8ZEN | pdb_00008zen

Cryo-EM structure of Adr-2-Adbp-1-dsRBD0 complex

• PDB DOI: https://doi.org/10.2210/pdb8ZEN/pdb
• EM Map EMD-60040: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN
• Organism(s): Caenorhabditis elegans
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-05-06 Released: 2025-05-14 
• Deposition Author(s): Liu, Z.M., Mu, J.Q., Wu, C.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.99 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of Adr-2-Adbp-1-dsRBD0 complex

Liu, Z.M., Mu, J.Q., Wu, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 160.21 kDa 
• Atom Count: 8,388 
• Modeled Residue Count: 1,069 
• Deposited Residue Count: 1,424 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adr-2-binding protein 1	A [auth B], D [auth E]	217	Caenorhabditis elegans	Mutation(s): 0  Gene Names: adbp-1, 2L737, VW02B12L.4
UniProt
Find proteins for G5EDW1 (Caenorhabditis elegans) Explore G5EDW1  Go to UniProtKB:  G5EDW1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Double-stranded RNA-specific adenosine deaminase adr-2	B [auth C], C [auth D]	495	Caenorhabditis elegans	Mutation(s): 0  Gene Names: adr-2, T20H4.4 EC: 3.5.4.37
UniProt
Find proteins for Q22618 (Caenorhabditis elegans) Explore Q22618  Go to UniProtKB:  Q22618

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP (Subject of Investigation/LOI)	E [auth C], G [auth D]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N
ZN (Subject of Investigation/LOI)	F [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.99 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: 2025-05-14 
Deposition Author(s): Liu, Z.M., Mu, J.Q., Wu, C.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release
  
• Version 1.1: 2025-07-23
  Changes: Data collection