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- EMDB-30190: The mitochondrial SAM-Mdm10 supercomplex in GDN micelle from S.cere -

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Basic information

Entry
Database: EMDB / ID: EMD-30190
TitleThe mitochondrial SAM-Mdm10 supercomplex in GDN micelle from S.cere
Map data
Sample
  • Complex: SAM-Mdm10 complex
    • Protein or peptide: Mitochondrial outer membrane beta-barrel protein
    • Protein or peptide: Sorting assembly machinery 35 kDa subunit
    • Protein or peptide: Sorting assembly machinery 37 kDa subunit
    • Protein or peptide: MDM10 isoform 1
KeywordsMitochondria / TRANSLOCASE
Function / homology
Function and homology information


ERMES complex / mitochondrial outer membrane translocase complex assembly / SAM complex / protein import into mitochondrial matrix / phospholipid transport / protein insertion into mitochondrial outer membrane / mitochondrion organization / mitochondrial outer membrane / mitochondrion / cytoplasm
Similarity search - Function
Mitochondrial distribution and morphology protein 10 / Mitochondrial distribution and morphology protein 10 / Sorting assembly machinery 35kDa subunit / Tom37, C-terminal domain / SAM35, subunit of SAM coomplex / Tom37 C-terminal domain / Mitochondrial outer membrane transport complex Sam37/metaxin, N-terminal domain / Outer mitochondrial membrane transport complex protein / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain
Similarity search - Domain/homology
MDM10 isoform 1 / Mitochondrial outer membrane beta-barrel protein / Sorting assembly machinery 35 kDa subunit / Sorting assembly machinery 37 kDa subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsTakeda H / Tsutsumi A
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
Japan Science and Technology Japan
Japan Agency for Medical Research and Development (AMED) Japan
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.
History
DepositionApr 3, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7btx
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30190.png

Downloads & links

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Map

FileDownload / File: emd_30190.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.045
Minimum - Maximum-0.16821305 - 0.30548275
Average (Standard dev.)0.00005907486 (±0.007812995)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 224.09999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z270270270
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/NS270270270
D min/max/mean-0.1680.3050.000

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Supplemental data

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Sample components

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Entire : SAM-Mdm10 complex

EntireName: SAM-Mdm10 complex
Components
  • Complex: SAM-Mdm10 complex
    • Protein or peptide: Mitochondrial outer membrane beta-barrel protein
    • Protein or peptide: Sorting assembly machinery 35 kDa subunit
    • Protein or peptide: Sorting assembly machinery 37 kDa subunit
    • Protein or peptide: MDM10 isoform 1

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Supramolecule #1: SAM-Mdm10 complex

SupramoleculeName: SAM-Mdm10 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Mitochondrial outer membrane beta-barrel protein

MacromoleculeName: Mitochondrial outer membrane beta-barrel protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 41.176824 KDa
SequenceString: TFTAKTGTNF GNDNDAEAYL QFEKLIDKKY LKLPTRVNLE ILRGTKIHSS FLFNSYSSLS PQSILNLKVF SQFYNWNTNK GLDIGQRGA RLSLRYEPLF LHKLLHNPHS NESPTLFHEW FLETCWRSTK ICSQGTSAPY MYSGTMLSQA GDQLRTILGH T FVLDKRDH ...String:
TFTAKTGTNF GNDNDAEAYL QFEKLIDKKY LKLPTRVNLE ILRGTKIHSS FLFNSYSSLS PQSILNLKVF SQFYNWNTNK GLDIGQRGA RLSLRYEPLF LHKLLHNPHS NESPTLFHEW FLETCWRSTK ICSQGTSAPY MYSGTMLSQA GDQLRTILGH T FVLDKRDH IMCPTKGSML KWSNELSPGK HLKTQLELNS VKSWMNDDFI TFSTTIKTGY LKNLSSQQSL PVHICDKFQS GG PSDIRGF QTFGLGPRDL YDAVGGDAFV SYGLSVFSRL PWKKVEKSNF RLHWFFNGGK LVNHDNTSLG NCIGQLSKEH STS TGIGLV LRHPMARFEL NFTLPITAHE NDLIRKGFQF GLGLAFL

UniProtKB: Mitochondrial outer membrane beta-barrel protein

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Macromolecule #2: Sorting assembly machinery 35 kDa subunit

