9UAQ | pdb_00009uaq

CryoEM structure of GFP-like protein from Aequorea coerulescens with Trimbody

• PDB DOI: https://doi.org/10.2210/pdb9UAQ/pdb
• EM Map EMD-63989: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): synthetic construct, Thermotoga maritima MSB8, Aequorea coerulescens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-04-01 Released: 2026-02-11 
• Deposition Author(s): Song, J.Y., Wang, W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.29 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

CryoEM structure of GFP-like protein from Aequorea coerulescens with Trimbody

Wang, W., Song, J.Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A3B3C3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 257.21 kDa 
• Atom Count: 18,042 
• Modeled Residue Count: 2,330 
• Deposited Residue Count: 2,334 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase	A, B, C	320	synthetic construct, Thermotoga maritima MSB8 This entity is chimeric	Mutation(s): 0
UniProt
Find proteins for Q9WXS1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WXS1  Go to UniProtKB:  Q9WXS1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GFP-nanobody-TAIL	D, E, F	233	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	G, H, I	225	Aequorea coerulescens	Mutation(s): 1
UniProt
Find proteins for Q6YGZ0 (Aequorea coerulescens) Explore Q6YGZ0  Go to UniProtKB:  Q6YGZ0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
GYS	G, H, I	L-PEPTIDE LINKING	C14 H15 N3 O5		SER, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.29 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: 2026-02-11 
Deposition Author(s): Song, J.Y., Wang, W.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2026-02-11
  Type: Initial release
  
• Version 2.0: 2026-03-18
  Changes: Data collection, Polymer sequence