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- PDB-5go4: Truncated mitofusin-1, nucleotide-free -

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Basic information

Entry
Database: PDB / ID: 5go4
TitleTruncated mitofusin-1, nucleotide-free
ComponentsMitofusin-1
KeywordsHYDROLASE / Mitochondrial Fusion
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 / Factors involved in megakaryocyte development and platelet production / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / 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 / Factors involved in megakaryocyte development and platelet production / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitochondrial outer membrane / GTPase activity / GTP binding / mitochondrion / identical protein binding / membrane
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 Å
AuthorsCao, Y.L. / Gao, S.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology of the People's Republic of China2013CB910500 China
National Natural Science Foundation of China31200553 China
Ministry of Education of the People's Republic of ChinaNCET-12-0567 China
CitationJournal: Nature / Year: 2017
Title: MFN1 structures reveal nucleotide-triggered dimerization critical for mitochondrial fusion
Authors: Cao, Y.L. / Meng, S. / Chen, Y. / Feng, J.X. / Gu, D.D. / Yu, B. / Li, Y.J. / Yang, J.Y. / Liao, S. / Chan, D.C. / Gao, S.
History
DepositionJul 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Structure summary
Revision 1.2Mar 8, 2017Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitofusin-1


Theoretical massNumber of molelcules
Total (without water)48,4171
Polymers48,4171
Non-polymers00
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20940 Å2
Unit cell
Length a, b, c (Å)51.799, 110.876, 112.400
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: 48417.094 Da / Num. of mol.: 1 / Fragment: UNP residues 1-365,UNP residues 696-741
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 3.46 Å3/Da / Density % sol: 64.47 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M sodium citrate tribasic dehydrate and 20~22% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.918 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.2→47 Å / Num. obs: 62925 / % possible obs: 99.4 % / Redundancy: 7.9 % / Net I/σ(I): 18.08

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.202→39.467 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 21.8
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2139 3219 5.12 %
Rwork0.1751 --
obs0.1771 62925 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.202→39.467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 0 184 3455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073351
X-RAY DIFFRACTIONf_angle_d0.7534523
X-RAY DIFFRACTIONf_dihedral_angle_d16.7522065
X-RAY DIFFRACTIONf_chiral_restr0.047515
X-RAY DIFFRACTIONf_plane_restr0.005585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2022-2.23510.26741550.23882356X-RAY DIFFRACTION92
2.2351-2.270.26771420.22852616X-RAY DIFFRACTION100
2.27-2.30720.26631350.22722655X-RAY DIFFRACTION100
2.3072-2.3470.23611240.21082641X-RAY DIFFRACTION100
2.347-2.38970.25111370.20212602X-RAY DIFFRACTION100
2.3897-2.43560.2211290.18812606X-RAY DIFFRACTION100
2.4356-2.48530.21791380.19392638X-RAY DIFFRACTION100
2.4853-2.53930.25451450.20282556X-RAY DIFFRACTION100
2.5393-2.59840.21541310.2042643X-RAY DIFFRACTION100
2.5984-2.66340.28491480.20632615X-RAY DIFFRACTION100
2.6634-2.73540.26291290.19982638X-RAY DIFFRACTION100
2.7354-2.81580.24451580.20652577X-RAY DIFFRACTION100
2.8158-2.90670.24541390.20362617X-RAY DIFFRACTION100
2.9067-3.01060.31291420.20022576X-RAY DIFFRACTION100
3.0106-3.1310.20661560.19712600X-RAY DIFFRACTION100
3.131-3.27350.29051080.19192635X-RAY DIFFRACTION100
3.2735-3.4460.21851210.18372656X-RAY DIFFRACTION100
3.446-3.66170.19971360.16752616X-RAY DIFFRACTION100
3.6617-3.94420.18841620.1512573X-RAY DIFFRACTION100
3.9442-4.34070.1731730.13532587X-RAY DIFFRACTION100
4.3407-4.96770.18181420.13292570X-RAY DIFFRACTION100
4.9677-6.25480.18611320.15662627X-RAY DIFFRACTION100
6.2548-39.47360.18961370.17372506X-RAY DIFFRACTION96
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)
11.4915-0.89190.20494.8336-2.52172.1011-0.0488-0.0462-0.0312-0.28940.0696-0.00080.1502-0.1006-0.04040.26950.0221-0.03730.3433-0.0230.271616.5083-7.141934.4783
23.2348-0.25260.11274.26221.41884.6568-0.122-0.3470.1060.32340.01110.1844-0.0495-0.3930.09410.28260.01210.01770.30980.03980.2971-1.422426.874423.6559
30.7007-1.87411.00497.6039-4.13842.7367-0.2489-0.11090.10260.4640.0965-0.5156-0.2037-0.03450.20320.217-0.0109-0.06920.3171-0.0240.308420.05725.845633.6937
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 73 )
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 284 )
3X-RAY DIFFRACTION3chain 'A' and (resid 285 through 736 )

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