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- EMDB-43045: Asymmetrical subunit from a Drp1 lattice on PA nanotubes -

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Basic information

Entry
Database: EMDB / ID: EMD-43045
TitleAsymmetrical subunit from a Drp1 lattice on PA nanotubes
Map dataDrp1 on Phosphatidic acid (PA)-containing nanotubes (NT)
Sample
  • Complex: Tetramer complex of Drp1 from a lattice
    • Protein or peptide: Dynamin-1-like protein
Keywordsmembrane remodeling GTPase / HYDROLASE
Function / homology
Function and homology information


mitochondrial membrane fission / regulation of ATP metabolic process / regulation of peroxisome organization / mitocytosis / dynamin GTPase / Apoptotic execution phase / regulation of mitophagy / peroxisome fission / mitochondrial fragmentation involved in apoptotic process / GTP-dependent protein binding ...mitochondrial membrane fission / regulation of ATP metabolic process / regulation of peroxisome organization / mitocytosis / dynamin GTPase / Apoptotic execution phase / regulation of mitophagy / peroxisome fission / mitochondrial fragmentation involved in apoptotic process / GTP-dependent protein binding / protein localization to mitochondrion / mitochondrial fission / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission / heart contraction / intracellular distribution of mitochondria / protein complex oligomerization / brush border / clathrin-coated pit / GTPase activator activity / positive regulation of protein secretion / mitochondrion organization / small GTPase binding / endocytosis / calcium ion transport / synaptic vesicle membrane / rhythmic process / peroxisome / regulation of gene expression / microtubule binding / mitochondrial outer membrane / microtubule / intracellular membrane-bounded organelle / GTPase activity / ubiquitin protein ligase binding / lipid binding / endoplasmic reticulum membrane / GTP binding / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / protein-containing complex / mitochondrion / identical protein binding / membrane / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Dynamin-1-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 14.73 Å
AuthorsRochon K / Peng R / Hutson AN / Stagg SM / Mears JA
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM125844 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM108753 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM143805 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31 GM139324 United States
CitationJournal: J Mol Biol / Year: 2025
Title: The Structure of the Drp1 Lattice on Membrane.
Authors: Ruizhi Peng / Kristy Rochon / Anelise N Hutson / Scott M Stagg / Jason A Mears /
Abstract: Mitochondrial health relies on the membrane fission mediated by dynamin-related protein 1 (Drp1). Previous structural studies of Drp1 on remodeled membranes were hampered by heterogeneity, leaving a ...Mitochondrial health relies on the membrane fission mediated by dynamin-related protein 1 (Drp1). Previous structural studies of Drp1 on remodeled membranes were hampered by heterogeneity, leaving a critical gap in the understanding of the mitochondrial fission mechanisms. Here we present a cryo-electron microscopy structure of full-length human Drp1 decorated on membrane tubules. Using the reconstruction of average subtracted tubular regions (RASTR) technique, we report that Drp1 forms a locally ordered lattice along the tubule without global helical symmetry. The filaments in the lattice are similar to dynamin rungs with conserved stalk interactions. Adjacent filaments are connected by GTPase domain interactions in a novel stacked conformation. We identified two states of the Drp1 lattice among the heterogenous dataset representing conformational changes around hinge 1. Additionally, we observed contact between Drp1 and membrane that can be assigned to the variable domain sequence. Together these structures revealed a putative mechanism by which Drp1 constricts mitochondria membranes in a stepwise, "ratchet" manner.
History
DepositionDec 6, 2023-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43045.png

Downloads & links

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Map

FileDownload / File: emd_43045.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDrp1 on Phosphatidic acid (PA)-containing nanotubes (NT)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.02 Å/pix.
x 448 pix.
= 904.96 Å		2.02 Å/pix.
x 448 pix.
= 904.96 Å		2.02 Å/pix.
x 448 pix.
= 904.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 816.0
Minimum - Maximum-2858.252700000000004 - 4612.292000000000371
Average (Standard dev.)0.44686237 (±242.158109999999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 904.95996 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43045_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_43045_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_43045_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Tetramer complex of Drp1 from a lattice

EntireName: Tetramer complex of Drp1 from a lattice
Components
  • Complex: Tetramer complex of Drp1 from a lattice
    • Protein or peptide: Dynamin-1-like protein

