+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32019 | ||||||||||||
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Title | Cryo-EM structure of SAM-Tom40 intermediate complex | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Mitochondrial protein assembly gate / TRANSLOCASE | ||||||||||||
Function / homology | Function and homology information mitochondrial outer membrane translocase complex assembly / SAM complex / membrane insertase activity / mitochondrial outer membrane translocase complex / protein import into mitochondrial matrix / phospholipid transport / porin activity / protein insertion into mitochondrial outer membrane / pore complex / protein transmembrane transporter activity ...mitochondrial outer membrane translocase complex assembly / SAM complex / membrane insertase activity / mitochondrial outer membrane translocase complex / protein import into mitochondrial matrix / phospholipid transport / porin activity / protein insertion into mitochondrial outer membrane / pore complex / protein transmembrane transporter activity / monoatomic ion transport / mitochondrion organization / mitochondrial intermembrane space / protein-containing complex assembly / mitochondrial outer membrane / mitochondrion / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae S288C (yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
Authors | Takeda H / Tsutsumi A / Kikkawa M / Endo T | ||||||||||||
Funding support | Japan, 3 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32019.map.gz | 19.2 MB | EMDB map data format | |
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Header (meta data) | emd-32019-v30.xml emd-32019.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32019_fsc.xml | 7.1 KB | Display | FSC data file |
Images | emd_32019.png | 105.7 KB | ||
Filedesc metadata | emd-32019.cif.gz | 6.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32019 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32019 | HTTPS FTP |
-Validation report
Summary document | emd_32019_validation.pdf.gz | 436.6 KB | Display | EMDB validaton report |
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Full document | emd_32019_full_validation.pdf.gz | 436.2 KB | Display | |
Data in XML | emd_32019_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | emd_32019_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32019 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32019 | HTTPS FTP |
-Related structure data
Related structure data | 7vkuMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_32019.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.245 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : SAM-Tom40
Entire | Name: SAM-Tom40 |
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Components |
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-Supramolecule #1: SAM-Tom40
Supramolecule | Name: SAM-Tom40 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
-Macromolecule #1: Sorting assembly machinery 50 kDa subunit
Macromolecule | Name: Sorting assembly machinery 50 kDa subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Molecular weight | Theoretical: 54.47384 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: 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 |
-Macromolecule #2: Sorting assembly machinery 35 kDa subunit
Macromolecule | Name: Sorting assembly machinery 35 kDa subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Molecular weight | Theoretical: 37.44607 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: 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 |
-Macromolecule #3: Sorting assembly machinery 37 kDa subunit
Macromolecule | Name: Sorting assembly machinery 37 kDa subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Molecular weight | Theoretical: 37.537797 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: 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 |
-Macromolecule #4: Mitochondrial import receptor subunit TOM40
Macromolecule | Name: Mitochondrial import receptor subunit TOM40 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Molecular weight | Theoretical: 42.071141 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 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 |