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- EMDB-40967: Cryo-EM structure of a full-length, native Drp1 dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-40967
TitleCryo-EM structure of a full-length, native Drp1 dimer
Map dataDrp1 cryoEM native dimer map
Sample
  • Complex: Dimer complex of native, full length Drp1
    • Protein or peptide: Dynamin-1-like protein
KeywordsDynamin-related protein 1 / Drp1 / mitochondrial fission / GTPase / Cytosolic Protein
Function / homology
Function and homology information


mitochondrial membrane fission / regulation of ATP metabolic process / regulation of peroxisome organization / mitocytosis / Apoptotic execution phase / dynamin GTPase / peroxisome fission / regulation of mitophagy / mitochondrial fragmentation involved in apoptotic process / GTP-dependent protein binding ...mitochondrial membrane fission / regulation of ATP metabolic process / regulation of peroxisome organization / mitocytosis / Apoptotic execution phase / dynamin GTPase / peroxisome fission / regulation of mitophagy / 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 / localization / positive regulation of intrinsic apoptotic signaling pathway / clathrin-coated pit / GTPase activator activity / mitochondrion organization / release of cytochrome c from mitochondria / positive regulation of protein secretion / synaptic vesicle membrane / small GTPase binding / peroxisome / endocytosis / calcium ion transport / rhythmic process / protein complex oligomerization / microtubule binding / regulation of gene expression / protein-containing complex assembly / microtubule / mitochondrial outer membrane / membrane fusion / molecular adaptor activity / positive regulation of apoptotic process / intracellular membrane-bounded organelle / GTPase activity / lipid binding / ubiquitin protein ligase binding / endoplasmic reticulum membrane / GTP binding / 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 / 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: 5.97 Å
AuthorsRochon K / Mears JA
Funding support United States, 2 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)F31 GM139324 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for regulated assembly of the mitochondrial fission GTPase Drp1.
Authors: Kristy Rochon / Brianna L Bauer / Nathaniel A Roethler / Yuli Buckley / Chih-Chia Su / Wei Huang / Rajesh Ramachandran / Maria S K Stoll / Edward W Yu / Derek J Taylor / Jason A Mears /
Abstract: Mitochondrial fission is a critical cellular event to maintain organelle function. This multistep process is initiated by the enhanced recruitment and oligomerization of dynamin-related protein 1 ...Mitochondrial fission is a critical cellular event to maintain organelle function. This multistep process is initiated by the enhanced recruitment and oligomerization of dynamin-related protein 1 (Drp1) at the surface of mitochondria. As such, Drp1 is essential for inducing mitochondrial division in mammalian cells, and homologous proteins are found in all eukaryotes. As a member of the dynamin superfamily of proteins (DSPs), controlled Drp1 self-assembly into large helical polymers stimulates its GTPase activity to promote membrane constriction. Still, little is known about the mechanisms that regulate correct spatial and temporal assembly of the fission machinery. Here we present a cryo-EM structure of a full-length Drp1 dimer in an auto-inhibited state. This dimer reveals two key conformational rearrangements that must be unlocked through intramolecular rearrangements to achieve the assembly-competent state observed in previous structures. This structural insight provides understanding into the mechanism for regulated self-assembly of the mitochondrial fission machinery.
History
DepositionJun 2, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40967.png

Downloads & links

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Map

FileDownload / File: emd_40967.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDrp1 cryoEM native dimer map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 352 pix.
= 376.64 Å		1.07 Å/pix.
x 352 pix.
= 376.64 Å		1.07 Å/pix.
x 352 pix.
= 376.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.41
Minimum - Maximum-3.0283384 - 4.9830236
Average (Standard dev.)0.0007357812 (±0.047322724)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 376.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Drp1 cryoEM native dimer half map B

Fileemd_40967_half_map_1.map
AnnotationDrp1 cryoEM native dimer half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Drp1 cryoEM native dimer half map A

Fileemd_40967_half_map_2.map
AnnotationDrp1 cryoEM native dimer half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dimer complex of native, full length Drp1

EntireName: Dimer complex of native, full length Drp1
Components
  • Complex: Dimer complex of native, full length Drp1
    • Protein or peptide: Dynamin-1-like protein

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Supramolecule #1: Dimer complex of native, full length Drp1

SupramoleculeName: Dimer complex of native, full length Drp1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
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: 2 / Enantiomer: LEVO / EC number: dynamin GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 81.984094 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 PSAVSRDKSS KVPSALAPAS QEPSPAASAE ADGKLI QDS RRETKNVASG GGGVGDGVQE PTTGNWRGML KTSKAEELLA EEKSKPIPIM PASPQKGHAV NLLDVPVPVA RKLSARE QR DCEVIERLIK SYFLIVRKNI QDSVPKAVMH FLVNHVKDTL QSELVGQLYK SSLLDDLLTE SEDMAQRRKE AADMLKAL Q GASQIIAEIR ETHLW

UniProtKB: Dynamin-1-like protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration.05 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
25.0 mMHEPES
150.0 mMKCl
5.0 mMMgCl2
10.0 mMBME

Details: 25 mM HEPES (KOH) pH 7.5, 0.15 M KCl, 5 mM MgCl2, 10 mM Beta-mercaptoethanol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 4560 / Average electron dose: 47.76 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 883690
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 71611
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4bej


Chain - Chain ID: A / Chain - Source name: AlphaFold
Details: Dimer built aligning two AlphaFold Chains to the 4BEJ chains A and B
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-8t1h:
Cryo-EM structure of a full-length, native Drp1 dimer

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