7BQD

Solution NMR structure of NF8 (knot fold); de novo designed protein with a novel fold

• PDB DOI: https://doi.org/10.2210/pdb7BQD/pdb
• BMRB: 36333

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-03-24 Released: 2021-03-24 
• Deposition Author(s): Kobayashi, N., Sugiki, T., Fujiwara, T., Minami, S., Koga, R., Chikenji, G., Koga, N.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

Exploration of novel alpha-beta-protein folds through de novo design

Minami, S., Kobayashi, N., Sugiki, T., Nagashima, T., Fujiwara, T., Koga, R., Chikenji, G., Koga, N.

(2023) Nat Struct Mol Biol 

• DOI: https://doi.org/10.1038/s41594-023-01029-0

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 10.3 kDa 
• Atom Count: 725 
• Modelled Residue Count: 88 
• Deposited Residue Count: 88 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NF8	A	88	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-24 
Deposition Author(s): Kobayashi, N., Sugiki, T., Fujiwara, T., Minami, S., Koga, R., Chikenji, G., Koga, N.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18K06152
Japan Agency for Medical Research and Development (AMED)	Japan	JP19am0101072
Japan Society for the Promotion of Science (JSPS)	Japan	18H05420
Japan Society for the Promotion of Science (JSPS)	Japan	15H05592
Japan Society for the Promotion of Science (JSPS)	Japan	19H03166

Revision History  

• Version 1.0: 2021-03-24
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Database references, Other
• Version 1.2: 2023-07-05
  Changes: Database references
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references