5YPS

The structural basis of histone chaperoneVps75


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 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 75
A, B, C, D, E
A, B, C, D, E, F
250Pneumocystis carinii B80Mutation(s): 3 
Gene Names: T552_02523
UniProt
Find proteins for A0A0W4ZF97 (Pneumocystis carinii (strain B80))
Explore A0A0W4ZF97 
Go to UniProtKB:  A0A0W4ZF97
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0W4ZF97
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
EA [auth D]
FA [auth D]
GA [auth D]
I [auth A]
J [auth A]
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
Query on PGE

Download Ideal Coordinates CCD File 
BA [auth C]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AB [auth F]
BB [auth F]
HA [auth D]
L [auth A]
RA [auth E]
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
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth C]
CB [auth F]
DB [auth F]
EB [auth F]
IA [auth D]
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)
Query on CA

Download Ideal Coordinates CCD File 
CA [auth D]
DA [auth D]
G [auth A]
H [auth A]
LA [auth E]
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
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
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 = 141.672α = 90
b = 76.404β = 90
c = 130.448γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing
PHENIXmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Key Research and Development Program of ChinaChina2017YFA0505900
The General Program of National Natural Science Foundation of ChinaChina31370735
The General Program of National Natural Science Foundation of ChinaChina3167040397
The Province Science and Technology Support Program,China2015JQO029

Revision History  (Full details and data files)

  • 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