[English] 日本語
Yorodumi
- EMDB-8874: Structural Basis of Mitochondrial Receptor Binding and Constricti... -

+
Open data


ID or keywords:

Loading...

-
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 / dynamin GTPase / Apoptotic execution phase / peroxisome fission / mitochondrial fragmentation involved in apoptotic process / regulation of mitophagy / GTP-dependent protein binding ...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 / regulation of mitophagy / GTP-dependent protein binding / protein localization to mitochondrion / mitochondrial fission / regulation of mitochondrion organization / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission / heart contraction / intracellular distribution of mitochondria / necroptotic process / brush border / protein complex oligomerization / positive regulation of protein targeting to membrane / clathrin-coated pit / GTPase activator activity / mitochondrion organization / positive regulation of protein secretion / small GTPase binding / synaptic vesicle membrane / endocytosis / calcium ion transport / rhythmic process / peroxisome / regulation of gene expression / microtubule binding / mitochondrial outer membrane / microtubule / 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 / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Mitochondrial dynamics protein MID49/MID51 / : / Mitochondrial dynamics protein MID51-like, C-terminal 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 ...Mitochondrial dynamics protein MID49/MID51 / : / Mitochondrial dynamics protein MID51-like, C-terminal 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. / Mab-21-like / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 / 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 / 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

-
Structure visualization

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

emd_8874.png

Downloads & links

-
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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

-
Supplemental data

-
Mask #1

Fileemd_8874_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: additional map

Fileemd_8874_additional_1.map
Annotationadditional map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Supplemental map: emd 8874 additional 2.map

Fileemd_8874_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half-map 1

Fileemd_8874_half_map_1.map
Annotationhalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half-map 2

Fileemd_8874_half_map_2.map
Annotationhalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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

-
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

-
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

-
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

-
Macromolecule #4: MAGNESIUM ION

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

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

-
Electron microscopy

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

-
Image processing

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
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more