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- PDB-9avb: Fis1 Wild type -

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Basic information

Entry
Database: PDB / ID: 9avb
TitleFis1 Wild type
ComponentsMitochondrial fission 1 protein
KeywordsUNKNOWN FUNCTION / Fis1 / Drp1 / mitochondrial fission / activated Fis1 / SP11
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
Mitochondrial fission 1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 1, 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

Downloads & links

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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)30,2304
Polymers30,1592
Non-polymers712
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-19 kcal/mol
Surface area12990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.330, 58.330, 156.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 15079.348 Da / Num. of mol.: 2
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.54 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 25% PEG 5KMME, 0.15M NaCl, 0.033M HEPES(pH 7.5), 0.033M ADA (pH 6.5), 0.033M Tris.HCl (pH 8.0)
PH range: 6.5-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98726 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 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: 0.98726 Å / Relative weight: 1
ReflectionResolution: 1.95→30.91 Å / Num. obs: 21571 / % possible obs: 98.6 % / Redundancy: 13.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.092 / Net I/σ(I): 18.55
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.95-22.44815870.6632.5431
2-2.061.90315130.7221.9821
2.06-2.121.31915170.8761.3671
2.12-2.181.04214500.9091.0791
2.18-2.250.73214350.9640.7581
2.25-2.330.49413830.9820.5121
2.33-2.420.39113540.9840.4051
2.42-2.520.28512710.9910.2961
2.52-2.630.23311830.9890.2431
2.63-2.760.18211810.9940.1891
2.76-2.910.13211330.9980.1371
2.91-3.080.09710650.9980.1011
3.08-3.30.0769790.9990.0791
3.3-3.560.0599450.9990.0611
3.56-3.90.0478370.9980.0491
3.9-4.360.0437700.9990.0451
4.36-5.040.046980.9990.0411
5.04-6.170.0415740.9990.0431
6.17-8.720.0374500.9990.0381
8.72-30.910.0352460.9990.0371

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→30.91 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2306 1079 5 %
Rwork0.1847 --
obs0.1869 21564 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→30.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 2 142 2148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072077
X-RAY DIFFRACTIONf_angle_d0.9632787
X-RAY DIFFRACTIONf_dihedral_angle_d4.845279
X-RAY DIFFRACTIONf_chiral_restr0.051301
X-RAY DIFFRACTIONf_plane_restr0.009358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.040.33461320.2862503X-RAY DIFFRACTION98
2.04-2.150.28071350.23552563X-RAY DIFFRACTION98
2.15-2.280.22571340.20252557X-RAY DIFFRACTION99
2.28-2.460.29441350.19412557X-RAY DIFFRACTION99
2.46-2.70.28761340.20272550X-RAY DIFFRACTION98
2.7-3.090.23561370.192596X-RAY DIFFRACTION100
3.09-3.90.21231350.17352558X-RAY DIFFRACTION98
3.9-30.910.20151370.16722601X-RAY DIFFRACTION99

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