6RR0 | pdb_00006rr0

Crystal structure of the Sir4 H-BRCT domain in complex with Ubp10 pT123 peptide

PDB DOI: https://doi.org/10.2210/pdb6RR0/pdb

Classification: NUCLEAR PROTEIN
Organism(s): Saccharomyces cerevisiae, Saccharomyces cerevisiae S288C
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-05-16 Released: 2019-09-18
Deposition Author(s): Deshpande, I., Keusch, J.J., Challa, K., Iesmantavicius, V., Gasser, S.M., Gut, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free:
0.218 (Depositor), 0.231 (DCC)
R-Value Work:
0.196 (Depositor), 0.205 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The Sir4 H-BRCT domain interacts with phospho-proteins to sequester and repress yeast heterochromatin.

Deshpande, I., Keusch, J.J., Challa, K., Iesmantavicius, V., Gasser, S.M., Gut, H.

(2019) EMBO J 38: e101744-e101744

PubMed: 31515872 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.15252/embj.2019101744
Primary Citation Related Structures:
6QSZ, 6QTM, 6RR0, 6RRV

PubMed Abstract:
In Saccharomyces cerevisiae, the silent information regulator (SIR) proteins Sir2/3/4 form a complex that suppresses transcription in subtelomeric regions and at the homothallic mating-type (HM) loci. Here, we identify a non-canonical BRCA1 C-terminal domain (H-BRCT) in Sir4, which is responsible for tethering telomeres to the nuclear periphery. We show that Sir4 H-BRCT and the closely related Dbf4 H-BRCT serve as selective phospho-epitope recognition domains that bind to a variety of phosphorylated target peptides. We present detailed structural information about the binding mode of established Sir4 interactors (Esc1, Ty5, Ubp10) and identify several novel interactors of Sir4 H-BRCT, including the E3 ubiquitin ligase Tom1. Based on these findings, we propose a phospho-peptide consensus motif for interaction with Sir4 H-BRCT and Dbf4 H-BRCT. Ablation of the Sir4 H-BRCT phospho-peptide interaction disrupts SIR-mediated repression and perinuclear localization. In conclusion, the Sir4 H-BRCT domain serves as a hub for recruitment of phosphorylated target proteins to heterochromatin to properly regulate silencing and nuclear order.

Organizational Affiliation

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.

Macromolecule Content

Total Structure Weight: 113.47 kDa
Atom Count: 7,527
Modeled Residue Count: 868
Deposited Residue Count: 973
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Regulatory protein SIR4	A, B, C, D, E A, B, C, D, E, F, G	127	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SIR4, ASD1, STE9, UTH2, YDR227W, YD9934.12
UniProt
Find proteins for P11978 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P11978 Go to UniProtKB: P11978
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11978
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 10	H, I, J, K, L H, I, J, K, L, M, N	12	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.19.12
UniProt
Find proteins for P53874 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53874 Go to UniProtKB: P53874
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53874
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A]	O [auth A], P [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain O [auth A] Focus chain P [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO Query on TPO	H, I, J, K, L H, I, J, K, L, M, N	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.218 (Depositor), 0.231 (DCC)
R-Value Work: 0.196 (Depositor), 0.205 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.04	α = 90
b = 75.28	β = 97.24
c = 95.91	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-09-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-09-18
Type: Initial release
Version 1.1: 2019-09-25
Changes: Data collection, Database references
Version 1.2: 2019-10-23
Changes: Data collection, Database references
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Structure summary