3GYP | pdb_00003gyp

Rtt106p

• PDB DOI: https://doi.org/10.2210/pdb3GYP/pdb

• Classification: CHAPERONE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-04-04 Released: 2009-12-08 
• Deposition Author(s): Liu, Y., Huang, H., Shi, Y., Teng, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.274 (Depositor), 0.293 (DCC) 
• R-Value Work: 
  0.218 (Depositor) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

Structural analysis of Rtt106p reveals a DNA-binding role required for heterochromatin silencing

Liu, Y., Huang, H., Zhou, B.O., Wang, S.S., Hu, Y., Li, X., Liu, J., Zang, J., Niu, L., Wu, J., Zhou, J.Q., Teng, M., Shi, Y.

(2010) J Biological Chem 285: 4251-4262

• PubMed: 20007951 
• DOI: https://doi.org/10.1074/jbc.M109.055996
• Primary Citation Related Structures: 
  3GYO, 3GYP


• PubMed Abstract: 
  

  Rtt106p is a Saccharomyces cerevisiae histone chaperone with roles in heterochromatin silencing and nucleosome assembly. The molecular mechanism by which Rtt106p engages in chromatin dynamics remains unclear. Here, we report the 2.5 A crystal structure of the core domain of Rtt106p, which adopts an unusual "double pleckstrin homology" domain architecture that represents a novel structural mode for histone chaperones. A histone H3-H4-binding region and a novel double-stranded DNA-binding region have been identified. Mutagenesis studies reveal that the histone and DNA binding activities of Rtt106p are involved in Sir protein-mediated heterochromatin formation. Our results uncover the structural basis of the diverse functions of Rtt106p and provide new insights into its cellular roles.

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Organizational Affiliation: 
• From the Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 and.
the State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, the Graduate School, Chinese Academy of Sciences, Shanghai 200031, China.
From the Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 and. Electronic address: [e-mail].
From the Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 and. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 29.92 kDa 
• Atom Count: 1,801 
• Modeled Residue Count: 225 
• Deposited Residue Count: 261 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone chaperone RTT106	A	261	Saccharomyces cerevisiae	Mutation(s): 1  Gene Names: RTT106
UniProt
Find proteins for P40161 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40161  Go to UniProtKB:  P40161

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BME	B [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.274 (Depositor), 0.293 (DCC) 
• R-Value Work:  0.218 (Depositor) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.417	α = 90
b = 54.006	β = 90
c = 109.51	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-08 
Deposition Author(s): Liu, Y., Huang, H., Shi, Y., Teng, M.

Revision History  

• Version 1.0: 2009-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.4: 2024-05-29
  Changes: Data collection