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- EMDB-32019: Cryo-EM structure of SAM-Tom40 intermediate complex -

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Basic information

Entry
Database: EMDB / ID: EMD-32019
TitleCryo-EM structure of SAM-Tom40 intermediate complex
Map data
Sample
  • Complex: SAM-Tom40
    • 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
    • Protein or peptide: Mitochondrial import receptor subunit TOM40
KeywordsMitochondrial protein assembly gate / TRANSLOCASE
Function / homology
Function and homology information


SAM complex / membrane insertase activity / mitochondrial outer membrane translocase complex assembly / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / phospholipid transport / porin activity / pore complex / protein import into mitochondrial matrix / protein transmembrane transporter activity ...SAM complex / membrane insertase activity / mitochondrial outer membrane translocase complex assembly / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / phospholipid transport / porin activity / pore complex / protein import into mitochondrial matrix / 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 outer membrane transport complex Sam37/metaxin, N-terminal domain / : / Outer mitochondrial membrane transport complex protein / Mitochondrial import receptor subunit Tom40, fungi / Tom40 / Eukaryotic porin/Tom40 ...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 / Mitochondrial import receptor subunit Tom40, fungi / Tom40 / Eukaryotic porin/Tom40 / Eukaryotic porin / 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 / Sorting assembly machinery 37 kDa subunit / Sorting assembly machinery 50 kDa subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsTakeda H / Tsutsumi A / Kikkawa M / Endo T
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: Nat Struct Mol Biol / Year: 2023
Title: Author Correction: A multipoint guidance mechanism for β-barrel folding on the SAM complex.
Authors: Hironori Takeda / Jon V Busto / Caroline Lindau / Akihisa Tsutsumi / Kentaro Tomii / Kenichiro Imai / Yu Yamamori / Takatsugu Hirokawa / Chie Motono / Iniyan Ganesan / Lena-Sophie Wenz / ...Authors: Hironori Takeda / Jon V Busto / Caroline Lindau / Akihisa Tsutsumi / Kentaro Tomii / Kenichiro Imai / Yu Yamamori / Takatsugu Hirokawa / Chie Motono / Iniyan Ganesan / Lena-Sophie Wenz / Thomas Becker / Masahide Kikkawa / Nikolaus Pfanner / Nils Wiedemann / Toshiya Endo /
History
DepositionOct 1, 2021-
Header (metadata) releaseJan 4, 2023-
Map releaseJan 4, 2023-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32019.png

Downloads & links

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Map

FileDownload / File: emd_32019.map.gz / Format: CCP4 / Size: 30.5 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 200 pix.
= 249. Å		1.25 Å/pix.
x 200 pix.
= 249. Å		1.25 Å/pix.
x 200 pix.
= 249. 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: 0.06
Minimum - Maximum-0.20191672 - 0.42213887
Average (Standard dev.)-0.0002914935 (±0.0096141)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : SAM-Tom40

EntireName: SAM-Tom40
Components
  • Complex: SAM-Tom40
    • 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
    • Protein or peptide: Mitochondrial import receptor subunit TOM40

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Supramolecule #1: SAM-Tom40

SupramoleculeName: SAM-Tom40 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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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)
Molecular weightTheoretical: 54.47384 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MTSSSGVDNE ISLDSPMPIF NESSTLKPIR VAGVVTTGTD HIDPSVLQAY LDDTIMKSIT LGQLVKNADV LNKRLCQHHI ALNAKQSFH FQGNTYISDE KETHDVVPLM EVVSQLDILP PKTFTAKTGT NFGNDNDAEA YLQFEKLIDK KYLKLPTRVN L EILRGTKI ...String:
MTSSSGVDNE ISLDSPMPIF NESSTLKPIR VAGVVTTGTD HIDPSVLQAY LDDTIMKSIT LGQLVKNADV LNKRLCQHHI ALNAKQSFH FQGNTYISDE KETHDVVPLM EVVSQLDILP PKTFTAKTGT NFGNDNDAEA YLQFEKLIDK KYLKLPTRVN L EILRGTKI HSSFLFNSYS SLSPQSILNL KVFSQFYNWN TNKGLDIGQR GARLSLRYEP LFLHKLLHNP HSNESPTLFH EW FLETCWR STKICSQGTS APYMYSGTML SQAGDQLRTI LGHTFVLDKR DHIMCPTKGS MLKWSNELSP GKHLKTQLEL NSV KSWMND DFITFSTTIK TGYLKNLSSQ QSLPVHICDK FQSGGPSDIR GFQTFGLGPR DLYDAVGGDA FVSYGLSVFS RLPW KKVEK SNFRLHWFFN GGKLVNHDNT SLGNCIGQLS KEHSTSTGIG LVLRHPMARF ELNFTLPITA HENDLIRKGF QFGLG LAFL

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)
Molecular weightTheoretical: 37.44607 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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)
Molecular weightTheoretical: 37.537797 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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: 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)
Molecular weightTheoretical: 42.071141 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSAPTPLAEA SQIPTIPALS PLTAKQSKGN FFSSNPISSF VVDTYKQLHS HRQSLELVNP GTVENLNKEV SRDVFLSQYF FTGLRADLN KAFSMNPAFQ TSHTFSIGSQ ALPKYAFSAL FANDNLFAQG NIDNDLSVSG RLNYGWDKKN ISKVNLQISD G QPTMCQLE ...String:
MSAPTPLAEA SQIPTIPALS PLTAKQSKGN FFSSNPISSF VVDTYKQLHS HRQSLELVNP GTVENLNKEV SRDVFLSQYF FTGLRADLN KAFSMNPAFQ TSHTFSIGSQ ALPKYAFSAL FANDNLFAQG NIDNDLSVSG RLNYGWDKKN ISKVNLQISD G QPTMCQLE QDYQASDFSV NVKTLNPSFS EKGEFTGVAV ASFLQSVTPQ LALGLETLYS RTDGSAPGDA GVSYLTRYVS KK QDWIFSG QLQANGALIA SLWRKVAQNV EAGIETTLQA GMVPITDPLM GTPIGIQPTV EGSTTIGAKY EYRQSVYRGT LDS NGKVAC FLERKVLPTL SVLFCGEIDH FKNDTKIGCG LQFETAGNQE LLMLQQGLDA DGNPLQALPQ L

UniProtKB: Mitochondrial import receptor subunit TOM40

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.5
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: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23542
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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