8VK8

Structure of UbV.d2.1 in complex with Ube2d2

• PDB DOI: https://doi.org/10.2210/pdb8VK8/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-01-08 Released: 2024-09-25 
• Deposition Author(s): Middleton, A.J.
• Funding Organization(s): Health Research Council (HRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 0.295 
• R-Value Work: 0.247 
• R-Value Observed: 0.249 

Starting Models: experimental

Literature

Structural and biophysical characterisation of ubiquitin variants that inhibit the ubiquitin conjugating enzyme Ube2d2

McAlpine, J.M.R.B., Zhu, G., Pudjihartono, N., Teyra, J., Currie, M.J., Tillett, Z.D., Dobson, R.C.J., Sidhu, S.S., Day, C.L., Middleton, A.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: assay for oligomerization

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: assay for oligomerization

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors.

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content

• Total Structure Weight: 103.23 kDa 
• Atom Count: 6,499 
• Modelled Residue Count: 815 
• Deposited Residue Count: 926 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 D2	A, D, G	152	Homo sapiens	Mutation(s): 3  Gene Names: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P62837 (Homo sapiens) Explore P62837  Go to UniProtKB:  P62837
PHAROS:  P62837 GTEx:  ENSG00000131508

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin variant D2.1	B, C, E, F, H	94	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 0.295 
• R-Value Work: 0.247 
• R-Value Observed: 0.249 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.774	α = 90
b = 129.774	β = 90
c = 123.106	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Middleton, A.J.

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Funding Organization	Location	Grant Number
Health Research Council (HRC)	New Zealand	--

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release