8R1F | pdb_00008r1f

Monomeric E6AP-E6-p53 ternary complex

• PDB DOI: https://doi.org/10.2210/pdb8R1F/pdb
• EM Map EMD-18809: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): Homo sapiens, Saccharomyces cerevisiae S288C, Human papillomavirus 16
• Expression System: Trichoplusia ni, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-11-01 Released: 2023-12-06 
• Deposition Author(s): Sandate, C.R., Chakraborty, D., Kater, L., Kempf, G., Thoma, N.H.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.67 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into viral hijacking of p53 by E6 and E6AP

Sandate, C.R., Chakraborty, D., Kater, L., Kempf, G., Thoma, N.H.

(2023) bioRxiv 

• DOI: https://doi.org/10.1101/2023.11.01.565136

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 181.83 kDa 
• Atom Count: 8,366 
• Modeled Residue Count: 1,025 
• Deposited Residue Count: 1,582 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-protein ligase E3A	A	899	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
Ubiquitin-like protein SMT3,Protein E6	B	266	Saccharomyces cerevisiae S288C, Human papillomavirus 16 This entity is chimeric	Mutation(s): 4  Gene Names: SMT3, YDR510W, D9719.15, E6
UniProt
Find proteins for P03126 (Human papillomavirus type 16) Explore P03126  Go to UniProtKB:  P03126
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12306  Go to UniProtKB:  Q12306
UniProt Groups	P03126Q12306

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellular tumor antigen p53	C	417	Homo sapiens	Mutation(s): 0  Gene Names: TP53, P53
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens) Explore P04637  Go to UniProtKB:  P04637
PHAROS:  P04637 GTEx:  ENSG00000141510

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth B], E [auth B], F [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.67 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	v.4
MODEL REFINEMENT	cryoSPARC	v.3 or v.4
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-12-06 
Deposition Author(s): Sandate, C.R., Chakraborty, D., Kater, L., Kempf, G., Thoma, N.H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-12-06
  Type: Initial release
  
• Version 1.1: 2024-06-19
  Changes: Database references
• Version 1.2: 2025-07-09
  Changes: Data collection, Structure summary