6O2D | pdb_00006o2d

Schizosaccharomyces pombe Cnp3 Cupin Domain

• PDB DOI: https://doi.org/10.2210/pdb6O2D/pdb

• Classification: CELL CYCLE
• Organism(s): Schizosaccharomyces pombe
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-02-22 Released: 2019-08-21 
• Deposition Author(s): Chik, J.K., Cho, U.S.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 
  0.251 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

Structures of CENP-C cupin domains at regional centromeres reveal unique patterns of dimerization and recruitment functions for the inner pocket.

Chik, J.K., Moiseeva, V., Goel, P.K., Meinen, B.A., Koldewey, P., An, S., Mellone, B.G., Subramanian, L., Cho, U.S.

(2019) J Biological Chem 294: 14119-14134

• PubMed: 31366733 
• DOI: https://doi.org/10.1074/jbc.RA119.008464
• Primary Citation Related Structures: 
  6O2D, 6O2K


• PubMed Abstract: 
  

  The successful assembly and regulation of the kinetochore are critical for the equal and accurate segregation of genetic material during the cell cycle. CENP-C (centromere protein C), a conserved inner kinetochore component, has been broadly characterized as a scaffolding protein and is required for the recruitment of multiple kinetochore proteins to the centromere. At its C terminus, CENP-C harbors a conserved cupin domain that has an established role in protein dimerization. Although the crystal structure of the Saccharomyces cerevisiae Mif2 ^CENP-C cupin domain has been determined, centromeric organization and kinetochore composition vary greatly between S. cerevisiae (point centromere) and other eukaryotes (regional centromere). Therefore, whether the structural and functional role of the cupin domain is conserved throughout evolution requires investigation. Here, we report the crystal structures of the Schizosaccharomyces pombe and Drosophila melanogaster CENP-C cupin domains at 2.52 and 1.81 Å resolutions, respectively. Although the central jelly roll architecture is conserved among the three determined CENP-C cupin domain structures, the cupin domains from organisms with regional centromeres contain additional structural features that aid in dimerization. Moreover, we found that the S. pombe Cnp3 ^CENP-C jelly roll fold harbors an inner binding pocket that is used to recruit the meiosis-specific protein Moa1. In summary, our results unveil the evolutionarily conserved and unique features of the CENP-C cupin domain and uncover the mechanism by which it functions as a recruitment factor.

---

Organizational Affiliation: 
• Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109.
Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109.
School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom.
Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109.
Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269.
School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom [e-mail].
Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109 [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 36.1 kDa 
• Atom Count: 2,251 
• Modeled Residue Count: 282 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inner kinetochore subunit cnp3	A, B	158	Schizosaccharomyces pombe	Mutation(s): 0  Gene Names: cnp3, SPBC1861.01c, SPBC56F2.13
UniProt
Find proteins for Q9USR9 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q9USR9  Go to UniProtKB:  Q9USR9

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free:  0.251 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.16	α = 90
b = 55.16	β = 90
c = 206.64	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
AutoSol	phasing
XDS	data scaling
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-08-21 
Deposition Author(s): Chik, J.K., Cho, U.S.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01-DK111465
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32-GM007315

Revision History  

• Version 1.0: 2019-08-21
  Type: Initial release
  
• Version 1.1: 2019-09-25
  Changes: Data collection, Database references
• Version 1.2: 2019-10-02
  Changes: Data collection, Database references
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2024-10-23
  Changes: Data collection, Database references, Structure summary