5W4D | pdb_00005w4d

C. japonica N-domain, Selenomethionine mutant

PDB DOI: https://doi.org/10.2210/pdb5W4D/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Caenorhabditis japonica
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2017-06-10 Released: 2018-06-13
Deposition Author(s): Aoki, S.T., Bingman, C.A., Kimble, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.190 (Depositor), 0.194 (DCC)
R-Value Work:
0.157 (Depositor), 0.162 (DCC)
R-Value Observed:
0.158 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

C. elegans germ granules require both assembly and localized regulators for mRNA repression.

Aoki, S.T., Lynch, T.R., Crittenden, S.L., Bingman, C.A., Wickens, M., Kimble, J.

(2021) Nat Commun 12: 996-996

PubMed: 33579952 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-21278-1
Primary Citation Related Structures:
5W4A, 5W4D

PubMed Abstract:
Cytoplasmic RNA-protein (RNP) granules have diverse biophysical properties, from liquid to solid, and play enigmatic roles in RNA metabolism. Nematode P granules are paradigmatic liquid droplet granules and central to germ cell development. Here we analyze a key P granule scaffolding protein, PGL-1, to investigate the functional relationship between P granule assembly and function. Using a protein-RNA tethering assay, we find that reporter mRNA expression is repressed when recruited to PGL-1. We determine the crystal structure of the PGL-1 N-terminal region to 1.5 Å, discover its dimerization, and identify key residues at the dimer interface. Mutations of those interface residues prevent P granule assembly in vivo, de-repress PGL-1 tethered mRNA, and reduce fertility. Therefore, PGL-1 dimerization lies at the heart of both P granule assembly and function. Finally, we identify the P granule-associated Argonaute WAGO-1 as crucial for repression of PGL-1 tethered mRNA. We conclude that P granule function requires both assembly and localized regulators.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University, Indianapolis, IN, USA. staoki@iu.edu.

Macromolecule Content

Total Structure Weight: 100.31 kDa
Atom Count: 7,578
Modeled Residue Count: 846
Deposited Residue Count: 864
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P-granule scaffold protein	A, B, C, D	216	Caenorhabditis japonica	Mutation(s): 2

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A]	I [auth A], L [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Interactions & Density Focus chain I [auth A] Focus chain L [auth B]
PG5 Query on PG5 Download:Ideal Coordinates CCD File SDF format, chain X [auth C] MOL2 format, chain X [auth C] mmCIF format, chain X [auth C]	X [auth C]	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE C₈ H₁₈ O₄ YFNKIDBQEZZDLK-UHFFFAOYSA-N		Interactions Focus chain X [auth C] Interactions & Density Focus chain X [auth C]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain G [auth A] SDF format, chain AA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain G [auth A] MOL2 format, chain AA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain G [auth A] mmCIF format, chain AA [auth D]	AA [auth D], G [auth A], Q [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain G [auth A] Focus chain Q [auth B] Interactions & Density Focus chain AA [auth D] Focus chain G [auth A] Focus chain Q [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain R [auth B] SDF format, chain K [auth A] SDF format, chain H [auth A] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain R [auth B] MOL2 format, chain K [auth A] MOL2 format, chain H [auth A] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain R [auth B] mmCIF format, chain K [auth A] mmCIF format, chain H [auth A]	H [auth A], K [auth A], R [auth B], V [auth C], W [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain H [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain V [auth C] Focus chain W [auth C]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain U [auth C] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] MOL2 format, chain Z [auth D] MOL2 format, chain U [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] mmCIF format, chain Z [auth D] mmCIF format, chain U [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B]	N [auth B], O [auth B], P [auth B], U [auth C], Z [auth D]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain Z [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain M [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain Y [auth D] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain Y [auth D] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] M [auth B] S [auth C] T [auth C] E [auth A], F [auth A], M [auth B], S [auth C], T [auth C], Y [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]