9D1Z

Structure of G75Q Ubiquitin bound to KLHDC3-EloB/C

• PDB DOI: https://doi.org/10.2210/pdb9D1Z/pdb

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


• Deposited: 2024-08-08 Released: 2024-11-20 
• Deposition Author(s): Schulman, B.A., Scott, D.C.
• Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.190 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 

Starting Model: in silico

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., Chuiron, K., Nourse, A., Lee, C., Paulo, J.A., Miller, D.J., Elledge, S.J., Haper, J.W., Kleiger, G., Schulman, B.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 77.99 kDa 
• Atom Count: 5,741 
• Modelled Residue Count: 642 
• Deposited Residue Count: 684 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch domain-containing protein 3	A	383	Homo sapiens	Mutation(s): 1  Gene Names: KLHDC3, PEAS
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQ90 (Homo sapiens) Explore Q9BQ90  Go to UniProtKB:  Q9BQ90
PHAROS:  Q9BQ90 GTEx:  ENSG00000124702

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-B	B	104	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	121	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	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth A], H [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.190 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.949	α = 90
b = 120.873	β = 90
c = 152.949	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

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

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	AG011085

Revision History  

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