8CXK | pdb_00008cxk

Structure of the C. elegans HIM-3 R93Y mutant

• PDB DOI: https://doi.org/10.2210/pdb8CXK/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-05-21 Released: 2023-05-17 
• Deposition Author(s): Ego, K.M., Russo, A., Giacopazzi, S., Deshong, A., Menon, M., Ortiz, V., Bhalla, N., Corbett, K.D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.164 (Depositor), 0.164 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.144 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

Literature

The conserved AAA ATPase PCH-2 distributes its regulation of meiotic prophase events through multiple meiotic HORMADs in C. elegans.

Russo, A.E., Giacopazzi, S., Deshong, A., Menon, M., Ortiz, V., Ego, K.M., Corbett, K.D., Bhalla, N.

(2023) PLoS Genet 19: e1010708-e1010708

• PubMed: 37058535 
• DOI: https://doi.org/10.1371/journal.pgen.1010708
• Primary Citation Related Structures: 
  8CXK


• PubMed Abstract: 
  

  During meiotic prophase, the essential events of homolog pairing, synapsis, and recombination are coordinated with meiotic progression to promote fidelity and prevent aneuploidy. The conserved AAA+ ATPase PCH-2 coordinates these events to guarantee crossover assurance and accurate chromosome segregation. How PCH-2 accomplishes this coordination is poorly understood. Here, we provide evidence that PCH-2 decelerates pairing, synapsis and recombination in C. elegans by remodeling meiotic HORMADs. We propose that PCH-2 converts the closed versions of these proteins, which drive these meiotic prophase events, to unbuckled conformations, destabilizing interhomolog interactions and delaying meiotic progression. Further, we find that PCH-2 distributes this regulation among three essential meiotic HORMADs in C. elegans: PCH-2 acts through HTP-3 to regulate pairing and synapsis, HIM-3 to promote crossover assurance, and HTP-1 to control meiotic progression. In addition to identifying a molecular mechanism for how PCH-2 regulates interhomolog interactions, our results provide a possible explanation for the expansion of the meiotic HORMAD family as a conserved evolutionary feature of meiosis. Taken together, our work demonstrates that PCH-2's remodeling of meiotic HORMADs has functional consequences for the rate and fidelity of homolog pairing, synapsis, recombination and meiotic progression, ensuring accurate meiotic chromosome segregation.

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Organizational Affiliation: 
• Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California, United States of America.
Department of Cellular and Molecular Medicine, University of California, San Diego, California, United States of America.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.17 kDa 
• Atom Count: 2,186 
• Modeled Residue Count: 242 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HORMA domain-containing protein	A	291	Caenorhabditis elegans	Mutation(s): 1  Gene Names: him-3, CELE_ZK381.1, ZK381.1
UniProt
Find proteins for G5EBG0 (Caenorhabditis elegans) Explore G5EBG0  Go to UniProtKB:  G5EBG0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.164 (Depositor), 0.164 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.144 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.234	α = 90
b = 73.234	β = 90
c = 110.816	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-17 
Deposition Author(s): Ego, K.M., Russo, A., Giacopazzi, S., Deshong, A., Menon, M., Ortiz, V., Bhalla, N., Corbett, K.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM144121

Revision History  

• Version 1.0: 2023-05-17
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description