7YKA | pdb_00007yka

Crystal structure of Fis1 (Mitochondrial fission 1 protein)

• PDB DOI: https://doi.org/10.2210/pdb7YKA/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-07-22 Released: 2023-08-02 
• Deposition Author(s): Duc, N.M., Bong, S.M., Lee, B.I.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.250 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Fis1 and Bap31 provides information on protein-protein interactions at mitochondria-associated ER membranes

Nguyen, M.D., Kim, Y., Bae, S.H., Kim, S., Yeo, H.K., Ha, N.C., Cho, G., Moon, S., Cho, K.H., Jang, H., Bong, S.M., Lee, B.I.

(2025) Commun Biol 8: 1161

• DOI: https://doi.org/10.1038/s42003-025-08625-4

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.61 kDa 
• Atom Count: 1,990 
• Modeled Residue Count: 240 
• Deposited Residue Count: 240 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial fission 1 protein	A	118	Homo sapiens	Mutation(s): 0  Gene Names: FIS1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3D6 (Homo sapiens) Explore Q9Y3D6  Go to UniProtKB:  Q9Y3D6
PHAROS:  Q9Y3D6 GTEx:  ENSG00000214253

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fis1	B	122	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3D6 (Homo sapiens) Explore Q9Y3D6  Go to UniProtKB:  Q9Y3D6
PHAROS:  Q9Y3D6 GTEx:  ENSG00000214253

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.250 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.822	α = 90
b = 56.283	β = 100.065
c = 57.012	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-02 
Deposition Author(s): Duc, N.M., Bong, S.M., Lee, B.I.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2019R1A2C1002545
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2018R1A5A2023127
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021R1F1A1060596

Revision History  

• Version 1.0: 2023-08-02
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection
• Version 1.2: 2025-08-13
  Changes: Database references, Structure summary
• Version 1.3: 2026-03-04
  Changes: Refinement description