3Q66 | pdb_00003q66

Structure of the Vps75-Rtt109 histone chaperone-lysine acetyltransferase complex (Full-length proteins in space group P6122)

PDB DOI: https://doi.org/10.2210/pdb3Q66/pdb

Classification: CHAPERONE/TRANSFERASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-12-30 Released: 2011-03-23
Deposition Author(s): Su, D., Thompson, J.R., Mer, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free:
0.247 (Depositor), 0.236 (DCC)
R-Value Work:
0.206 (Depositor), 0.198 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structure and histone binding properties of the Vps75-Rtt109 chaperone-lysine acetyltransferase complex.

Su, D., Hu, Q., Zhou, H., Thompson, J.R., Xu, R.M., Zhang, Z., Mer, G.

(2011) J Biological Chem 286: 15625-15629

PubMed: 21454705 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.C111.220715
Primary Citation Related Structures:
3Q66, 3Q68

PubMed Abstract:
The histone chaperone Vps75 presents the remarkable property of stimulating the Rtt109-dependent acetylation of several histone H3 lysine residues within (H3-H4)(2) tetramers. To investigate this activation mechanism, we determined x-ray structures of full-length Vps75 in complex with full-length Rtt109 in two crystal forms. Both structures show similar asymmetric assemblies of a Vps75 dimer bound to an Rtt109 monomer. In the Vps75-Rtt109 complexes, the catalytic site of Rtt109 is confined to an enclosed space that can accommodate the N-terminal tail of histone H3 in (H3-H4)(2). Investigation of Vps75-Rtt109-(H3-H4)(2) and Vps75-(H3-H4)(2) complexes by NMR spectroscopy-probed hydrogen/deuterium exchange suggests that Vps75 guides histone H3 in the catalytic enclosure. These findings clarify the basis for the enhanced acetylation of histone H3 tail residues by Vps75-Rtt109.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA.

Macromolecule Content

Total Structure Weight: 112.31 kDa
Atom Count: 7,413
Modeled Residue Count: 885
Deposited Residue Count: 970
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting-associated protein 75	A, C [auth B]	264	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: N0890, VPS75, YNL246W
UniProt
Find proteins for P53853 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53853 Go to UniProtKB: P53853
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53853
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone acetyltransferase RTT109	B [auth C]	442	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: KIM2, L1377, REM50, RTT109, YLL002W EC: 2.3.1.48
UniProt
Find proteins for Q07794 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q07794 Go to UniProtKB: Q07794
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q07794
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain D [auth A] MOL2 format, chain E [auth C] MOL2 format, chain D [auth A] mmCIF format, chain E [auth C] mmCIF format, chain D [auth A]	D [auth A], E [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY Query on ALY	B [auth C]	L-PEPTIDE LINKING	C₈ H₁₆ N₂ O₃		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free: 0.247 (Depositor), 0.236 (DCC)
R-Value Work: 0.206 (Depositor), 0.198 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.385	α = 90
b = 99.385	β = 90
c = 479.605	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-03-23

Deposition Author(s):

Su, D.

Thompson, J.R.

Mer, G.

Revision History (Full details and data files)

Version 1.0: 2011-03-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-12-06
Changes: Data collection
Version 1.4: 2024-10-09
Changes: Structure summary