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- EMDB-21916: Mitochondrial SAM complex - dimer 2 in detergent -

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Basic information

Entry
Database: EMDB / ID: EMD-21916
TitleMitochondrial SAM complex - dimer 2 in detergent
Map data
Sample
  • Complex: Mitochondrial SAM complex - dimer 2 in detergent
    • Protein or peptide: Sam35
    • Protein or peptide: Tom37 domain-containing protein
    • Protein or peptide: Bac_surface_Ag domain-containing protein
KeywordsMitochondrial SAM complex / Sam35 / Sam37 / Sam50. / MEMBRANE PROTEIN
Function / homology
Function and homology information


SAM complex / protein transport / mitochondrial outer membrane
Similarity search - Function
Metaxin, glutathione S-transferase domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase N-terminal domain / Mitochondrial outer membrane transport complex Sam37/metaxin, N-terminal domain / : / Outer mitochondrial membrane transport complex protein / Thioredoxin-like fold / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain
Similarity search - Domain/homology
Mitochondrial outer membrane transport complex Sam37/metaxin N-terminal domain-containing protein / Thioredoxin-like fold domain-containing protein / Bacterial surface antigen (D15) domain-containing protein
Similarity search - Component
Biological speciesThermothelomyces thermophilus (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsNi X / Botos I
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Nat Commun / Year: 2020
Title: Structural insight into mitochondrial β-barrel outer membrane protein biogenesis.
Authors: Kathryn A Diederichs / Xiaodan Ni / Sarah E Rollauer / Istvan Botos / Xiaofeng Tan / Martin S King / Edmund R S Kunji / Jiansen Jiang / Susan K Buchanan /
Abstract: In mitochondria, β-barrel outer membrane proteins mediate protein import, metabolite transport, lipid transport, and biogenesis. The Sorting and Assembly Machinery (SAM) complex consists of three ...In mitochondria, β-barrel outer membrane proteins mediate protein import, metabolite transport, lipid transport, and biogenesis. The Sorting and Assembly Machinery (SAM) complex consists of three proteins that assemble as a 1:1:1 complex to fold β-barrel proteins and insert them into the mitochondrial outer membrane. We report cryoEM structures of the SAM complex from Myceliophthora thermophila, which show that Sam50 forms a 16-stranded transmembrane β-barrel with a single polypeptide-transport-associated (POTRA) domain extending into the intermembrane space. Sam35 and Sam37 are located on the cytosolic side of the outer membrane, with Sam35 capping Sam50, and Sam37 interacting extensively with Sam35. Sam35 and Sam37 each adopt a GST-like fold, with no functional, structural, or sequence similarity to their bacterial counterparts. Structural analysis shows how the Sam50 β-barrel opens a lateral gate to accommodate its substrates.
History
DepositionMay 4, 2020-
Header (metadata) releaseAug 12, 2020-
Map releaseAug 12, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / 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
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6wum
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21916.png

Downloads & links

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Map

FileDownload / File: emd_21916.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 208 pix.
= 220.48 Å		1.06 Å/pix.
x 208 pix.
= 220.48 Å		1.06 Å/pix.
x 208 pix.
= 220.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.6
Minimum - Maximum-2.0294948 - 3.3203545
Average (Standard dev.)0.024457235 (±0.13078666)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 220.47998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z208208208
origin x/y/z0.0000.0000.000
length x/y/z220.480220.480220.480
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS208208208
D min/max/mean-2.0293.3200.024

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Supplemental data

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Sample components

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Entire : Mitochondrial SAM complex - dimer 2 in detergent

EntireName: Mitochondrial SAM complex - dimer 2 in detergent
Components
  • Complex: Mitochondrial SAM complex - dimer 2 in detergent
    • Protein or peptide: Sam35
    • Protein or peptide: Tom37 domain-containing protein
    • Protein or peptide: Bac_surface_Ag domain-containing protein

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Supramolecule #1: Mitochondrial SAM complex - dimer 2 in detergent

SupramoleculeName: Mitochondrial SAM complex - dimer 2 in detergent / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermothelomyces thermophilus (fungus)

