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- PDB-9ayd: Mitochondrial fission 1 (Fis1) protein structure Y38E mutation 1.53A -

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Basic information

Entry
Database: PDB / ID: 9ayd
TitleMitochondrial fission 1 (Fis1) protein structure Y38E mutation 1.53A
ComponentsMitochondrial fission 1 protein
KeywordsUNKNOWN FUNCTION / Fis1 structure / Mitochondrial fission / Drug design
Function / homology
Function and homology information


negative regulation of fatty acid transport / negative regulation of ATP metabolic process / Class I peroxisomal membrane protein import / peroxisome fission / mitochondrial fission / peroxisomal membrane / protein targeting to mitochondrion / positive regulation of intrinsic apoptotic signaling pathway / mitochondrion organization / peroxisome ...negative regulation of fatty acid transport / negative regulation of ATP metabolic process / Class I peroxisomal membrane protein import / peroxisome fission / mitochondrial fission / peroxisomal membrane / protein targeting to mitochondrion / positive regulation of intrinsic apoptotic signaling pathway / mitochondrion organization / peroxisome / molecular adaptor activity / mitochondrial outer membrane / apoptotic process / 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
ACETATE ION / TRIETHYLENE GLYCOL / Mitochondrial fission 1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsMathews, I.I. / Pokhrel, S. / Wakatsuki, S.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133894 United States
CitationJournal: Nat Commun / Year: 2025
Title: A hidden cysteine in Fis1 targeted to prevent excessive mitochondrial fission and dysfunction under oxidative stress.
Authors: Pokhrel, S. / Heo, G. / Mathews, I. / Yokoi, S. / Matsui, T. / Mitsutake, A. / Wakatsuki, S. / Mochly-Rosen, D.
History
DepositionMar 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,4505
Polymers30,0912
Non-polymers3593
Water3,459192
1
A: Mitochondrial fission 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2553
Polymers15,0451
Non-polymers2092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitochondrial fission 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1952
Polymers15,0451
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.500, 81.440, 47.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-372-

HOH

21B-373-

HOH

31B-397-

HOH

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Components

#1: Protein Mitochondrial fission 1 protein / FIS1 homolog / hFis1 / Tetratricopeptide repeat protein 11 / TPR repeat protein 11


Mass: 15045.287 Da / Num. of mol.: 2 / Mutation: Y38E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FIS1, TTC11, CGI-135 / Cell (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3D6
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.18 Å3/Da / Density % sol: 43.64 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1M Sodium Acetate (pH 4.5), 30% PEG smear low

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2022
Details: Rh coated collimating mirrors, K-B focusing mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.53→38.861 Å / Num. obs: 40271 / % possible obs: 99.2 % / Redundancy: 12.8 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.063 / Net I/σ(I): 22.25
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.53-1.572.37529610.752.4671
1.57-1.611.95628410.8292.0321
1.61-1.661.56327910.8551.6251
1.66-1.711.3927150.881.4471
1.71-1.771.19825960.8891.2521
1.77-1.830.81125290.9630.8421
1.83-1.90.5524820.9850.5721
1.9-1.980.39723860.9920.4121
1.98-2.060.26822700.9940.2791
2.06-2.160.16321680.9970.1691
2.16-2.280.11420710.9980.1191
2.28-2.420.07919830.9990.0831
2.42-2.590.06218660.9990.0641
2.59-2.790.05117550.9990.0531
2.79-3.060.04415940.9990.0461
3.06-3.420.03314600.9990.0351
3.42-3.950.027130310.0281
3.95-4.840.024111310.0251
4.84-6.840.02387010.0241
6.84-38.8610.025170.9990.0211

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→38.86 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.737 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 2014 5 %RANDOM
Rwork0.18093 ---
obs0.1832 38258 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.962 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å2-0 Å20 Å2
2--1.63 Å2-0 Å2
3----0.67 Å2
Refinement stepCycle: 1 / Resolution: 1.53→38.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 24 192 2330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0122242
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162237
X-RAY DIFFRACTIONr_angle_refined_deg1.1371.6473006
X-RAY DIFFRACTIONr_angle_other_deg0.4031.595175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1665274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.756514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.2910461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0620.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022601
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02499
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5952.7321076
X-RAY DIFFRACTIONr_mcbond_other1.5782.731075
X-RAY DIFFRACTIONr_mcangle_it2.234.9081356
X-RAY DIFFRACTIONr_mcangle_other2.2294.911357
X-RAY DIFFRACTIONr_scbond_it1.8453.2411166
X-RAY DIFFRACTIONr_scbond_other1.8443.2421167
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5235.7421651
X-RAY DIFFRACTIONr_long_range_B_refined3.278580.362708
X-RAY DIFFRACTIONr_long_range_B_other2.981587.652668
X-RAY DIFFRACTIONr_rigid_bond_restr2.65334473
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 148 -
Rwork0.232 2808 -
obs--99.36 %

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