2M6N | pdb_00002m6n

3D solution structure of EMI1 (Early Mitotic Inhibitor 1)

• PDB DOI: https://doi.org/10.2210/pdb2M6N/pdb
• BMRB: 19147

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-04-06 Released: 2013-05-29 
• Deposition Author(s): Frye, J.J., Brown, N.G., Petzold, G., Watson, E.R., Royappa, G.R., Nourse, A., Jarvis, M., Kriwacki, R.W., Peters, J., Stark, H., Schulman, B.A.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

Electron microscopy structure of human APC/C(CDH1)-EMI1 reveals multimodal mechanism of E3 ligase shutdown.

Frye, J.J., Brown, N.G., Petzold, G., Watson, E.R., Grace, C.R., Nourse, A., Jarvis, M.A., Kriwacki, R.W., Peters, J.M., Stark, H., Schulman, B.A.

(2013) Nat Struct Mol Biol 20: 827-835

• PubMed: 23708605 
• DOI: https://doi.org/10.1038/nsmb.2593
• Primary Citation Related Structures: 
  2M6N


• PubMed Abstract: 
  

  The anaphase-promoting complex/cyclosome (APC/C) is a ~1.5-MDa multiprotein E3 ligase enzyme that regulates cell division by promoting timely ubiquitin-mediated proteolysis of key cell-cycle regulatory proteins. Inhibition of human APC/C(CDH1) during interphase by early mitotic inhibitor 1 (EMI1) is essential for accurate coordination of DNA synthesis and mitosis. Here, we report a hybrid structural approach involving NMR, electron microscopy and enzymology, which reveal that EMI1's 143-residue C-terminal domain inhibits multiple APC/C(CDH1) functions. The intrinsically disordered D-box, linker and tail elements, together with a structured zinc-binding domain, bind distinct regions of APC/C(CDH1) to synergistically both block the substrate-binding site and inhibit ubiquitin-chain elongation. The functional importance of intrinsic structural disorder is explained by enabling a small inhibitory domain to bind multiple sites to shut down various functions of a 'molecular machine' nearly 100 times its size.

---

Organizational Affiliation: 
• 1Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 9.74 kDa 
• Atom Count: 363 
• Modeled Residue Count: 46 
• Deposited Residue Count: 86 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
F-box only protein 5	A	86	Homo sapiens	Mutation(s): 0  Gene Names: FBXO5, EMI1, FBX5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKT4 (Homo sapiens) Explore Q9UKT4  Go to UniProtKB:  Q9UKT4
PHAROS:  Q9UKT4 GTEx:  ENSG00000112029

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-29 
Deposition Author(s): Frye, J.J., Brown, N.G., Petzold, G., Watson, E.R., Royappa, G.R., Nourse, A., Jarvis, M., Kriwacki, R.W., Peters, J., Stark, H., Schulman, B.A.

Revision History  

• Version 1.0: 2013-05-29
  Type: Initial release
  
• Version 1.1: 2013-06-12
  Changes: Database references
• Version 1.2: 2013-07-17
  Changes: Database references
• Version 1.3: 2024-05-01
  Changes: Data collection, Database references, Derived calculations