6H86

Rebuilt and re-refined PDB entry 4R3Q: Crystal structure of SYCE3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in:4R3Q


Literature

A molecular model for self-assembly of the synaptonemal complex protein SYCE3.

Dunne, O.M.Davies, O.R.

(2019) J Biol Chem 294: 9260-9275

  • DOI: 10.1074/jbc.RA119.008404
  • Primary Citation of Related Structures:  
    6H86

  • PubMed Abstract: 
  • The synaptonemal complex (SC) is a supramolecular protein assembly that mediates homologous chromosome synapsis during meiosis. This zipper-like structure assembles in a continuous manner between homologous chromosome axes, enforcing a 100-nm separation along their entire length and providing the necessary three-dimensional framework for cross-over formation ...

    The synaptonemal complex (SC) is a supramolecular protein assembly that mediates homologous chromosome synapsis during meiosis. This zipper-like structure assembles in a continuous manner between homologous chromosome axes, enforcing a 100-nm separation along their entire length and providing the necessary three-dimensional framework for cross-over formation. The mammalian SC comprises eight components-synaptonemal complex protein 1-3 (SYCP1-3), synaptonemal complex central element protein 1-3 (SYCE1-3), testis-expressed 12 (TEX12), and six6 opposite strand transcript 1 (SIX6OS1)-arranged in transverse and longitudinal structures. These largely α-helical, coiled-coil proteins undergo heterotypic interactions, coupled with recursive self-assembly of SYCP1, SYCE2-TEX12, and SYCP2-SYCP3, to achieve the vast supramolecular SC structure. Here, we report a novel self-assembly mechanism of the SC central element component SYCE3, identified through multi-angle light scattering and small-angle X-ray scattering (SAXS) experiments. These analyses revealed that SYCE3 adopts a dimeric four-helical bundle structure that acts as the building block for concentration-dependent self-assembly into a series of discrete higher-order oligomers. We observed that this is achieved through staggered lateral interactions between self-assembly surfaces of SYCE3 dimers and through end-on interactions that likely occur through intermolecular domain swapping between dimer folds. These mechanisms are combined to achieve potentially limitless SYCE3 assembly, particularly favoring formation of dodecamers of three laterally associated end-on tetramers. Our findings extend the family of self-assembling proteins within the SC and reveal additional means for structural stabilization of the SC central element.


    Related Citations: 
    • Structural insight into the central element assembly of the synaptonemal complex.
      Lu, J., Gu, Y., Feng, J., Zhou, W., Yang, X., Shen, Y.
      (2014) Sci Rep 4: 7059

    Organizational Affiliation

    From the Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom owen.davies@newcastle.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Synaptonemal complex central element protein 3A, B88Mus musculusMutation(s): 0 
Gene Names: Syce3Tseg2
UniProt
Find proteins for B5KM66 (Mus musculus)
Explore B5KM66 
Go to UniProtKB:  B5KM66
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.576α = 90
b = 75.576β = 90
c = 101.511γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXmodel building
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-08-02 
  • Released Date: 2019-05-08 
  • Deposition Author(s): Davies, O.R.

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom104158/Z/14/Z
Royal SocietyUnited KingdomRG170118

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-06-19
    Changes: Data collection, Database references