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- PDB-1t3j: Mitofusin domain HR2 V686M/I708M mutant -

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Basic information

Entry
Database: PDB / ID: 1t3j
TitleMitofusin domain HR2 V686M/I708M mutant
Componentsmitofusin 1
KeywordsMEMBRANE PROTEIN / coiled coil antiparallel / dimer
Function / homology
Function and homology information


: / mitochondrial fusion => GO:0008053 / : / : / outer mitochondrial membrane protein complex / PINK1-PRKN Mediated Mitophagy / positive regulation of mitochondrial fusion / mitochondrion localization / positive regulation of dendritic spine morphogenesis / Factors involved in megakaryocyte development and platelet production ...: / mitochondrial fusion => GO:0008053 / : / : / outer mitochondrial membrane protein complex / PINK1-PRKN Mediated Mitophagy / positive regulation of mitochondrial fusion / mitochondrion localization / positive regulation of dendritic spine morphogenesis / Factors involved in megakaryocyte development and platelet production / GTP metabolic process / positive regulation of mitochondrial membrane potential / mitochondrial fusion / intracellular distribution of mitochondria / negative regulation of mitochondrial fission / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitochondrial outer membrane / mitochondrial inner membrane / membrane => GO:0016020 / GTPase activity / GTP binding / mitochondrion / identical protein binding
Similarity search - Function
Mitofusin-1 / Fzo/mitofusin HR2 domain / fzo-like conserved region / Mitofusin family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Dynamin / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Mitofusin-1 / Fzo/mitofusin HR2 domain / fzo-like conserved region / Mitofusin family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Dynamin / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsKoshiba, T. / Detmer, S.A. / Kaiser, J.T. / Chen, H. / McCaffery, J.M. / Chan, D.C.
CitationJournal: Science / Year: 2004
Title: Structural basis of mitochondrial tethering by mitofusin complexes
Authors: Koshiba, T. / Detmer, S.A. / Kaiser, J.T. / Chen, H. / McCaffery, J.M. / Chan, D.C.
History
DepositionApr 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mitofusin 1


Theoretical massNumber of molelcules
Total (without water)11,1071
Polymers11,1071
Non-polymers00
Water59433
1
A: mitofusin 1

A: mitofusin 1


Theoretical massNumber of molelcules
Total (without water)22,2152
Polymers22,2152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation19_655-x+5/4,-z+1/4,-y+1/41
Buried area2890 Å2
ΔGint-30 kcal/mol
Surface area9360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)162.830, 162.830, 162.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132
DetailsThe second part of the dimer is generated by the twofold axis: -X+1/4, -Z+1/4, -Y+1/4

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Components

#1: Protein mitofusin 1


Mass: 11107.447 Da / Num. of mol.: 1 / Mutation: V686M, I708M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: MFN1 / Plasmid: pET28a(+),pET28-MFN1-HR2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q811U4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 4.09 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: Isopropanol, TRIS, Ammonium Acetate, PEG 200, pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9795, 0.9797, 0.9641, 0.9800
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 22, 2004
RadiationMonochromator: Si(111) double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97971
30.96411
40.981
ReflectionResolution: 2.5→27.52 Å / Num. all: 6772 / Num. obs: 6772 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 44.1 Å2 / Limit h max: 65 / Limit h min: 5 / Limit k max: 46 / Limit k min: 5 / Limit l max: 37 / Limit l min: 0 / Observed criterion F max: 2907765.71 / Observed criterion F min: 14.9 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 25.2
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 5.6 / Num. unique all: 319 / Rsym value: 0.463 / % possible all: 99.2

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→14.86 Å / Rfactor Rfree error: 0.011 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 669 9.9 %random
Rwork0.241 ---
all-6772 --
obs-6772 99.5 %-
Solvent computationSolvent model: bulk solvent / Bsol: 52.5258 Å2 / ksol: 0.388799 e/Å3
Displacement parametersBiso max: 99.67 Å2 / Biso mean: 52.81 Å2 / Biso min: 26.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.36 Å
Luzzati d res high-2.5
Refinement stepCycle: LAST / Resolution: 2.5→14.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms513 0 0 33 546
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_torsion_deg17.1
X-RAY DIFFRACTIONx_torsion_impr_deg0.77
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.5-2.610.397708.60.3247430.047813813100
2.61-2.750.377759.20.3067400.04481881599.6
2.75-2.920.288809.70.2777490.032829829100
2.92-3.150.2669211.10.2417390.028831831100
3.15-3.460.315839.90.247530.03583883699.8
3.46-3.950.254829.60.2067710.02885485399.9
3.95-4.950.25839.70.2067740.027857857100
4.95-14.860.29910411.40.2628060.02993991096.8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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