6LZ1

Structure of S.pombe alpha-mannosidase Ams1

• PDB DOI: https://doi.org/10.2210/pdb6LZ1/pdb
• EM Map EMD-30021: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Schizosaccharomyces pombe 972h-
• Expression System: Schizosaccharomyces pombe
• Mutation(s): No 


• Deposited: 2020-02-17 Released: 2020-09-09 
• Deposition Author(s): Zhang, J., Ye, K.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC), Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Cryo-EM structure of fission yeast tetrameric alpha-mannosidase Ams1.

Zhang, J., Wang, Y.Y., Du, L.L., Ye, K.

(2020) FEBS Open Bio 10: 2437-2451

• PubMed: 32981237 
• DOI: https://doi.org/10.1002/2211-5463.12988
• Primary Citation of Related Structures:  
  6LZ1


• PubMed Abstract: 
  

  Fungal α-mannosidase Ams1 and its mammalian homolog MAN2C1 hydrolyze terminal α-linked mannoses in free oligosaccharides released from misfolded glycoproteins or lipid-linked oligosaccharide donors. Ams1 is transported by selective autophagy into vacuoles. Here, we determine the tetrameric structure of Ams1 from the fission yeast Schizosaccharomyces pombe at 3.2 Å resolution by cryo-electron microscopy. Distinct from a low resolution structure of S. cerevisiae Ams1, S. pombe Ams1 has a prominent N-terminal tail that mediates tetramerization and an extra β-sheet domain. Ams1 shares a conserved active site with other enzymes in glycoside hydrolase family 38, to which Ams1 belongs, but contains extra N-terminal domains involved in tetramerization. The atomic structure of Ams1 reported here will aid understanding of its enzymatic activity and transport mechanism.

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Organizational Affiliation: 

Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

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: 517.07 kDa 
• Atom Count: 34,492 
• Modelled Residue Count: 4,304 
• Deposited Residue Count: 4,532 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ams1	A, B, C, D	1,133	Schizosaccharomyces pombe 972h-	Mutation(s): 0  Gene Names: ams1, mns2, SPAC513.05 EC: 3.2.1.24
UniProt
Find proteins for Q9UT61 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q9UT61  Go to UniProtKB:  Q9UT61

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: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2.1
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-09 
Deposition Author(s): Zhang, J., Ye, K.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2017YFA0504600
National Natural Science Foundation of China (NSFC)	China	91940302, 91540201, 31430024, 31325007
Chinese Academy of Sciences	China	XDB37010201

Revision History  

• Version 1.0: 2020-09-09
  Type: Initial release
  
• Version 1.1: 2020-10-28
  Changes: Database references
• Version 1.2: 2021-03-10
  Changes: Database references
• Version 1.3: 2024-03-27
  Changes: Data collection, Database references, Refinement description