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- PDB-3uux: Crystal structure of yeast Fis1 in complex with Mdv1 fragment con... -

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Basic information

Entry
Database: PDB / ID: 3uux
TitleCrystal structure of yeast Fis1 in complex with Mdv1 fragment containing N-terminal extension and coiled coil domains
Components
  • Mitochondria fission 1 protein
  • Mitochondrial division protein 1
KeywordsAPOPTOSIS / Tetratricopeptide repeat / mitochondrial fission / mitochondria and cytoplasm
Function / homology
Function and homology information


Class I peroxisomal membrane protein import / peroxisome organization / peroxisome fission / : / mitochondrial fission / peroxisomal membrane / positive regulation of mitochondrial fission / ubiquitin binding / peroxisome / molecular adaptor activity ...Class I peroxisomal membrane protein import / peroxisome organization / peroxisome fission / : / mitochondrial fission / peroxisomal membrane / positive regulation of mitochondrial fission / ubiquitin binding / peroxisome / molecular adaptor activity / mitochondrial outer membrane / apoptotic process / lipid binding / mitochondrion
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #220 / 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 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #220 / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Tetratricopeptide repeat domain / Helix non-globular / Special / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / 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 S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.9 Å
AuthorsZhang, Y. / Chan, N.C. / Gristick, H. / Chan, D.C.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal structure of mitochondrial fission complex reveals scaffolding function for mitochondrial division 1 (mdv1) coiled coil.
Authors: Zhang, Y. / Chan, N.C. / Ngo, H.B. / Gristick, H. / Chan, D.C.
History
DepositionNov 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)84,5434
Polymers84,5434
Non-polymers00
Water00
1
A: Mitochondria fission 1 protein
B: Mitochondrial division protein 1


Theoretical massNumber of molelcules
Total (without water)42,2712
Polymers42,2712
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-16 kcal/mol
Surface area16220 Å2
MethodPISA
2
C: Mitochondria fission 1 protein
D: Mitochondrial division protein 1

C: Mitochondria fission 1 protein
D: Mitochondrial division protein 1


Theoretical massNumber of molelcules
Total (without water)84,5434
Polymers84,5434
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area13260 Å2
ΔGint-82 kcal/mol
Surface area26250 Å2
MethodPISA
3
A: Mitochondria fission 1 protein
B: Mitochondrial division protein 1

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


Theoretical massNumber of molelcules
Total (without water)84,5434
Polymers84,5434
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area12710 Å2
ΔGint-85 kcal/mol
Surface area26900 Å2
MethodPISA
4
C: Mitochondria fission 1 protein
D: Mitochondrial division protein 1


Theoretical massNumber of molelcules
Total (without water)42,2712
Polymers42,2712
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-15 kcal/mol
Surface area15830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.676, 174.676, 167.301
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13B
23D

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPGLUGLUAA5 - 1275 - 127
21ASPASPGLUGLUCC5 - 1275 - 127
12ALAALAASPASPBB225 - 290153 - 218
22ALAALAASPASPDD225 - 290153 - 218
13THRTHRGLUGLUBB146 - 16074 - 88
23THRTHRGLUGLUDD146 - 16074 - 88

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 15128.260 Da / Num. of mol.: 2 / Fragment: cytoplasmic portion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: FIS1, MDV2, YIL065C / 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: 27143.021 Da / Num. of mol.: 2 / Fragment: N-terminal extension and coiled coil / Mutation: K215A, K216A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: MDV1, FIS2, GAG3, NET2, YJL112W, J0802 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P47025
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.77 Å3/Da / Density % sol: 67.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.54M sodium citrate, 0.1M cacodylate, 4% acetonitrile, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 8, 2010
RadiationMonochromator: Side-scattering cuberoot I-beam bent single crystal, asymetric cut 12.2 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.896→123.514 Å / Num. all: 11999 / Num. obs: 11999 / % possible obs: 98.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 14.5 % / Rsym value: 0.076 / Net I/σ(I): 25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.9-4.118.10.5191.51367016920.51998.1
4.11-4.369.40.2413.21544816460.24199.9
4.36-4.66130.15452037915720.154100
4.66-5.0318.10.145.52593014330.14100
5.03-5.52180.1495.22430113490.149100
5.52-6.1717.90.145.52182512220.14100
6.17-7.1217.30.0898.41883210870.089100
7.12-8.7217.20.04315.5161039350.043100
8.72-12.3316.40.02922.3120837370.029100
12.33-19.80815.40.03319.650073260.03376.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å10 Å
Translation4 Å10 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.9→123.51 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.2503 / WRfactor Rwork: 0.2399 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7906 / SU B: 37.203 / SU ML: 0.517 / SU Rfree: 0.7063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.706 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT; IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1178 9.8 %RANDOM
Rwork0.2695 ---
obs0.2709 11999 98.64 %-
all-12164 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 159.89 Å2 / Biso mean: 126.7367 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-6.9 Å20 Å2-0 Å2
2--6.9 Å2-0 Å2
3----13.81 Å2
Refinement stepCycle: LAST / Resolution: 3.9→123.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4076 0 0 0 4076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224139
X-RAY DIFFRACTIONr_angle_refined_deg1.9441.9755600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7085511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20725.228197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.71515727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7231522
X-RAY DIFFRACTIONr_chiral_restr0.130.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213106
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT POSITIONAL / Weight position: 0.03

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A9820.04
2B5260.04
3B1090.03
LS refinement shellResolution: 3.896→3.997 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 72 -
Rwork0.332 707 -
all-779 -
obs-707 95.12 %

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