8IYA

Complex of SETDB1-derived peptide bound to UBE2E1

• PDB DOI: https://doi.org/10.2210/pdb8IYA/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-04-04 Released: 2024-01-03 
• Deposition Author(s): Du, Y.X., Liu, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.247 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Literature

Complex of SETDB1-derived peptide bound to UBE2E1

Wu, X.W., Du, Y.X., Liu, L.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: mass spectrometry

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59.96 kDa 
• Atom Count: 3,913 
• Modelled Residue Count: 491 
• Deposited Residue Count: 528 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 E1	A [auth B], B [auth A], C	170	Homo sapiens	Mutation(s): 4  Gene Names: UBE2E1, UBCH6 EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P51965 (Homo sapiens) Explore P51965  Go to UniProtKB:  P51965
PHAROS:  P51965 GTEx:  ENSG00000170142

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase SETDB1	D, E, F	6	Homo sapiens	Mutation(s): 0  Gene Names: SETDB1, ESET, KIAA0067, KMT1E EC: 2.1.1.366
UniProt & NIH Common Fund Data Resources
Find proteins for Q15047 (Homo sapiens) Explore Q15047  Go to UniProtKB:  Q15047
PHAROS:  Q15047 GTEx:  ENSG00000143379

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth B], H [auth A], I [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.247 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.747	α = 90
b = 50.077	β = 91.754
c = 109.248	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHENIX	phasing
Aimless	data processing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-03 
Deposition Author(s): Du, Y.X., Liu, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22137005, 92253302, 22227810

Revision History  

• Version 1.0: 2024-01-03
  Type: Initial release