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- EMDB-30986: Cryo-EM structure of the yeast mitochondrial SAM-Tom40/Tom5/Tom6 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-30986
TitleCryo-EM structure of the yeast mitochondrial SAM-Tom40/Tom5/Tom6 complex at 3.0 angstrom
Map data
Sample
  • Complex: SAM-Tom40/Tom5/Tom6 complex
    • Complex: Sorting assembly machinery subunits
      • Protein or peptide: Sorting assembly machinery 50 kDa subunit
      • Protein or peptide: Sorting assembly machinery 35 kDa subunit
      • Protein or peptide: Sorting assembly machinery 37 kDa subunit
    • Complex: Mitochondrial import receptor subunits
      • Protein or peptide: Mitochondrial import receptor subunit TOM40
      • Protein or peptide: Mitochondrial import receptor subunit TOM5
      • Protein or peptide: Mitochondrial import receptor subunit TOM6
KeywordsTRANSLOCASE
Function / homology
Function and homology information


mitochondrial outer membrane translocase complex assembly / SAM complex / membrane insertase activity / mitochondrial outer membrane translocase complex / mitochondrial respiratory chain complex assembly / protein import into mitochondrial matrix / phospholipid transport / protein targeting to mitochondrion / protein insertion into mitochondrial outer membrane / porin activity ...mitochondrial outer membrane translocase complex assembly / SAM complex / membrane insertase activity / mitochondrial outer membrane translocase complex / mitochondrial respiratory chain complex assembly / protein import into mitochondrial matrix / phospholipid transport / protein targeting to mitochondrion / protein insertion into mitochondrial outer membrane / porin activity / pore complex / protein transmembrane transporter activity / monoatomic ion transport / mitochondrion organization / mitochondrial intermembrane space / protein-containing complex assembly / mitochondrial outer membrane / mitochondrion / cytoplasm / cytosol
Similarity search - Function
Sorting assembly machinery 35kDa subunit / Tom37, C-terminal domain / SAM35, subunit of SAM coomplex / Tom37 C-terminal domain / Mitochondrial import receptor subunit Tom6 / Mitochondrial import receptor subunit Tom6, fungal / Mitochondrial import receptor subunit Tom40, fungi / Mitochondrial outer membrane transport complex Sam37/metaxin, N-terminal domain / Outer mitochondrial membrane transport complex protein / Mitochondrial outer membrane translocase complex, subunit Tom5 ...Sorting assembly machinery 35kDa subunit / Tom37, C-terminal domain / SAM35, subunit of SAM coomplex / Tom37 C-terminal domain / Mitochondrial import receptor subunit Tom6 / Mitochondrial import receptor subunit Tom6, fungal / Mitochondrial import receptor subunit Tom40, fungi / Mitochondrial outer membrane transport complex Sam37/metaxin, N-terminal domain / Outer mitochondrial membrane transport complex protein / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase / Tom40 / Eukaryotic porin/Tom40 / Eukaryotic porin / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Porin domain superfamily
Similarity search - Domain/homology
Sorting assembly machinery 35 kDa subunit / Mitochondrial import receptor subunit TOM40 / Mitochondrial import receptor subunit TOM6 / Sorting assembly machinery 37 kDa subunit / Sorting assembly machinery 50 kDa subunit / Mitochondrial import receptor subunit TOM5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsWang Q / Guan ZY
CitationJournal: Science / Year: 2021
Title: Structural insight into the SAM-mediated assembly of the mitochondrial TOM core complex.
Authors: Qiang Wang / Zeyuan Guan / Liangbo Qi / Jinjin Zhuang / Chen Wang / Sixing Hong / Ling Yan / Yan Wu / Xiaoqian Cao / Jianbo Cao / Junjie Yan / Tingting Zou / Zhu Liu / Delin Zhang / Chuangye Yan / Ping Yin /
Abstract: β barrel outer membrane proteins (β-OMPs) play vital roles in mitochondria, chloroplasts, and Gram-negative bacteria. Evolutionarily conserved complexes such as the mitochondrial sorting and ...β barrel outer membrane proteins (β-OMPs) play vital roles in mitochondria, chloroplasts, and Gram-negative bacteria. Evolutionarily conserved complexes such as the mitochondrial sorting and assembly machinery (SAM) mediate the assembly of β-OMPs. We investigated the SAM-mediated assembly of the translocase of the outer membrane (TOM) core complex. Cryo–electron microscopy structures of SAM–fully folded Tom40 and the SAM-Tom40/Tom5/Tom6 complexes at ~3-angstrom resolution reveal that Sam37 stabilizes the mature Tom40 mainly through electrostatic interactions, thus facilitating subsequent TOM assembly. These results support the β barrel switching model and provide structural insights into the assembly and release of β barrel complexes.
History
DepositionFeb 13, 2021-
Header (metadata) releaseSep 1, 2021-
Map releaseSep 1, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7e4i
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30986.png

Downloads & links

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Map

FileDownload / File: emd_30986.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.087 Å
Density
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.6
Minimum - Maximum-4.855578 - 6.53388
Average (Standard dev.)0.00053093635 (±0.115804814)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 304.36002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0871.0871.087
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z304.360304.360304.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-4.8566.5340.001

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Supplemental data

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Sample components

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Entire : SAM-Tom40/Tom5/Tom6 complex