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Supramolecule #1: Tetramer complex of Drp1 from a lattice

SupramoleculeName: Tetramer complex of Drp1 from a lattice / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Asymmetrical subunit of GMP-PCP bound Drp1 lattice on Phosphatidic acid (PA)-containing nanotubes
Source (natural)Organism: Homo sapiens (human) / Strain: DNM1L, DLP1, DRP1
Molecular weightTheoretical: 164 KDa

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Macromolecule #1: Dynamin-1-like protein

MacromoleculeName: Dynamin-1-like protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: dynamin GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.608789 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPHMGGSMEA LIPVINKLQD VFNTVGADII QLPQIVVVGT QSSGKSSVLE SLVGRDLLPR GTGIVTRRPL ILQLVHVSQE DKRKTTGEE NGVEAEEWGK FLHTKNKLYT DFDEIRQEIE NETERISGNN KGVSPEPIHL KIFSPNVVNL TLVDLPGMTK V PVGDQPKD ...String:
GPHMGGSMEA LIPVINKLQD VFNTVGADII QLPQIVVVGT QSSGKSSVLE SLVGRDLLPR GTGIVTRRPL ILQLVHVSQE DKRKTTGEE NGVEAEEWGK FLHTKNKLYT DFDEIRQEIE NETERISGNN KGVSPEPIHL KIFSPNVVNL TLVDLPGMTK V PVGDQPKD IELQIRELIL RFISNPNSII LAVTAANTDM ATSEALKISR EVDPDGRRTL AVITKLDLMD AGTDAMDVLM GR VIPVKLG IIGVVNRSQL DINNKKSVTD SIRDEYAFLQ KKYPSLANRN GTKYLARTLN RLLMHHIRDC LPELKTRINV LAA QYQSLL NSYGEPVDDK SATLLQLITK FATEYCNTIE GTAKYIETSE LCGGARICYI FHETFGRTLE SVDPLGGLNT IDIL TAIRN ATGPRPALFV PEVSFELLVK RQIKRLEEPS LRCVELVHEE MQRIIQHCSN YSTQELLRFP KLHDAIVEVV TCLLR KRLP VTNEMVHNLV AIELAYINTK HPDFADACGL MNNNIEEQRR NRLARELPSA VSRDKSSKVP SALAPASQEP SPAASA EAD GKLIQDSRRE TKNVASGGGG VGDGVQEPTT GNWRGMLKTS KAEELLAEEK SKPIPIMPAS PQKGHAVNLL DVPVPVA RK LSAREQRDCE VIERLIKSYF LIVRKNIQDS VPKAVMHFLV NHVKDTLQSE LVGQLYKSSL LDDLLTESED MAQRRKEA A DMLKALQGAS QIIAEIRETH LW

UniProtKB: Dynamin-1-like protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
25.0 mMHEPES
150.0 mMPotassium chlorideKCl
5.0 mMMagnesium dichlorideMgCl2
10.0 mMBME
2.0 mMGMP-PCP
500.0 uMPA Nanotubes

Details: Primary Buffer: 25 mM HEPES (KOH) pH 7.5, 0.15 M KCl, 5 mM MgCl2, 10 mM Beta-mercaptoethanol Nanotubes: 40% D-galactosyl-beta-1-N-nervonyl-erythro-sphingosine (GC), 35% ...Details: Primary Buffer: 25 mM HEPES (KOH) pH 7.5, 0.15 M KCl, 5 mM MgCl2, 10 mM Beta-mercaptoethanol Nanotubes: 40% D-galactosyl-beta-1-N-nervonyl-erythro-sphingosine (GC), 35% phosphatidylethanolamine (PE), 25% phosphatidic acid (PA) Final Sample: Protein diluted to 0.4mg/ml and incubated with 500 uM NTs, 2mM GMPPCP and 2mM MgCl2
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Details: 25mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III
DetailsDrp1 was incubated with nanotubes and GMPPCP to form decorated lipid templates

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Detector mode: INTEGRATING / Number real images: 1941 / Average exposure time: 1.093 sec. / Average electron dose: 58.49 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: RASTR azimuthal average
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 14.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 13215
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cisTEM
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-8v8t:
Asymmetrical subunit from a Drp1 lattice on PA nanotubes

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