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- PDB-5gns: Structures of human Mitofusin 1 provide insight into mitochondria... -

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Basic information

Entry
Database: PDB / ID: 5gns
TitleStructures of human Mitofusin 1 provide insight into mitochondrial tethering
ComponentsMitofusin-1
KeywordsHYDROLASE / Mitofusin 1 / BDLP-like folding
Function / homology
Function and homology information


RHOT2 GTPase cycle / outer mitochondrial membrane protein complex / mitochondrion localization / GTP metabolic process / positive regulation of mitochondrial membrane potential / mitochondrial fusion / PINK1-PRKN Mediated Mitophagy / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Factors involved in megakaryocyte development and platelet production / mitochondrial outer membrane ...RHOT2 GTPase cycle / outer mitochondrial membrane protein complex / mitochondrion localization / GTP metabolic process / positive regulation of mitochondrial membrane potential / mitochondrial fusion / PINK1-PRKN Mediated Mitophagy / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Factors involved in megakaryocyte development and platelet production / mitochondrial outer membrane / GTPase activity / GTP binding / mitochondrion / membrane / identical protein binding
Similarity search - Function
Fzo/mitofusin HR2 domain / fzo-like conserved region / 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-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.702 Å
AuthorsQi, Y. / Yan, L. / Yu, C. / Guo, X. / Zhou, X. / Hu, X. / Huang, X. / Rao, Z. / Lou, Z. / Hu, J.
Funding support China, Armenia, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31225006 China
the National Basic Research Program of China2012CB910302 China
an International Early Career Scientist grant from Howard Hughes Medical InstituteArmenia
CitationJournal: To Be Published
Title: Structures of human Mitofusin 1 provide insight into mitochondrial tethering
Authors: Qi, Y. / Yan, L. / Yu, C. / Guo, X. / Zhou, X. / Hu, X. / Huang, X. / Rao, Z. / Lou, Z. / Hu, J.
History
DepositionJul 24, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_prerelease_seq
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitofusin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8582
Polymers47,3351
Non-polymers5231
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-1 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.657, 74.671, 94.756
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mitofusin-1 / Fzo homolog / Transmembrane GTPase MFN1


Mass: 47334.785 Da / Num. of mol.: 1 / Fragment: UNP residues 1-364 / Mutation: K88A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MFN1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IWA4, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 200mM sodium phosphate monobasic monohydrate, 20%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 122150 / % possible obs: 99.1 % / Redundancy: 14.1 % / Net I/σ(I): 10.2

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.702→40.005 Å / SU ML: 0.37 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 29.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.283 1436 9.95 %
Rwork0.212 --
obs0.219 14425 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.702→40.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3011 0 32 8 3051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013127
X-RAY DIFFRACTIONf_angle_d1.3884216
X-RAY DIFFRACTIONf_dihedral_angle_d17.6521172
X-RAY DIFFRACTIONf_chiral_restr0.051479
X-RAY DIFFRACTIONf_plane_restr0.007535
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.702-2.79860.32371370.24131281X-RAY DIFFRACTION100
2.7986-2.91060.33361430.25081244X-RAY DIFFRACTION100
2.9106-3.0430.35981450.2581279X-RAY DIFFRACTION100
3.043-3.20340.32421450.23121277X-RAY DIFFRACTION100
3.2034-3.4040.32831430.22161305X-RAY DIFFRACTION100
3.404-3.66670.29421360.2191290X-RAY DIFFRACTION100
3.6667-4.03530.29891420.20591289X-RAY DIFFRACTION100
4.0353-4.61850.24391480.18221303X-RAY DIFFRACTION100
4.6185-5.8160.25351450.20161320X-RAY DIFFRACTION100
5.816-40.00930.26421520.21311401X-RAY DIFFRACTION100

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