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Macromolecule #1: Sam35

MacromoleculeName: Sam35 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermothelomyces thermophilus (fungus)
Molecular weightTheoretical: 36.64843 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MASIPSAAPS WRKMQIPRPL QRLFDYFPLR IYEPNELPER SQQLTSGDLP TLYVFSTDSD ARLGLPSFNP GCLKWQTLLR LANLDFRIL PSTNHSSPTG SLPFLLPPRT SPTASPAPIP ASGLLSFARK NPWRPGKAAD LDLGHLDADL PPRAQAYLAL I THSLRNAW ...String:
MASIPSAAPS WRKMQIPRPL QRLFDYFPLR IYEPNELPER SQQLTSGDLP TLYVFSTDSD ARLGLPSFNP GCLKWQTLLR LANLDFRIL PSTNHSSPTG SLPFLLPPRT SPTASPAPIP ASGLLSFARK NPWRPGKAAD LDLGHLDADL PPRAQAYLAL I THSLRNAW LCALYLDPTH DALLRRLYVD PASSSRAVRA ALLHQLRRAA AEQVATASSG GGKIVSLAPV DSADGIDEEA VY RSARDAL DALASLLRES ETAWFGTERP GSFDAALFSY THLMVEYMSE EEDTESAKGR VSLGRMVKEA GNGELAEHRE RML GVAWPE WDGYRR

UniProtKB: Thioredoxin-like fold domain-containing protein

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Macromolecule #2: Tom37 domain-containing protein

MacromoleculeName: Tom37 domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermothelomyces thermophilus (fungus)
Molecular weightTheoretical: 49.458762 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSSAWSHPQF EKGGGSGGGS GGSAWSHPQF EKGGMAVQLH VWGPAFGLPS IDAECLAAIA YLAQTLGSAD YQLIQSSPSA VPTQHLPTL YDSRTSTWIG GFTSITAHLH THPPPTFQSA PQPTDGSSST TTTTTTTTTA ASATADGTAY TAFLSAHAAP L LALSLYVS ...String:
MSSAWSHPQF EKGGGSGGGS GGSAWSHPQF EKGGMAVQLH VWGPAFGLPS IDAECLAAIA YLAQTLGSAD YQLIQSSPSA VPTQHLPTL YDSRTSTWIG GFTSITAHLH THPPPTFQSA PQPTDGSSST TTTTTTTTTA ASATADGTAY TAFLSAHAAP L LALSLYVS SANYGAATRP AYSAVLPLPL PWTEPPAVRA AMARRAAHLG LSSLDADAAA ERARAEERRA AADGWVAVPP HA TAGRAAG GGGGGGGGGG KGGGVAAVLT PEQKSRIRLE EAAREVLDVL AEVDWAAGGG GRQVAAEVRC LAFGYLALML LPD VPRPWL REIMEGRYPA LCTFVRDFRA RVFPQGGKLL PWADGGAQAS ASASASASAV ALRFVRAVMA EVPLVGEWWS RWWT ARKKR EVLASKGAKP APSNDLLLLL GAGLGLTVVG AGVFFYRGLP PFGEAVQVWR KPVVGLSSFG AAGAMFSGAL YGLD

UniProtKB: Mitochondrial outer membrane transport complex Sam37/metaxin N-terminal domain-containing protein

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Macromolecule #3: Bac_surface_Ag domain-containing protein

MacromoleculeName: Bac_surface_Ag domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermothelomyces thermophilus (fungus)
Molecular weightTheoretical: 53.380969 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MASSLGFGGS NAVDKVNATT TPGTVATPNS GPTKMLDEHI LTPASISTLE VHGATNTRRS LLDQIFKPVL EDTAAAGTTL GQVLDRVGA ATKKLARFDI FKEEGFGVFL SEAAPPQSAP PTDRTDLDIS IRVKEKSRLV FSAGTDFGNA EGSAYTNAVV R NIFGGAET ...String:
MASSLGFGGS NAVDKVNATT TPGTVATPNS GPTKMLDEHI LTPASISTLE VHGATNTRRS LLDQIFKPVL EDTAAAGTTL GQVLDRVGA ATKKLARFDI FKEEGFGVFL SEAAPPQSAP PTDRTDLDIS IRVKEKSRLV FSAGTDFGNA EGSAYTNAVV R NIFGGAET LTVNASTGTR TRSAYNATFS TPINGNPDLR LSVEALRSAT QKPWASHEEH LTGANLRLAW LTEKGDTHAL AY SSVWRQL TGLAPTASPT VRADAGDSLK SSLTHTFTRD RRDNPMLPQS GYLFRSVSEL AGWGPLNGDV SFAKTEVEAS GAL PVAIPG LAGKSGVSVG GGLRLGVLYP LPLGYSLTGA AQPSRINDRF QLGGPNDVRG FKIGGLGPHD GVDAVGGDVF AAGS VNALL PLPRTGPDSP LRLQLYANAG RLVALNSKGT DKEGKEGLAM DSAAVFKGVK SAVGKLTNGI PSLAAGVGLV YAHPV ARFE LNFSLPLVLR RGEEGRKGLQ VGVGISFL

UniProtKB: Bacterial surface antigen (D15) domain-containing protein

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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
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 69.0 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: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 60472
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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