9E2K | pdb_00009e2k

Variediene synthase with one cyclase (conformation 1)

• PDB DOI: https://doi.org/10.2210/pdb9E2K/pdb
• EM Map EMD-47455: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Aspergillus stellatus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-22 Released: 2025-05-21 
• Deposition Author(s): Wenger, E.S., Christianson, D.W.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Variediene synthase hexameric prenyltransferase core

Wenger, E.S., Christianson, D.W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A5B1 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 495.6 kDa 
• Atom Count: 15,520 
• Modeled Residue Count: 1,939 
• Deposited Residue Count: 4,350 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Variediene synthase	A, B, C, D, E, F	725	Aspergillus stellatus	Mutation(s): 0  Gene Names: EvVS EC: 4.2.3.218 (PDB Primary Data), 4.2.3.219 (PDB Primary Data), 2.5.1.29 (PDB Primary Data), 2.5.1.81 (PDB Primary Data)
UniProt
Find proteins for A0A0P0ZD79 (Emericella variicolor) Explore A0A0P0ZD79  Go to UniProtKB:  A0A0P0ZD79

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
POP (Subject of Investigation/LOI)	G [auth B]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-21 
Deposition Author(s): Wenger, E.S., Christianson, D.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	574961-0089

Revision History  

• Version 1.0: 2025-05-21
  Type: Initial release