rtt109-mediated acetylation of H3K9 and H3K27.

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Organizational Affiliation: 

1State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan P. R. China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: mass spectrometry

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 183.18 kDa 
• Atom Count: 10,574 
• Modelled Residue Count: 1,206 
• Deposited Residue Count: 1,500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting-associated protein 75	A, B, C, D, E, F	250	Pneumocystis carinii B80	Mutation(s): 3  Gene Names: T552_02523
UniProt
Find proteins for A0A0W4ZF97 (Pneumocystis carinii (strain B80)) Explore A0A0W4ZF97  Go to UniProtKB:  A0A0W4ZF97

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	EA [auth D], FA [auth D], GA [auth D], I [auth A], J [auth A], K [auth A], NA [auth E], OA [auth E], PA [auth E], QA [auth E], R [auth B], S [auth B], T [auth B], X [auth C], XA [auth F], Y [auth C], YA [auth F], Z [auth C], ZA [auth F]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PGE	BA [auth C]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	AB [auth F], BB [auth F], HA [auth D], L [auth A], RA [auth E], U [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	AA [auth C], CB [auth F], DB [auth F], EB [auth F], IA [auth D], JA [auth D], KA [auth D], M [auth A], N [auth A], SA [auth E], TA [auth E], UA [auth E], V [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	CA [auth D], DA [auth D], G [auth A], H [auth A], LA [auth E], MA [auth E], O [auth B], P [auth B], Q [auth B], VA [auth F], W [auth C], WA [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.236 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.672	α = 90
b = 76.404	β = 90
c = 130.448	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
HKL-2000	data scaling
PHASER	phasing
PHENIX	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-11-07 
Deposition Author(s): Chen, Y., Zhang, Y., Dou, Y., Wang, M., Xu, S., Jiang, H., Limper, A., Su, D.

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Funding Organization	Location	Grant Number
National Key Research and Development Program of China	China	2017YFA0505900
The General Program of National Natural Science Foundation of China	China	31370735
The General Program of National Natural Science Foundation of China	China	3167040397
The Province Science and Technology Support Program,	China	2015JQO029

Revision History  

• Version 1.0: 2018-11-07
  Type: Initial release
  
• Version 1.1: 2019-05-29
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2020-06-10
  Changes: Database references, Structure summary