6L9J | pdb_00006l9j

Structure of yeast Snf5 and Swi3 subcomplex

PDB DOI: https://doi.org/10.2210/pdb6L9J/pdb

Classification: GENE REGULATION
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-11-10 Released: 2020-11-11
Deposition Author(s): Long, J., Zhou, H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free:
0.280 (Depositor), 0.281 (DCC)
R-Value Work:
0.229 (Depositor), 0.230 (DCC)
R-Value Observed:
0.231 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Snf5 and Swi3 subcomplex formation is required for SWI/SNF complex function in yeast.

Zhou, H., Chen, G., Dong, C., Zhao, X., Shen, Z., Chen, F., Liu, B., Long, J.

(2020) Biochem Biophys Res Commun 526: 934-940

PubMed: 32284172 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2020.03.169
Primary Citation Related Structures:
6L9J

PubMed Abstract:
The SWI/SNF chromatin remodeling complex, which alters nucleosome positions by either evicting histones or sliding nucleosomes on DNA, is highly conserved from yeast to humans, and 20% of all human cancers have mutations in various subunits of the SWI/SNF complex. Here, we reported the crystal structure of the yeast Snf5-Swi3 subcomplex at a resolution of 2.65 Å. Our results showed that the Snf5-Swi3 subcomplex assembles into a heterotrimer with one Snf5 molecule bound to two distinct Swi3 molecules. In addition, we demonstrated that Snf5-Swi3 subcomplex formation is required for SWI/SNF function in yeast. These findings shed light on the important role of the Snf5-Swi3 subcomplex in the assembly and functional integrity of the SWI/SNF complex.

Organizational Affiliation

State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China. Electronic address: haozhou@nankai.edu.cn.

Macromolecule Content

Total Structure Weight: 280.93 kDa
Atom Count: 13,673
Modeled Residue Count: 1,605
Deposited Residue Count: 2,404
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SWI/SNF chromatin-remodeling complex subunit SNF5	A, D, G, J	227	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: SNF5, SWI10, TYE4, YBR289W, YBR2036
UniProt
Find proteins for P18480 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P18480 Go to UniProtKB: P18480
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P18480
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SWI/SNF complex subunit SWI3	B, C, E, F, H B, C, E, F, H, I, K, L	187	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: SWI3, TYE2, YJL176C, J0495
UniProt
Find proteins for P32591 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32591 Go to UniProtKB: P32591
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32591
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth E] SDF format, chain N [auth E] SDF format, chain O [auth E] SDF format, chain P [auth E] SDF format, chain Q [auth F] SDF format, chain R [auth H] SDF format, chain S [auth K] SDF format, chain T [auth L] SDF format, chain U [auth L] MOL2 format, chain M [auth E] MOL2 format, chain N [auth E] MOL2 format, chain O [auth E] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth H] MOL2 format, chain S [auth K] MOL2 format, chain T [auth L] MOL2 format, chain U [auth L] mmCIF format, chain M [auth E] mmCIF format, chain N [auth E] mmCIF format, chain O [auth E] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain R [auth H] mmCIF format, chain S [auth K] mmCIF format, chain T [auth L] mmCIF format, chain U [auth L]	M [auth E] N [auth E] O [auth E] P [auth E] Q [auth F] M [auth E], N [auth E], O [auth E], P [auth E], Q [auth F], R [auth H], S [auth K], T [auth L], U [auth L]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth H] Focus chain S [auth K] Focus chain T [auth L] Focus chain U [auth L] Interactions & Density Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth H] Focus chain S [auth K] Focus chain T [auth L] Focus chain U [auth L]