6DD8 | pdb_00006dd8

Structure of mouse SYCP3, P21 form

• PDB DOI: https://doi.org/10.2210/pdb6DD8/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-09 Released: 2018-08-01 
• Deposition Author(s): Rosenberg, S.C., Munoz, I.C., Uson, I., 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: 2.60 Å
• R-Value Free: 
  0.323 (Depositor), 0.330 (DCC) 
• R-Value Work: 
  0.254 (Depositor), 0.263 (DCC) 
• R-Value Observed: 
  0.257 (Depositor) 

Literature

A conserved filamentous assembly underlies the structure of the meiotic chromosome axis.

West, A.M., Rosenberg, S.C., Ur, S.N., Lehmer, M.K., Ye, Q., Hagemann, G., Caballero, I., Uson, I., MacQueen, A.J., Herzog, F., Corbett, K.D.

(2019) Elife 8

• PubMed: 30657449 
• DOI: https://doi.org/10.7554/eLife.40372
• Primary Citation Related Structures: 
  6DD8, 6DD9


• PubMed Abstract: 
  

  The meiotic chromosome axis plays key roles in meiotic chromosome organization and recombination, yet the underlying protein components of this structure are highly diverged. Here, we show that 'axis core proteins' from budding yeast (Red1), mammals (SYCP2/SYCP3), and plants (ASY3/ASY4) are evolutionarily related and play equivalent roles in chromosome axis assembly. We first identify 'closure motifs' in each complex that recruit meiotic HORMADs, the master regulators of meiotic recombination. We next find that axis core proteins form homotetrameric (Red1) or heterotetrameric (SYCP2:SYCP3 and ASY3:ASY4) coiled-coil assemblies that further oligomerize into micron-length filaments. Thus, the meiotic chromosome axis core in fungi, mammals, and plants shares a common molecular architecture, and likely also plays conserved roles in meiotic chromosome axis assembly and recombination control.

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Organizational Affiliation: 
• Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, United States.
Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, United States.
Department of Chemistry, University of California, San Diego, La Jolla, United States.
Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona, Spain.
Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, United States.
Ludwig Institute for Cancer Research, La Jolla, United States.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 71.3 kDa 
• Atom Count: 4,123 
• Modeled Residue Count: 494 
• Deposited Residue Count: 576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptonemal complex protein 3	A, B, C, D	144	Mus musculus	Mutation(s): 0  Gene Names: Sycp3, mCG_16771
UniProt & NIH Common Fund Data Resources
Find proteins for P70281 (Mus musculus) Explore P70281  Go to UniProtKB:  P70281
IMPC:  MGI:109542

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.323 (Depositor), 0.330 (DCC) 
• R-Value Work:  0.254 (Depositor), 0.263 (DCC) 
• R-Value Observed: 0.257 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/583

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.81	α = 90
b = 49.396	β = 90.8
c = 150.264	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
Arcimboldo	phasing
RESOLVE	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-08-01 
Deposition Author(s): Rosenberg, S.C., Munoz, I.C., Uson, I., 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	R01 GM104141

Revision History  

• Version 1.0: 2018-08-01
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Data collection, Database references
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Structure summary