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- EMDB-30191: The mitochondrial SAM-Mdm10 supercomplex in Nanodisc from S.cere -

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Basic information

Entry
Database: EMDB / ID: EMD-30191
TitleThe mitochondrial SAM-Mdm10 supercomplex in Nanodisc from S.cere
Map data
SampleSAM-Mdm10 complex
  • Mitochondrial outer membrane beta-barrel protein
  • (Sorting assembly machinery ...) x 2
  • MDM10 isoform 1
Function / homology
Function and homology information


ERMES complex / SAM complex / mitochondrial outer membrane translocase complex assembly / phospholipid transport / outer membrane / protein insertion into mitochondrial outer membrane / mitochondrion organization / mitochondrial outer membrane / mitochondrion / integral component of membrane / cytoplasm
Surface antigen D15-like / Tom37, C-terminal domain / Mitochondrial distribution and morphology protein 10 / Sorting assembly machinery 35kDa subunit / Mitochondrial outer membrane transport complex Sam37/metaxin, N-terminal domain / Bacterial surface antigen (D15)
MDM10 isoform 1 / Mitochondrial outer membrane beta-barrel protein / Sorting assembly machinery 35 kDa subunit / Sorting assembly machinery 37 kDa subunit
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsTakeda H / Tsutsumi A / Nishizawa T / Nureki O / Kikkawa M / Endo T
Funding support3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)
Japan Agency for Medical Research and Development (AMED)
Japan Science and Technology
CitationJournal: Nature / Year: 2021
Title: Mitochondrial sorting and assembly machinery operates by β-barrel switching.
Authors: Hironori Takeda / Akihisa Tsutsumi / Tomohiro Nishizawa / Caroline Lindau / Jon V Busto / Lena-Sophie Wenz / Lars Ellenrieder / Kenichiro Imai / Sebastian P Straub / Waltraut Mossmann / Jian ...Authors: Hironori Takeda / Akihisa Tsutsumi / Tomohiro Nishizawa / Caroline Lindau / Jon V Busto / Lena-Sophie Wenz / Lars Ellenrieder / Kenichiro Imai / Sebastian P Straub / Waltraut Mossmann / Jian Qiu / Yu Yamamori / Kentaro Tomii / Junko Suzuki / Takeshi Murata / Satoshi Ogasawara / Osamu Nureki / Thomas Becker / Nikolaus Pfanner / Nils Wiedemann / Masahide Kikkawa / Toshiya Endo /
Abstract: The mitochondrial outer membrane contains so-called β-barrel proteins, which allow communication between the cytosol and the mitochondrial interior. Insertion of β-barrel proteins into the outer ...The mitochondrial outer membrane contains so-called β-barrel proteins, which allow communication between the cytosol and the mitochondrial interior. Insertion of β-barrel proteins into the outer membrane is mediated by the multisubunit mitochondrial sorting and assembly machinery (SAM, also known as TOB). Here we use cryo-electron microscopy to determine the structures of two different forms of the yeast SAM complex at a resolution of 2.8-3.2 Å. The dimeric complex contains two copies of the β-barrel channel protein Sam50-Sam50a and Sam50b-with partially open lateral gates. The peripheral membrane proteins Sam35 and Sam37 cap the Sam50 channels from the cytosolic side, and are crucial for the structural and functional integrity of the dimeric complex. In the second complex, Sam50b is replaced by the β-barrel protein Mdm10. In cooperation with Sam50a, Sam37 recruits and traps Mdm10 by penetrating the interior of its laterally closed β-barrel from the cytosolic side. The substrate-loaded SAM complex contains one each of Sam50, Sam35 and Sam37, but neither Mdm10 nor a second Sam50, suggesting that Mdm10 and Sam50b function as placeholders for a β-barrel substrate released from Sam50a. Our proposed mechanism for dynamic switching of β-barrel subunits and substrate explains how entire precursor proteins can fold in association with the mitochondrial machinery for β-barrel assembly.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionApr 3, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateFeb 17, 2021-
Current statusFeb 17, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7bty
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30191.png

Downloads & links

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Map

FileDownload / File: emd_30191.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 180 pix.
= 224.1 Å		1.25 Å/pix.
x 180 pix.
= 224.1 Å		1.25 Å/pix.
x 180 pix.
= 224.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.245 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.5344711 - 0.7539808
Average (Standard dev.)-4.6169156e-05 (±0.018324407)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 224.1 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2451.2451.245
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z224.100224.100224.100
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.5340.754-0.000

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Supplemental data

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Sample components

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Entire SAM-Mdm10 complex

EntireName: SAM-Mdm10 complex / Number of components: 5

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Component #1: protein, SAM-Mdm10 complex

ProteinName: SAM-Mdm10 complex / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #2: protein, Mitochondrial outer membrane beta-barrel protein

ProteinName: Mitochondrial outer membrane beta-barrel protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 41.176824 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #3: protein, Sorting assembly machinery 35 kDa subunit

ProteinName: Sorting assembly machinery 35 kDa subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.44607 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #4: protein, Sorting assembly machinery 37 kDa subunit

ProteinName: Sorting assembly machinery 37 kDa subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.537797 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #5: protein, MDM10 isoform 1

ProteinName: MDM10 isoform 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 56.296719 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 299 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 128400
3D reconstructionSoftware: RELION / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

7bty

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