5YPS | pdb_00005yps

The structural basis of histone chaperoneVps75


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.236 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5YPS

This is version 1.3 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 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.

Macromolecule Content 

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

Macromolecules

Find similar proteins by:|  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 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
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
  • Version 1.3: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Structure summary