9L3L | pdb_00009l3l

Crystal structure of the C lobe of E6AP in complex with K48-linked diUb

• PDB DOI: https://doi.org/10.2210/pdb9L3L/pdb

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


• Deposited: 2024-12-18 Released: 2025-12-24 
• Deposition Author(s): Wu, X.W., Cai, H.Y., 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: 2.59 Å
• R-Value Free: 
  0.269 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Models: experimental

Literature

Structural Insights into the Role of the C-Lobe of E6AP in Catalyzing K48-Linked Ubiquitin Chain Formation

Wu, X.W., Cai, H.Y., Du, Y.X., Liu, L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.29 kDa 
• Atom Count: 2,075 
• Modeled Residue Count: 257 
• Deposited Residue Count: 257 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-protein ligase E3A	A	108	Homo sapiens	Mutation(s): 0  Gene Names: UBE3A, E6AP, EPVE6AP, HPVE6A EC: 2.3.2.26
UniProt & NIH Common Fund Data Resources
Find proteins for Q05086 (Homo sapiens) Explore Q05086  Go to UniProtKB:  Q05086
PHAROS:  Q05086 GTEx:  ENSG00000114062

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Donor Ubiquitin	B	76	Homo sapiens	Mutation(s): 0  Gene Names: RPS27A, UBA80, UBCEP1
UniProt & NIH Common Fund Data Resources
Find proteins for P62979 (Homo sapiens) Explore P62979  Go to UniProtKB:  P62979
PHAROS:  P62979 GTEx:  ENSG00000143947

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Acceptor Ubiquitin	C	73	Homo sapiens	Mutation(s): 0  Gene Names: RPS27A, UBA80, UBCEP1
UniProt & NIH Common Fund Data Resources
Find proteins for P62979 (Homo sapiens) Explore P62979  Go to UniProtKB:  P62979
PHAROS:  P62979 GTEx:  ENSG00000143947

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SLZ	C	L-PEPTIDE LINKING	C5 H12 N2 O2 S		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free:  0.269 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.07	α = 90
b = 121.69	β = 90
c = 81.32	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Wu, X.W., Cai, H.Y., Du, Y.X., Liu, L.

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

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release