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- PDB-6jsj: Structural analysis of a trimeric assembly of the mitochondrial d... -

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Basic information

Entry
Database: PDB / ID: 6jsj
TitleStructural analysis of a trimeric assembly of the mitochondrial dynamin-like GTPase Mgm1
ComponentsDynamin-like GTPase MGM1, mitochondrial
KeywordsHYDROLASE / Mitochondria / Fusion / Mgm1
Function / homology
Function and homology information


mitochondrial inner boundary membrane / mitochondrial outer membrane fusion / mitochondrial inner membrane fusion / Regulation of Apoptosis / mitochondrion inheritance / heme transport / cardiolipin binding / mitochondrial genome maintenance / phosphatidic acid binding / mitochondrial membrane organization ...mitochondrial inner boundary membrane / mitochondrial outer membrane fusion / mitochondrial inner membrane fusion / Regulation of Apoptosis / mitochondrion inheritance / heme transport / cardiolipin binding / mitochondrial genome maintenance / phosphatidic acid binding / mitochondrial membrane organization / phosphatidylinositol-3,5-bisphosphate binding / mitochondrial fusion / phosphatidylserine binding / mitochondrial crista / mitochondrion organization / mitochondrial intermembrane space / microtubule binding / microtubule / mitochondrial inner membrane / membrane fusion / GTPase activity / GTP binding / mitochondrion / membrane / cytoplasm
Similarity search - Function
Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain / Dynamin, GTPase / Dynamin / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin, N-terminal ...Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain / Dynamin, GTPase / Dynamin / 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'-DIPHOSPHATE / IODIDE ION / Dynamin-like GTPase MGM1, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsYan, L. / Li, L.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFC0840302 China
National Natural Science Foundation of China (NSFC)31700659 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural analysis of a trimeric assembly of the mitochondrial dynamin-like GTPase Mgm1.
Authors: Yan, L. / Qi, Y. / Ricketson, D. / Li, L. / Subramanian, K. / Zhao, J. / Yu, C. / Wu, L. / Sarsam, R. / Wong, M. / Lou, Z. / Rao, Z. / Nunnari, J. / Hu, J.
History
DepositionApr 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dynamin-like GTPase MGM1, mitochondrial
B: Dynamin-like GTPase MGM1, mitochondrial
C: Dynamin-like GTPase MGM1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,70431
Polymers237,2023
Non-polymers4,50228
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15360 Å2
ΔGint-24 kcal/mol
Surface area89590 Å2
Unit cell
Length a, b, c (Å)152.940, 152.940, 236.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Dynamin-like GTPase MGM1, mitochondrial / Mitochondrial genome maintenance protein 1


Mass: 79067.180 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: MGM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P32266
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


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


Mass: 126.904 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: I
Has ligand of interestY

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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: 2.91 Å3/Da / Density % sol: 57.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 100mM potassium iodide, 8% PEG3350, 250mM NaCl, 10mM Tris (pH 8.0), 2mM magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 46877 / % possible obs: 99.9 % / Redundancy: 18 % / Biso Wilson estimate: 125.97 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.07
Reflection shellResolution: 3.2→3.32 Å / Num. unique obs: 3404 / CC1/2: 0.815

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Processing

Software
NameVersionClassification
PHENIXv1.0refinement
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→49.17 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.877 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.541
RfactorNum. reflection% reflectionSelection details
Rfree0.306 2292 4.89 %RANDOM
Rwork0.243 ---
obs0.246 46876 100 %-
Displacement parametersBiso max: 300 Å2 / Biso mean: 135.73 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--13.6426 Å20 Å20 Å2
2---13.6426 Å20 Å2
3---27.2852 Å2
Refine analyzeLuzzati coordinate error obs: 0.54 Å
Refinement stepCycle: final / Resolution: 3.2→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14973 0 109 0 15082
Biso mean--179.91 --
Num. residues----1868
LS refinement shellResolution: 3.2→3.28 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2723 155 4.56 %
Rwork0.2476 3245 -
all0.2487 3400 -
obs--99.91 %

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