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- PDB-2pqn: Crystal structure of yeast Fis1 complexed with a fragment of yeas... -

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Basic information

Entry
Database: PDB / ID: 2pqn
TitleCrystal structure of yeast Fis1 complexed with a fragment of yeast Mdv1
Components
  • Mitochondria fission 1 protein
  • Mitochondrial division protein 1
KeywordsAPOPTOSIS / TPR domain / protein-protein complex
Function / homology
Function and homology information


Class I peroxisomal membrane protein import / peroxisome organization / peroxisome fission / mitochondrial genome maintenance / mitochondrial fission / positive regulation of mitochondrial fission / ubiquitin binding / peroxisome / mitochondrial outer membrane / apoptotic process / mitochondrion
Similarity search - Function
Mitochondrial division protein 1 / Mitochondrial division protein 1 / 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 repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...Mitochondrial division protein 1 / Mitochondrial division protein 1 / 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 repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Mitochondrial fission 1 protein / Mitochondrial division protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsZhang, Y. / Chan, D.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Structural basis for recruitment of mitochondrial fission complexes by Fis1.
Authors: Zhang, Y. / Chan, D.C.
History
DepositionMay 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondria fission 1 protein
B: Mitochondrial division protein 1


Theoretical massNumber of molelcules
Total (without water)21,1662
Polymers21,1662
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.172, 57.388, 69.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Mitochondria fission 1 protein / Mitochondrial division protein 2


Mass: 15128.260 Da / Num. of mol.: 1 / Fragment: cytosolic portion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FIS1, MDV2 / Plasmid: pBB75 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P40515
#2: Protein Mitochondrial division protein 1 / Mitochondria fission 2 protein


Mass: 6037.681 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MDV1, FIS2, GAG3, NET2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P47025
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.05 Å3/Da / Density % sol: 40.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG3350, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 12, 2006
Details: Flat collimating mirror, double crystal monochromator, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 9834 / % possible obs: 98.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 13
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.359 / % possible all: 89.5

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Phasing

Phasing MRMethod rotation: fast direct / Method translation: STRIPtrans_method

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PDB_EXTRACT2data extraction
Blu-Icedata collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Y8M

1y8m


Resolution: 2.15→29.81 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 11.018 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23306 765 8.1 %RANDOM
Rwork0.19769 ---
obs0.20062 8653 95.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.17 Å2
Baniso -1Baniso -2Baniso -3
1-1.96 Å20 Å20 Å2
2---1.76 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1185 0 0 41 1226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221214
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9751642
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8455146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31124.91559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.66415221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.449156
X-RAY DIFFRACTIONr_chiral_restr0.0960.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02911
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.2578
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2853
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.264
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8221.5757
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33621175
X-RAY DIFFRACTIONr_scbond_it2.0563536
X-RAY DIFFRACTIONr_scangle_it3.1764.5466
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.147→2.203 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 52 -
Rwork0.218 494 -
obs--87.5 %
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)
118.787411.7053-0.768831.4631-9.23447.0751-0.48081.1588-1.1606-0.79530.3162-2.6254-0.79081.76730.16460.0471-0.23650.21660.3346-0.141-0.00317.6156.499-16.828
25.5033-0.10790.26794.70291.47243.07180.0108-0.08380.2277-0.1734-0.04940.1272-0.07370.04280.0386-0.2418-0.02320.02410.0162-0.00190.13137.43811.511-5.92
319.189816.0861-7.899120.6866-3.684110.157-0.53250.79911.3018-1.26130.58540.642-0.9512-0.2146-0.05290.0986-0.1094-0.0396-0.11640.13450.19118.62421.663-17.289
49.61222.68650.4466.73312.92047.8027-0.40180.94730.1399-1.13340.46890.0477-0.51510.8301-0.06720.0722-0.05940.10660.13770.0717-0.122110.2737.746-26.62
57.36331.14136.08784.8480.801616.74540.10660.0005-0.01880.026-0.0711-0.00460.0935-0.0545-0.0354-0.2161-0.01870.02980.0154-0.06260.280919.05711.599-2.031
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA4 - 144 - 14
22AA15 - 6315 - 63
33AA64 - 7664 - 76
44AA77 - 12977 - 129
55BB146 - 16429 - 47

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