9D8P

Focused map of Cryo-EM structure of Ubiquitin C-degron bound to KLHDC10-EloB/C

• PDB DOI: https://doi.org/10.2210/pdb9D8P/pdb
• EM Map EMD-46645: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-08-19 Released: 2024-11-20 
• Deposition Author(s): Chittori, S., Scott, D.C., Schulman, B.A.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for C-degron selectivity across KLHDCX-family E3 ubiquitin ligases

Scott, D.C., Chittori, S., Purser, N., King, M.T., Maiwald, S., Churion, K., Nourse, A., Lee, C., Paulo, J.A., Miller, D.J., Elledge, S.J., Harper, J.W., Kleiger, G., Schulman, B.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 79.93 kDa 
• Atom Count: 4,073 
• Modelled Residue Count: 537 
• Deposited Residue Count: 708 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch domain-containing protein 10	A	402	Homo sapiens	Mutation(s): 0  Gene Names: KLHDC10, KIAA0265
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PID8 (Homo sapiens) Explore Q6PID8  Go to UniProtKB:  Q6PID8
PHAROS:  Q6PID8 GTEx:  ENSG00000128607

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-B	B	118	Homo sapiens	Mutation(s): 0  Gene Names: ELOB, TCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens) Explore Q15370  Go to UniProtKB:  Q15370
PHAROS:  Q15370 GTEx:  ENSG00000103363

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-C	C	112	Homo sapiens	Mutation(s): 0  Gene Names: ELOC, TCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens) Explore Q15369  Go to UniProtKB:  Q15369
PHAROS:  Q15369 GTEx:  ENSG00000154582

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-C	D	76	Homo sapiens	Mutation(s): 1  Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48 GTEx:  ENSG00000150991

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-20 
Deposition Author(s): Chittori, S., Scott, D.C., Schulman, B.A.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	5R01CA247365

Revision History  

• Version 1.0: 2024-11-20
  Type: Initial release