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- PDB-5wp9: Structural Basis of Mitochondrial Receptor Binding and Constricti... -

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Basic information

Entry
Database: PDB / ID: 5wp9
TitleStructural Basis of Mitochondrial Receptor Binding and Constriction by Dynamin-Related Protein 1
Components
  • Dynamin-1-like protein
  • Mitochondrial dynamics protein MID49
KeywordsPROTEIN FIBRIL / Mitochondrial division / Dynamin related-protein-1 / Nucleotide / MID49
Function / homology
Function and homology information


: / mitochondrial membrane fission / regulation of ATP metabolic process / regulation of peroxisome organization / mitocytosis / 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 / dynamin GTPase / Apoptotic execution phase / peroxisome fission / mitochondrial fragmentation involved in apoptotic process / : / GTP-dependent protein binding / regulation of autophagy of mitochondrion / 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 / mitochondrial outer membrane / microtubule / 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
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Dynamin-1-like protein / Mitochondrial dynamics protein MID49
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.22 Å
AuthorsKalia, R. / Wang, R.Y.R. / Yusuf, A. / Thomas, P.V. / Agard, D.A. / Shaw, J.M. / Frost, A.
Funding support United States, 4items
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, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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 / _citation_author.name
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 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

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Assembly

Deposited unit
A: Dynamin-1-like protein
B: Mitochondrial dynamics protein MID49
C: Dynamin-1-like protein
D: Mitochondrial dynamics protein MID49
E: Dynamin-1-like protein
F: Mitochondrial dynamics protein MID49
G: Dynamin-1-like protein
H: Mitochondrial dynamics protein MID49
I: Dynamin-1-like protein
J: Mitochondrial dynamics protein MID49
K: Dynamin-1-like protein
L: Mitochondrial dynamics protein MID49
M: Dynamin-1-like protein
N: Mitochondrial dynamics protein MID49
O: Dynamin-1-like protein
P: Mitochondrial dynamics protein MID49
hetero molecules


Theoretical massNumber of molelcules
Total (without water)929,98832
Polymers925,62416
Non-polymers4,36416
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area46020 Å2
ΔGint-245 kcal/mol
Surface area324630 Å2
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 20 / Rise per n subunits: 54.8 Å / Rotation per n subunits: -0.8 °)

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Components

#1: Protein
Dynamin-1-like protein / Dnm1p/Vps1p-like protein / DVLP / Dynamin family member proline-rich carboxyl-terminal domain less ...Dnm1p/Vps1p-like protein / DVLP / Dynamin family member proline-rich carboxyl-terminal domain less / Dymple / Dynamin-like protein / Dynamin-like protein 4 / Dynamin-like protein IV / HdynIV / Dynamin-related protein 1


Mass: 79546.453 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNM1L, DLP1, DRP1 / Production host: Escherichia coli (E. coli) / References: UniProt: O00429, dynamin GTPase
#2: Protein
Mitochondrial dynamics protein MID49 / Mitochondrial dynamics protein of 49 kDa / Mitochondrial elongation factor 2 / Smith-Magenis ...Mitochondrial dynamics protein of 49 kDa / Mitochondrial elongation factor 2 / Smith-Magenis syndrome chromosomal region candidate gene 7 protein


Mass: 36156.570 Da / Num. of mol.: 8 / Fragment: UNP residues 126-454
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIEF2, MID49, SMCR7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96C03
#3: Chemical
ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: DRP1-MID49 / Type: COMPLEX
Details: CryoEM structure of Dynamin-Related Protein 1 in complex with Adaptor MID49
Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 115.56 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 31000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 300 nm / Cs: 2 mm / C2 aperture diameter: 30 µm
Image recordingElectron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: SerialEM / Category: image acquisition
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -0.8 ° / Axial rise/subunit: 54.8 Å / Axial symmetry: C1
3D reconstructionResolution: 4.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 412684 / Symmetry type: HELICAL

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