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- EMDB-8874: Structural Basis of Mitochondrial Receptor Binding and Constricti... -

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Basic information

Entry
Database: EMDB / ID: EMD-8874
TitleStructural Basis of Mitochondrial Receptor Binding and Constriction by Dynamin-Related Protein 1
Map datasummed map, B-factored to -225, low-pass filtered to 4.0 Ang
Sample
  • Complex: DRP1-MID49
    • Protein or peptide: Dynamin-1-like protein
    • Protein or peptide: Mitochondrial dynamics protein MID49
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsMitochondrial division / Dynamin related-protein-1 / Nucleotide / MID49 / PROTEIN FIBRIL
Function / homology
Function and homology information


: / mitochondrial membrane fission / regulation of ATP metabolic process / regulation of peroxisome organization / mitocytosis / regulation of mitophagy / dynamin GTPase / Apoptotic execution phase / peroxisome fission / mitochondrial fragmentation involved in apoptotic process ...: / mitochondrial membrane fission / regulation of ATP metabolic process / regulation of peroxisome organization / mitocytosis / regulation of mitophagy / dynamin GTPase / Apoptotic execution phase / peroxisome fission / mitochondrial fragmentation involved in apoptotic process / GTP-dependent protein binding / protein localization to mitochondrion / mitochondrial fission / positive regulation of neutrophil chemotaxis / regulation of mitochondrion organization / positive regulation of mitochondrial fission / intracellular distribution of mitochondria / heart contraction / necroptotic process / positive regulation of release of cytochrome c from mitochondria / brush border / positive regulation of protein targeting to membrane / localization / positive regulation of intrinsic apoptotic signaling pathway / clathrin-coated pit / mitochondrion organization / GTPase activator activity / release of cytochrome c from mitochondria / positive regulation of protein secretion / synaptic vesicle membrane / small GTPase binding / peroxisome / endocytosis / rhythmic process / calcium ion transport / protein complex oligomerization / microtubule binding / regulation of gene expression / protein-containing complex assembly / microtubule / mitochondrial outer membrane / membrane fusion / membrane => GO:0016020 / molecular adaptor activity / positive regulation of apoptotic process / intracellular membrane-bounded organelle / GTPase activity / lipid binding / ubiquitin protein ligase binding / GTP binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / mitochondrion / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain ...Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / 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 / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Dynamin-1-like protein / Mitochondrial dynamics protein MID49
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 4.22 Å
AuthorsKalia R / Wang RYR
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM110772-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM53466 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)S10OD020054 , 1S10OD021741 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM84970 United States
CitationJournal: Nature / Year: 2018
Title: Structural basis of mitochondrial receptor binding and constriction by DRP1.
Authors: Raghav Kalia / Ray Yu-Ruei Wang / Ali Yusuf / Paul V Thomas / David A Agard / Janet M Shaw / Adam Frost /
Abstract: Mitochondrial inheritance, genome maintenance and metabolic adaptation depend on organelle fission by dynamin-related protein 1 (DRP1) and its mitochondrial receptors. DRP1 receptors include the ...Mitochondrial inheritance, genome maintenance and metabolic adaptation depend on organelle fission by dynamin-related protein 1 (DRP1) and its mitochondrial receptors. DRP1 receptors include the paralogues mitochondrial dynamics proteins of 49 and 51 kDa (MID49 and MID51) and mitochondrial fission factor (MFF); however, the mechanisms by which these proteins recruit and regulate DRP1 are unknown. Here we present a cryo-electron microscopy structure of full-length human DRP1 co-assembled with MID49 and an analysis of structure- and disease-based mutations. We report that GTP induces a marked elongation and rotation of the GTPase domain, bundle-signalling element and connecting hinge loops of DRP1. In this conformation, a network of multivalent interactions promotes the polymerization of a linear DRP1 filament with MID49 or MID51. After co-assembly, GTP hydrolysis and exchange lead to MID receptor dissociation, filament shortening and curling of DRP1 oligomers into constricted and closed rings. Together, these views of full-length, receptor- and nucleotide-bound conformations reveal how DRP1 performs mechanical work through nucleotide-driven allostery.
History
DepositionAug 3, 2017-
Header (metadata) releaseDec 20, 2017-
Map releaseJun 20, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 14.4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 14.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5wp9
  • Surface level: 14.4
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5wp9
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8874.png

Downloads & links

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Map

FileDownload / File: emd_8874.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsummed map, B-factored to -225, low-pass filtered to 4.0 Ang
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 350 pix.
= 427. Å		1.22 Å/pix.
x 350 pix.
= 427. Å		1.22 Å/pix.
x 350 pix.
= 427. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.22 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 14.4 / Movie #1: 14.4
Minimum - Maximum-85.834289999999996 - 104.265854000000004
Average (Standard dev.)0.027421337 (±2.837356)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 427.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.221.221.22
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z427.000427.000427.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-85.834104.2660.027

