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- PDB-9kff: Truncated Fzo1 with modified LD,transition-like state -

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Basic information

Entry
Database: PDB / ID: 9kff
TitleTruncated Fzo1 with modified LD,transition-like state
ComponentsMitofusin FZO1
KeywordsHYDROLASE / Fzo1 / dynamin / mitofusin
Function / homology
Function and homology information


peroxisomal-mitochondrial contact site / peroxisome-mitochondrion membrane tether activity / mitochondrial outer membrane fusion / Factors involved in megakaryocyte development and platelet production / RHOT2 GTPase cycle / mitochondrial inner membrane fusion / PINK1-PRKN Mediated Mitophagy / mitochondrion localization / mitochondrial fusion / intracellular distribution of mitochondria ...peroxisomal-mitochondrial contact site / peroxisome-mitochondrion membrane tether activity / mitochondrial outer membrane fusion / Factors involved in megakaryocyte development and platelet production / RHOT2 GTPase cycle / mitochondrial inner membrane fusion / PINK1-PRKN Mediated Mitophagy / mitochondrion localization / mitochondrial fusion / intracellular distribution of mitochondria / mitochondrial membrane / peroxisome / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitochondrial outer membrane / GTPase activity / GTP binding / mitochondrion
Similarity search - Function
Mitofusin family / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin, N-terminal / Dynamin family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / GUANOSINE-5'-DIPHOSPHATE / : / Mitofusin FZO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsGao, S. / Huang, S.-J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2320103002 China
National Natural Science Foundation of China (NSFC)82173098 China
CitationJournal: To Be Published
Title: A special latch in yeast mitofusin guarantees mitochondrial fusion by stabilizing self-assembly
Authors: Gao, S. / Huang, S.-J.
History
DepositionNov 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitofusin FZO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4906
Polymers51,7231
Non-polymers7685
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.115, 77.115, 283.551
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-1283-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Mitofusin FZO1 / Transmembrane GTPase FZO1


Mass: 51722.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FZO1, YBR179C, YBR1241 / Production host: Escherichia coli (E. coli)
References: UniProt: P38297, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement

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Non-polymers , 6 types, 304 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES(PH 6.5), 8%(w/v) PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Aug 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.12→48.61 Å / Num. obs: 28505 / % possible obs: 97.3 % / Redundancy: 6.4 % / CC1/2: 0.974 / Net I/σ(I): 9.8
Reflection shellResolution: 2.12→2.18 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2342 / CC1/2: 0.697 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→48.61 Å / SU ML: 0.1897 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.258
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.243 1994 7.01 %
Rwork0.2013 26436 -
obs0.2043 28430 96.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.51 Å2
Refinement stepCycle: LAST / Resolution: 2.12→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3222 0 46 299 3567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133328
X-RAY DIFFRACTIONf_angle_d1.14854491
X-RAY DIFFRACTIONf_chiral_restr0.0579520
X-RAY DIFFRACTIONf_plane_restr0.0077567
X-RAY DIFFRACTIONf_dihedral_angle_d9.2068439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.170.27071430.2331891X-RAY DIFFRACTION99.03
2.17-2.230.26551410.21851880X-RAY DIFFRACTION98.97
2.23-2.30.41361420.32591878X-RAY DIFFRACTION97.73
2.3-2.370.29281410.21011875X-RAY DIFFRACTION98.25
2.37-2.450.2311410.20011882X-RAY DIFFRACTION98.01
2.45-2.550.26191380.19931837X-RAY DIFFRACTION95.5
2.55-2.670.27251360.21331813X-RAY DIFFRACTION93.25
2.67-2.810.25661350.22271768X-RAY DIFFRACTION91.93
2.81-2.990.3051410.2161861X-RAY DIFFRACTION95.11
2.99-3.220.24711440.20851896X-RAY DIFFRACTION96.96
3.22-3.540.21771440.17521916X-RAY DIFFRACTION97.26
3.54-4.050.20671440.18161919X-RAY DIFFRACTION96.09
4.05-5.10.16491480.1491951X-RAY DIFFRACTION96.06
5.1-48.610.19741560.18642069X-RAY DIFFRACTION93.8
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)
10.948851036974-0.0601280669164-0.1744560907560.827407868261-0.2180723622770.654586342269-0.0770097277871-0.07638556102770.02509034056360.03784741993260.0109582125355-0.158797409786-0.06383203836940.0837614540807-0.274581171106-0.000129332433707-0.0578782775875-0.0180239989521-0.0299758921353-0.0296489749268-0.0209452186015-21.2841515022-19.85116871711.1312836998
20.0641782452075-0.004893601512580.03811560473110.155129148716-0.002028666419470.09240242396020.00279111835216-0.00471473100925-0.01526979283660.00462594540033-0.0230307410504-0.02199957809680.003619517388950.02701199040515.25373214088E-60.05365760313230.01180479393730.00693375538540.03363009279060.002483204273050.03999022001573.75472633646-18.10513746791.14626346344
30.03559956645110.052258239129-0.02048457794750.078453065623-0.04130839256630.0931470345159-0.0249962595463-0.08463424657420.01254393583470.007723744836720.0148308313054-0.0113921581602-0.03217582211390.0286355523087-4.64654314448E-50.05030754755430.006233039752020.006836985481060.0469627992841-0.02115004091250.0505932504166-22.9326494772-20.105867864919.0693174941
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 82 through 184 )82 - 1841 - 90
22chain 'A' and (resid 185 through 459 )185 - 45991 - 345
33chain 'A' and (resid 460 through 855 )460 - 855346 - 404

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