8PBA

Cryo-EM structure of Caenorhabditis elegans DPF-3 (apo)

• PDB DOI: https://doi.org/10.2210/pdb8PBA/pdb
• EM Map EMD-17582: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Caenorhabditis elegans
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2023-06-08 Released: 2024-06-26 
• Deposition Author(s): Gudipati, R.K., Cavadini, S., Kempf, G., Grosshans, H.
• Funding Organization(s): Swiss National Science Foundation, Other private, Polish National Science Centre

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.64 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of Caenorhabditis elegans DPF-3 (apo)

Gudipati, R.K., Cavadini, S., Kempf, G., Grosshans, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 212.93 kDa 
• Atom Count: 11,632 
• Modelled Residue Count: 1,444 
• Deposited Residue Count: 1,870 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl Peptidase Four (IV) family	A, B	935	Caenorhabditis elegans	Mutation(s): 0  Gene Names: dpf-3, CELE_K02F2.1, K02F2.1
UniProt
Find proteins for Q965K3 (Caenorhabditis elegans) Explore Q965K3  Go to UniProtKB:  Q965K3

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.64 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	RosettaEM

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-26 
Deposition Author(s): Gudipati, R.K., Cavadini, S., Kempf, G., Grosshans, H.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	182880
Other private		--
Polish National Science Centre	Poland	SONATA BIS 2021/42/E/NZ1/00336
Polish National Science Centre	Poland	OPUS 2022/45/B/NZ2/02183

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release