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- PDB-8u1z: Crystal structure of the Fis1 cytosolic domain bound to a peptide... -

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Basic information

Entry
Database: PDB / ID: 8u1z
TitleCrystal structure of the Fis1 cytosolic domain bound to a peptide inhibitor
Components
  • Mitochondrial fission 1 protein
  • inhibitor peptide
KeywordsPEPTIDE BINDING PROTEIN/INHIBITOR / tetracopipeptide repeat protein / mitochondria / inhibitor / fission / PEPTIDE BINDING PROTEIN-INHIBITOR complex
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 fragmentation involved in apoptotic process / protein targeting to mitochondrion / mitochondrial fission / peroxisomal membrane / autophagy of mitochondrion / positive regulation of intrinsic apoptotic signaling pathway ...negative regulation of fatty acid transport / negative regulation of ATP metabolic process / Class I peroxisomal membrane protein import / peroxisome fission / mitochondrial fragmentation involved in apoptotic process / protein targeting to mitochondrion / mitochondrial fission / peroxisomal membrane / autophagy of mitochondrion / positive regulation of intrinsic apoptotic signaling pathway / mitochondrion organization / peroxisome / mitochondrial outer membrane / molecular adaptor activity / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNolden, K.A. / Peterson, F.C. / Hill, R.B.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)TR001437 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM067180 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM080202 United States
CitationJournal: To Be Published
Title: Novel Fis1 inhibiting peptide reverses microvascular endothelial dysfunction in vessels from humans with type 2 diabetes
Authors: Nolden, K.A. / Kakarla, M. / Egner, J.M. / Wang, J. / Harwig, M.C. / Puppala, V.K. / Hofeld, B.C. / Arnold, L.A. / Trykall, D.Z. / Peterson, F.C. / Roberts, M.L. / Jenson, D.M. / Hill, R.B. / Widlansky, M.E.
History
DepositionSep 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: 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: inhibitor peptide


Theoretical massNumber of molelcules
Total (without water)16,2112
Polymers16,2112
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, 2D NMR titration study, microscale thermophoresis, intrinsic tryptophan fluorescence spectroscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-10 kcal/mol
Surface area8610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.798, 54.798, 103.198
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-217-

HOH

21A-257-

HOH

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Components

#1: Protein Mitochondrial fission 1 protein


Mass: 14505.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FIS1 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3D6
#2: Protein/peptide inhibitor peptide


Mass: 1704.966 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG3350, HEPES, sodium chloride, Silver Bullet D5 (Hampton Research HR2-996-41)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→48.4 Å / Num. obs: 14066 / % possible obs: 99 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.068 / Net I/σ(I): 15.85
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.8-1.852.13518130.2022.3521
1.85-1.91.65319980.3841.8011
1.9-1.951.31919600.6321.4151
1.95-2.010.94118830.7961.0081
2.01-2.080.58818300.9060.631
2.08-2.150.40117590.9430.431
2.15-2.230.29517140.9760.3161
2.23-2.320.21316460.9870.2281
2.32-2.430.17516010.9910.1881
2.43-2.550.12614970.9960.1351
2.55-2.680.10914420.9960.1161
2.68-2.850.08413590.9980.091
2.85-3.040.06612860.9980.0711
3.04-3.290.05411880.9980.0581
3.29-3.60.04310980.9990.0461
3.6-4.030.0379940.9990.0391
4.03-4.650.0328610.9990.0341
4.65-5.690.0327370.9990.0341
5.69-8.050.035850.9990.0331
8.05-48.40.0283200.9990.031

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NZN

1nzn


Resolution: 1.85→37.57 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2592 1398 9.97 %
Rwork0.2081 --
obs0.2131 14019 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→37.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1116 0 0 85 1201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061136
X-RAY DIFFRACTIONf_angle_d0.7881523
X-RAY DIFFRACTIONf_dihedral_angle_d13.145444
X-RAY DIFFRACTIONf_chiral_restr0.047163
X-RAY DIFFRACTIONf_plane_restr0.006194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.920.37721340.28021209X-RAY DIFFRACTION99
1.92-1.990.33251360.25961225X-RAY DIFFRACTION100
1.99-2.080.2821370.2131240X-RAY DIFFRACTION100
2.08-2.190.24361400.19631255X-RAY DIFFRACTION100
2.19-2.330.24551350.19571222X-RAY DIFFRACTION100
2.33-2.510.29281410.20551262X-RAY DIFFRACTION100
2.51-2.760.25991400.21891258X-RAY DIFFRACTION100
2.76-3.160.27571400.22691263X-RAY DIFFRACTION100
3.16-3.980.27671450.20461297X-RAY DIFFRACTION100
3.99-37.570.22281500.19641390X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0916-0.02260.10640.0827-0.18290.2352-0.2239-1.32320.60920.65260.2138-0.3722-0.60230.24170.00130.569-0.1095-0.06430.56610.03480.626915.954143.439828.9822
20.4081-0.3545-0.00750.3640.13210.44150.2530.37510.1828-0.17-0.17020.3059-0.3054-0.15330.00030.34320.0675-0.01050.4208-0.0580.4413-2.376133.639324.6934
31.55351.04180.6310.64810.54141.44490.03390.049-0.0386-0.06450.08610.08320.0636-0.1113-0.00010.28860.0099-0.01550.3003-0.0080.2827.504528.177633.2039
41.18410.5120.56351.2703-0.01871.24620.0741-0.138-0.11410.33860.1618-0.46160.28870.4238-0.00020.24440.0328-0.0080.3306-0.03550.326620.02429.005944.2784
50.33630.05090.00640.0231-0.06470.1812-0.01630.23750.469-0.5282-0.0918-0.7472-0.27760.5732-0.02730.3175-0.02440.05540.3286-0.01320.335814.574640.042639.3879
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 27 )
3X-RAY DIFFRACTION3chain 'A' and (resid 28 through 83 )
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 125 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 13 )

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