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- EMDB-30985: Cryo-EM structure of the yeast mitochondrial SAM-Tom40 complex at... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-30985 | |||||||||
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Title | Cryo-EM structure of the yeast mitochondrial SAM-Tom40 complex at 3.0 angstrom | |||||||||
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Function / homology | ![]() mitochondrial outer membrane translocase complex assembly / SAM complex / mitochondrial outer membrane translocase complex / protein import into mitochondrial matrix / phospholipid transport / protein insertion into mitochondrial outer membrane / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Wang Q / Guan ZY | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 79 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.9 KB 15.9 KB | Display Display | ![]() |
Images | ![]() | 75.5 KB | ||
Filedesc metadata | ![]() | 6.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7e4hMC ![]() 7e4iC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : SAM-Tom40 complex
Entire | Name: SAM-Tom40 complex |
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Components |
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-Supramolecule #1: SAM-Tom40 complex
Supramolecule | Name: SAM-Tom40 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() ![]() |
-Supramolecule #2: Sorting assembly machinery subunits
Supramolecule | Name: Sorting assembly machinery subunits / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() ![]() ![]() |
-Supramolecule #3: Mitochondrial import receptor subunit TOM40
Supramolecule | Name: Mitochondrial import receptor subunit TOM40 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4 |
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-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: ![]() ![]() ![]() |
Molecular weight | Theoretical: 54.544918 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-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: ![]() ![]() ![]() |
Molecular weight | Theoretical: 37.44607 KDa |
Recombinant expression | Organism: ![]() ![]() |
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: ![]() ![]() ![]() |
Molecular weight | Theoretical: 40.498754 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 ILEDYKDHDG DYKDHDIDYK DDDDK 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: ![]() ![]() ![]() |
Molecular weight | Theoretical: 46.444711 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGSDYKDDDD KMSAPTPLAE ASQIPTIPAL SPLTAKQSKG NFFSSNPISS FVVDTYKQL HSHRQSLELV NPGTVENLNK EVSRDVFLSQ YFFTGLRADL NKAFSMNPAF QTSHTFSIGS QALPKYAFSA L FANDNLFA ...String: MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGSDYKDDDD KMSAPTPLAE ASQIPTIPAL SPLTAKQSKG NFFSSNPISS FVVDTYKQL HSHRQSLELV NPGTVENLNK EVSRDVFLSQ YFFTGLRADL NKAFSMNPAF QTSHTFSIGS QALPKYAFSA L FANDNLFA QGNIDNDLSV SGRLNYGWDK KNISKVNLQI SDGQPTMCQL EQDYQASDFS VNVKTLNPSF SEKGEFTGVA VA SFLQSVT PQLALGLETL YSRTDGSAPG DAGVSYLTRY VSKKQDWIFS GQLQANGALI ASLWRKVAQN VEAGIETTLQ AGM VPITDP LMGTPIGIQP TVEGSTTIGA KYEYRQSVYR GTLDSNGKVA CFLERKVLPT LSVLFCGEID HFKNDTKIGC GLQF ETAGN QELLMLQQGL DADGNPLQAL PQL UniProtKB: Mitochondrial import receptor subunit TOM40 |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 2.5 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: RANDOM CONICAL TILT |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 240049 |