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Supplemental data

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Mask #1

Fileemd_8874_msk_1.map
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Additional map: additional map

Fileemd_8874_additional_1.map
Annotationadditional map
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Supplemental map: emd 8874 additional 2.map

Fileemd_8874_additional_2.map
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Half map: half-map 1

Fileemd_8874_half_map_1.map
Annotationhalf-map 1
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Half map: half-map 2

Fileemd_8874_half_map_2.map
Annotationhalf-map 2
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Sample components

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Entire : DRP1-MID49

EntireName: DRP1-MID49
Components
  • Complex: DRP1-MID49
    • Protein or peptide: Dynamin-1-like protein
    • Protein or peptide: Mitochondrial dynamics protein MID49
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: DRP1-MID49

SupramoleculeName: DRP1-MID49 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: CryoEM structure of Dynamin-Related Protein 1 in complex with Adaptor MID49
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 115.56 kDa/nm

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Macromolecule #1: Dynamin-1-like protein

MacromoleculeName: Dynamin-1-like protein / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: dynamin GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 79.546453 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEALIPVINK LQDVFNTVGA DIIQLPQIVV VGTQSSGKSS VLESLVGRDL LPRGTGIVTR RPLILQLVHV SQEDKRKTTG EENGVEAEE WGKFLHTKNK LYTDFDEIRQ EIENETERIS GNNKGVSPEP IHLKIFSPNV VNLTLVDLPG MTKVPVGDQP K DIELQIRE ...String:
MEALIPVINK LQDVFNTVGA DIIQLPQIVV VGTQSSGKSS VLESLVGRDL LPRGTGIVTR RPLILQLVHV SQEDKRKTTG EENGVEAEE WGKFLHTKNK LYTDFDEIRQ EIENETERIS GNNKGVSPEP IHLKIFSPNV VNLTLVDLPG MTKVPVGDQP K DIELQIRE LILRFISNPN SIILAVTAAN TDMATSEALK ISREVDPDGR RTLAVITKLD LMDAGTDAMD VLMGRVIPVK LG IIGVVNR SQLDINNKKS VTDSIRDEYA FLQKKYPSLA NRNGTKYLAR TLNRLLMHHI RDCLPELKTR INVLAAQYQS LLN SYGEPV DDKSATLLQL ITKFATEYCN TIEGTAKYIE TSELCGGARI CYIFHETFGR TLESVDPLGG LNTIDILTAI RNAT GPRPA LFVPEVSFEL LVKRQIKRLE EPSLRCVELV HEEMQRIIQH CSNYSTQELL RFPKLHDAIV EVVTCLLRKR LPVTN EMVH NLVAIELAYI NTKHPDFADA CGLMNNNIEE QRRNRLAREL PSAVSRDKLI QDSRRETKNV ASGGGGVGDG VQEPTT GNW RGMLKTSKAE ELLAEEKSKP IPIMPASPQK GHAVNLLDVP VPVARKLSAR EQRDCEVIER LIKSYFLIVR KNIQDSV PK AVMHFLVNHV KDTLQSELVG QLYKSSLLDD LLTESEDMAQ RRKEAADMLK ALQGASQIIA EIRETHLW

UniProtKB: Dynamin-1-like protein

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Macromolecule #2: Mitochondrial dynamics protein MID49

MacromoleculeName: Mitochondrial dynamics protein MID49 / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.15657 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TLQERLLAFE RDRVTIPAAQ VALAKQLAGD IALELQAYFR SKFPELPFGA FVPGGPLYDG LQAGAADHVR LLVPLVLEPG LWSLVPGVD TVARDPRCWA VRRTQLEFCP RGSSPWDRFL VGGYLSSRVL LELLRKALAA SVNWPAIGSL LGCLIRPSMA S EELLLEVQ ...String:
TLQERLLAFE RDRVTIPAAQ VALAKQLAGD IALELQAYFR SKFPELPFGA FVPGGPLYDG LQAGAADHVR LLVPLVLEPG LWSLVPGVD TVARDPRCWA VRRTQLEFCP RGSSPWDRFL VGGYLSSRVL LELLRKALAA SVNWPAIGSL LGCLIRPSMA S EELLLEVQ HERLELTVAV LVAVPGVDAD DRLLLAWPLE GLAGNLWLQD LYPVEAARLR ALDDHDAGTR RRLLLLLCAV CR GCSALGQ LGRGHLTQVV LRLGEDNVDW TEEALGERFL QALELLIGSL EQASLPCHFN PSVNLFSSLR EEEIDDIGYA LYS GLQEPE GLL

UniProtKB: Mitochondrial dynamics protein MID49

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Macromolecule #3: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 3 / Number of copies: 8 / Formula: GCP
Molecular weightTheoretical: 521.208 Da
Chemical component information

ChemComp-G2P:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP, energy-carrying molecule analogue*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 31000
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 54.8 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.8 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 412684

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