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- PDB-7yka: Crystal structure of Fis1 (Mitochondrial fission 1 protein) -

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Basic information

Entry
Database: PDB / ID: 7yka
TitleCrystal structure of Fis1 (Mitochondrial fission 1 protein)
Components
  • Fis1
  • Mitochondrial fission 1 protein
KeywordsAPOPTOSIS
Function / homology
Function and homology information


response to flavonoid / negative regulation of fatty acid transport / negative regulation of ATP metabolic process / response to fluoride / response to hypobaric hypoxia / Class I peroxisomal membrane protein import / peroxisome fission / mitochondrial fragmentation involved in apoptotic process / cellular response to peptide / cellular response to toxic substance ...response to flavonoid / negative regulation of fatty acid transport / negative regulation of ATP metabolic process / response to fluoride / response to hypobaric hypoxia / Class I peroxisomal membrane protein import / peroxisome fission / mitochondrial fragmentation involved in apoptotic process / cellular response to peptide / cellular response to toxic substance / mitochondrial fission / cellular response to lipid / peroxisomal membrane / protein targeting to mitochondrion / positive regulation of mitochondrial fission / response to muscle activity / positive regulation of intrinsic apoptotic signaling pathway / response to endoplasmic reticulum stress / mitochondrion organization / response to nutrient levels / cellular response to glucose stimulus / peroxisome / positive regulation of neuron apoptotic process / molecular adaptor activity / mitochondrial outer membrane / lipid binding / protein-containing complex / mitochondrion / identical protein binding / membrane / cytosol
Similarity search - Function
Mitochondria fission 1 protein / Fis1, N-terminal tetratricopeptide repeat / Fis1, C-terminal tetratricopeptide repeat / Mitochondria fission protein Fis1, cytosolic domain / Fis1 N-terminal tetratricopeptide repeat / Fis1 C-terminal tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Mitochondrial fission 1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDuc, N.M. / Bong, S.M. / Lee, B.I.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2019R1A2C1002545 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2018R1A5A2023127 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2021R1F1A1060596 Korea, Republic Of
CitationJournal: Commun Biol / Year: 2025
Title: Crystal structure of Fis1 and Bap31 provides information on protein-protein interactions at mitochondria-associated ER membranes
Authors: 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.
History
DepositionJul 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Aug 13, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondrial fission 1 protein
B: Fis1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,61111
Polymers28,0222
Non-polymers5899
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: AUC experiment monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.822, 56.283, 57.012
Angle α, β, γ (deg.)90.000, 100.065, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Mitochondrial fission 1 protein / FIS1 homolog / hFis1


Mass: 13803.808 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FIS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3D6
#2: Protein Fis1


Mass: 14218.286 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3D6
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 100 mM Imidazole pH 8.0 200 mM Zinc acetate 20% PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 12419 / % possible obs: 99.4 % / Redundancy: 6 % / Biso Wilson estimate: 29.47 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 15.6
Reflection shellResolution: 2.3→2.35 Å / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 830

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NZN

1nzn


Resolution: 2.3→39.75 Å / SU ML: 0.2958 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.9037
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2503 578 4.91 %
Rwork0.2262 11195 -
obs0.2274 11773 93.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.34 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1971 0 9 10 1990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00111999
X-RAY DIFFRACTIONf_angle_d0.29732676
X-RAY DIFFRACTIONf_chiral_restr0.0314290
X-RAY DIFFRACTIONf_plane_restr0.0021341
X-RAY DIFFRACTIONf_dihedral_angle_d11.5939786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.530.31861070.24132305X-RAY DIFFRACTION77.58
2.53-2.90.28171560.25782897X-RAY DIFFRACTION97.79
2.9-3.650.25461490.23122973X-RAY DIFFRACTION99.68
3.65-39.750.2251660.20873020X-RAY DIFFRACTION99.56

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