EntireName: SAM-Tom40/Tom5/Tom6 complex
Components
  • Complex: SAM-Tom40/Tom5/Tom6 complex
    • Complex: Sorting assembly machinery subunits
      • Protein or peptide: Sorting assembly machinery 50 kDa subunit
      • Protein or peptide: Sorting assembly machinery 35 kDa subunit
      • Protein or peptide: Sorting assembly machinery 37 kDa subunit
    • Complex: Mitochondrial import receptor subunits
      • Protein or peptide: Mitochondrial import receptor subunit TOM40
      • Protein or peptide: Mitochondrial import receptor subunit TOM5
      • Protein or peptide: Mitochondrial import receptor subunit TOM6

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Supramolecule #1: SAM-Tom40/Tom5/Tom6 complex

SupramoleculeName: SAM-Tom40/Tom5/Tom6 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)

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Supramolecule #2: Sorting assembly machinery subunits

SupramoleculeName: Sorting assembly machinery subunits / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)

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Supramolecule #3: Mitochondrial import receptor subunits

SupramoleculeName: Mitochondrial import receptor subunits / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#6

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Macromolecule #1: Sorting assembly machinery 50 kDa subunit

MacromoleculeName: Sorting assembly machinery 50 kDa subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c
Molecular weightTheoretical: 54.544918 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATSSSGVDN EISLDSPMPI FNESSTLKPI RVAGVVTTGT DHIDPSVLQA YLDDTIMKSI TLGQLVKNAD VLNKRLCQHH IALNAKQSF HFQGNTYISD EKETHDVVPL MEVVSQLDIL PPKTFTAKTG TNFGNDNDAE AYLQFEKLID KKYLKLPTRV N LEILRGTK ...String:
MATSSSGVDN EISLDSPMPI FNESSTLKPI RVAGVVTTGT DHIDPSVLQA YLDDTIMKSI TLGQLVKNAD VLNKRLCQHH IALNAKQSF HFQGNTYISD EKETHDVVPL MEVVSQLDIL PPKTFTAKTG TNFGNDNDAE AYLQFEKLID KKYLKLPTRV N LEILRGTK IHSSFLFNSY SSLSPQSILN LKVFSQFYNW NTNKGLDIGQ RGARLSLRYE PLFLHKLLHN PHSNESPTLF HE WFLETCW RSTKICSQGT SAPYMYSGTM LSQAGDQLRT ILGHTFVLDK RDHIMCPTKG SMLKWSNELS PGKHLKTQLE LNS VKSWMN DDFITFSTTI KTGYLKNLSS QQSLPVHICD KFQSGGPSDI RGFQTFGLGP RDLYDAVGGD AFVSYGLSVF SRLP WKKVE KSNFRLHWFF NGGKLVNHDN TSLGNCIGQL SKEHSTSTGI GLVLRHPMAR FELNFTLPIT AHENDLIRKG FQFGL GLAF L

UniProtKB: Sorting assembly machinery 50 kDa subunit

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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 S288c (yeast) / Strain: S288c
Molecular weightTheoretical: 37.44607 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 S288c (yeast) / Strain: S288c
Molecular weightTheoretical: 40.498754 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 ILEDYKDHDG DYKDHDIDYK DDDDK

UniProtKB: Sorting assembly machinery 37 kDa subunit

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Macromolecule #4: Mitochondrial import receptor subunit TOM40

MacromoleculeName: Mitochondrial import receptor subunit TOM40 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c
Molecular weightTheoretical: 43.947262 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASAPTPLAE ASQIPTIPAL SPLTAKQSKG NFFSSNPISS FVVDTYKQLH SHRQSLELVN PGTVENLNKE VSRDVFLSQY FFTGLRADL NKAFSMNPAF QTSHTFSIGS QALPKYAFSA LFANDNLFAQ GNIDNDLSVS GRLNYGWDKK NISKVNLQIS D GQPTMCQL ...String:
MASAPTPLAE ASQIPTIPAL SPLTAKQSKG NFFSSNPISS FVVDTYKQLH SHRQSLELVN PGTVENLNKE VSRDVFLSQY FFTGLRADL NKAFSMNPAF QTSHTFSIGS QALPKYAFSA LFANDNLFAQ GNIDNDLSVS GRLNYGWDKK NISKVNLQIS D GQPTMCQL EQDYQASDFS VNVKTLNPSF SEKGEFTGVA VASFLQSVTP QLALGLETLY SRTDGSAPGD AGVSYLTRYV SK KQDWIFS GQLQANGALI ASLWRKVAQN VEAGIETTLQ AGMVPITDPL MGTPIGIQPT VEGSTTIGAK YEYRQSVYRG TLD SNGKVA CFLERKVLPT LSVLFCGEID HFKNDTKIGC GLQFETAGNQ ELLMLQQGLD ADGNPLQALP QLLESAGKPI PNPL LGLDS T

UniProtKB: Mitochondrial import receptor subunit TOM40

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Macromolecule #5: Mitochondrial import receptor subunit TOM5

MacromoleculeName: Mitochondrial import receptor subunit TOM5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c
Molecular weightTheoretical: 6.196197 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MAMFGLPQQE VSEEEKRAHQ EQTEKTLKQA AYVAAFLWVS PMIWHLVKKQ WK

UniProtKB: Mitochondrial import receptor subunit TOM5

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Macromolecule #6: Mitochondrial import receptor subunit TOM6

MacromoleculeName: Mitochondrial import receptor subunit TOM6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c
Molecular weightTheoretical: 6.481539 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MADGMFAMPG AAAGAASPQQ PKSRFQAFKE SPLYTIALNG AFFVAGVAFI QSPLMDMLAP QL

UniProtKB: Mitochondrial import receptor subunit TOM6

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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

Concentration6 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: RANDOM CONICAL TILT
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0) / Number images used: 406531
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0)

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