MacromoleculeName: Sorting assembly machinery 35 kDa subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 37.44607 KDa
SequenceString: MVSSFSVPMP VKRIFDTFPL QTYAAQTDKD EAVALEIQRR SYTFTERGGG SSELTVEGTY KLGVYNVFLE ANTGAALATD PWCLFVQLA LCQKNGLVLP THSQEQTPSH TCNHEMLVLS RLSNPDEALP ILVEGYKKRI IRSTVAISEI MRSRILDDAE Q LMYYTLLD ...String:
MVSSFSVPMP VKRIFDTFPL QTYAAQTDKD EAVALEIQRR SYTFTERGGG SSELTVEGTY KLGVYNVFLE ANTGAALATD PWCLFVQLA LCQKNGLVLP THSQEQTPSH TCNHEMLVLS RLSNPDEALP ILVEGYKKRI IRSTVAISEI MRSRILDDAE Q LMYYTLLD TVLYDCWITQ IIFCASDAQF MELYSCQKLS GSIVTPLDVE NSLLQKLSAK SLKISLTKRN KFQFRHREIV KS MQGVYHN HHNSVNQEQV LNVLFENSKQ VLLGLKDMLK SDGQPTYLHL KIASYILCIT NVKEPIKLKT FVENECKELV QFA QDTLKN FVQ

UniProtKB: Sorting assembly machinery 35 kDa subunit

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Macromolecule #3: Sorting assembly machinery 37 kDa subunit

MacromoleculeName: Sorting assembly machinery 37 kDa subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 37.537797 KDa
SequenceString: MVKGSVHLWG KDGKASLISV DSIALVWFIK LCTSEEAKSM VAGLQIVFSN NTDLSSDGKL PVLILDNGTK VSGYVNIVQF LHKNICTSK YEKGTDYEED LAIVRKKDRL LEYSLLNYVD VEISRLTDYQ LFLNTKNYNE YTKKLFSKLL YFPMWYNTPL Q LRSQAREN ...String:
MVKGSVHLWG KDGKASLISV DSIALVWFIK LCTSEEAKSM VAGLQIVFSN NTDLSSDGKL PVLILDNGTK VSGYVNIVQF LHKNICTSK YEKGTDYEED LAIVRKKDRL LEYSLLNYVD VEISRLTDYQ LFLNTKNYNE YTKKLFSKLL YFPMWYNTPL Q LRSQAREN CEEIIGSLTL EDDEEFVESK AMESASQLAQ SKTFKIAHKN KIKGKQELQQ VKYNLQFDNR LQSCVSNWLA AR KKLDDSV ILSSDLLFLA NLYVQLGLPD GNRIRSKLEQ TFGSELLNSM SNKIDDFVHR PSNNLEQRDP QFREQGNVVM SLY NLACKY I

UniProtKB: Sorting assembly machinery 37 kDa subunit

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Macromolecule #4: MDM10 isoform 1

MacromoleculeName: MDM10 isoform 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 56.296719 KDa
SequenceString: MLPYMDQVLR AFYQSTHWST QNSYEDITAT SRTLLDFRIP SAIHLQISNK STPNTFNSLD FSTRSRINGS LSYLYSDAQQ LEKFMRNST DIPLQDATET YRQLQPNLNF SVSSANTLSS DNTTVDNDKK LLHDSKFVKK SLYYGRMYYP SSDLEAMIIK R LSPQTQFM ...String:
MLPYMDQVLR AFYQSTHWST QNSYEDITAT SRTLLDFRIP SAIHLQISNK STPNTFNSLD FSTRSRINGS LSYLYSDAQQ LEKFMRNST DIPLQDATET YRQLQPNLNF SVSSANTLSS DNTTVDNDKK LLHDSKFVKK SLYYGRMYYP SSDLEAMIIK R LSPQTQFM LKGVSSFKES LNVLTCYFQR DSHRNLQEWI FSTSDLLCGY RVLHNFLTTP SKFNTSLYNN SSLSLGAEFW LG LVSLSPG CSTTLRYYTH STNTGRPLTL TLSWNPLFGH ISSTYSAKTG TNSTFCAKYD FNLYSIESNL SFGCEFWQKK HHL LETNKN NNDKLEPISD ELVDINPNSR ATKLLHENVP DLNSAVNDIP STLDIPVHKQ KLLNDLTYAF SSSLRKIDEE RSTI EKFDN KINSSIFTSV WKLSTSLRDK TLKLLWEGKW RGFLISAGTE LVFTRGFQES LSDDEKNDNA ISISATDTEN GNIPV FPAK FGIQFQYST

UniProtKB: MDM10 isoform 1

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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

BufferpH: 7.5
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 299 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 186871
FSC plot (resolution estimation)

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