7VQO

Cryo-EM structure of Ams1 bound to the FW domain of Nbr1

• PDB DOI: https://doi.org/10.2210/pdb7VQO/pdb
• EM Map EMD-32091: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Thermochaetoides thermophila DSM 1495, Escherichia coli K-12
• Expression System: Schizosaccharomyces pombe 972h-
• Mutation(s): No 


• Deposited: 2021-10-20 Released: 2022-07-06 
• Deposition Author(s): Zhang, J., Ye, K.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Chinese Academy of Sciences, National Basic Research Program of China (973 Program)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.19 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structural mechanism of protein recognition by the FW domain of autophagy receptor Nbr1

Zhang, J., Wang, Y.Y., Pan, Z.Q., Li, Y., Sui, J., Du, L.L., Ye, K.

(2022) Nat Commun 13: 3650

• DOI: https://doi.org/10.1038/s41467-022-31439-5

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 726.97 kDa 
• Atom Count: 38,640 
• Modelled Residue Count: 4,720 
• Deposited Residue Count: 6,464 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ams1, Nbr1 and malE fusion protein	A, B, C, D	1,616	Thermochaetoides thermophila DSM 1495, Escherichia coli K-12	Mutation(s): 0  Gene Names: CTHT_0067100, CTHT_0062850, malE EC: 3.2.1.24
UniProt
Find proteins for G0SGP6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SGP6  Go to UniProtKB:  G0SGP6
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for G0SE85 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SE85  Go to UniProtKB:  G0SE85
UniProt Groups	G0SE85P0AEX9G0SGP6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.19 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	2.5
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-06 
Deposition Author(s): Zhang, J., Ye, K.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32071199, 91940302
Chinese Academy of Sciences	China	XDB37010201
National Basic Research Program of China (973 Program)	China	2017YFA0504600

Revision History  

• Version 1.0: 2022-07-06
  Type: Initial release
  
• Version 1.1: 2024-06-26
  Changes: Data collection, Refinement description