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- PDB-9kfe: Truncated Fzo1 with modified LB, GTP-bound -

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Basic information

Entry
Database: PDB / ID: 9kfe
TitleTruncated Fzo1 with modified LB, GTP-bound
ComponentsMitofusin FZO1,Mitofusin FZO1,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
GUANOSINE-5'-TRIPHOSPHATE / : / Mitofusin FZO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 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: Nat Commun / Year: 2025
Title: A special latch in yeast mitofusin guarantees mitochondrial fusion by stabilizing self-assembly.
Authors: Huang, S.J. / Ma, D.F. / Yu, C. / Li, J. / Tu, X. / Huang, Z. / Qi, Y. / Ou, J.Y. / Feng, J.X. / Yu, B. / Cao, Y.L. / Yue, J.X. / Hu, J. / Li, M. / Lu, Y. / Yan, L. / Gao, S.
History
DepositionNov 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitofusin FZO1,Mitofusin FZO1,Fzo1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8174
Polymers54,2301
Non-polymers5873
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-13 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.133, 77.133, 284.664
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-90-

TRP

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Components

#1: Protein Mitofusin FZO1,Mitofusin FZO1,Fzo1 / Transmembrane GTPase FZO1


Mass: 54230.426 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
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 150mM Cesium chloride, 17% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.81→48.7 Å / Num. obs: 12840 / % possible obs: 98.6 % / Redundancy: 5 % / CC1/2: 0.991 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.083 / Rrim(I) all: 0.154 / Net I/σ(I): 9.8
Reflection shellResolution: 2.81→2.97 Å / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 6.5 / Num. unique obs: 1775 / CC1/2: 0.787 / Rpim(I) all: 0.128 / Rrim(I) all: 0.236

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→38.22 Å / SU ML: 0.349 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2918
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2672 1259 10.01 %
Rwork0.2188 11320 -
obs0.2237 12579 96.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.97 Å2
Refinement stepCycle: LAST / Resolution: 2.81→38.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3114 0 34 1 3149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00173207
X-RAY DIFFRACTIONf_angle_d0.47044328
X-RAY DIFFRACTIONf_chiral_restr0.0371506
X-RAY DIFFRACTIONf_plane_restr0.0032542
X-RAY DIFFRACTIONf_dihedral_angle_d4.1174412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.930.33921310.28431181X-RAY DIFFRACTION93.58
2.93-3.060.3281400.2731258X-RAY DIFFRACTION99.57
3.06-3.220.30631410.25311275X-RAY DIFFRACTION99.79
3.22-3.420.29281390.22461245X-RAY DIFFRACTION99.64
3.42-3.690.23881430.20841290X-RAY DIFFRACTION99.51
3.69-4.060.27241430.19261284X-RAY DIFFRACTION99.44
4.06-4.640.20591420.16531282X-RAY DIFFRACTION98.75
4.64-5.840.25141360.20961207X-RAY DIFFRACTION90.07
5.85-38.220.22881440.20541298X-RAY DIFFRACTION88.96
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)
11.97690781740.791831191171-0.2299583026341.70149676530.2706470322421.91457736447-0.2111227587120.1363386958850.423899128464-0.4582807223740.04997026057460.0201023667974-0.260127025998-0.1136639490120.1223858045980.275974685056-0.0688467860802-0.0966948736230.05494896943510.03705991607440.150097483258-21.4587160737-21.806713078110.9123656913
20.5191112581370.2939309899350.3486783942481.155753921660.4500956266481.25625196519-0.03554117943140.0593816923802-0.108073057599-0.0821818264339-0.078856866691-0.03492169145570.1483705211530.1076110568580.02342286648830.1012460268660.03213509386010.04465533589090.005941918221-0.001497727430680.09020747456331.4652867916-19.0763701729-2.67630924852
31.862628605770.38931186253-0.05520499902360.9489438736260.06278044863540.6962107100920.0372807240602-0.2878035438880.09067839420940.155891775206-0.0834685416807-0.101242960090.01952889811160.09926305777170.1818671237750.1473691572670.0500077427841-0.08570990106710.03543802957230.04972665977420.0398389922409-6.37200962082-16.637020408415.9601968371
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 84 through 184 )84 - 1841 - 75
22chain 'A' and (resid 185 through 377 )185 - 37776 - 266
33chain 'A' and (resid 378 through 854 )378 - 854267 - 388

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