[English] 日本語
Yorodumi
- EMDB-49496: Thermothelomyces thermophilus SAM complex bound to darobactin A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49496
TitleThermothelomyces thermophilus SAM complex bound to darobactin A
Map datanon-sharpened map SAM complex bound to darobactin A
Sample
  • Complex: Thermothelomyces thermophilus SAM complex bound to darobactin A
    • Protein or peptide: Sam35
    • Protein or peptide: Sam50
    • Protein or peptide: Sam37
    • Protein or peptide: darobactin A
  • Ligand: ERGOSTEROL
Keywordsbeta-barrel / sorting and assembly machinery / MEMBRANE PROTEIN-ANTIBIOTIC complex
Function / homology
Function and homology information


SAM complex / protein insertion into mitochondrial outer membrane / mitochondrion organization / 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) / Photorhabdus khanii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsDiederichs K / Botos I / Buchanan SK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)ZIA DK036139 United States
CitationJournal: Nat Commun / Year: 2025
Title: The dynamic lateral gate of the mitochondrial β-barrel biogenesis machinery is blocked by darobactin A.
Authors: Kathryn A Diederichs / Istvan Botos / Scout Hayashi / Gvantsa Gutishvili / Vadim Kotov / Katie Kuo / Akira Iinishi / Gwendolyn Cooper / Benjamin Schwarz / Herve Celia / Thomas C Marlovits / ...Authors: Kathryn A Diederichs / Istvan Botos / Scout Hayashi / Gvantsa Gutishvili / Vadim Kotov / Katie Kuo / Akira Iinishi / Gwendolyn Cooper / Benjamin Schwarz / Herve Celia / Thomas C Marlovits / Kim Lewis / James C Gumbart / Joseph A Mindell / Susan K Buchanan /
Abstract: The folding and insertion of β-barrel proteins into the mitochondrial outer membrane is facilitated by the sorting and assembly machinery (SAM) complex. Here we report two 2.8 Å cryo-EM ...The folding and insertion of β-barrel proteins into the mitochondrial outer membrane is facilitated by the sorting and assembly machinery (SAM) complex. Here we report two 2.8 Å cryo-EM structures of the Thermothelomyces thermophilus SAM complex in the absence of substrate in which the Sam50 lateral gate adopts two different conformations: the first is a closed lateral gate as observed in previously published structures, while the second contains a Sam50 with the first four β-strands rotated outwards by approximately 45°, resulting in an open lateral gate. The observed monomeric open conformation contrasts our previous work where the open conformation was adopted by non-physiological up-down dimers. To understand how these lateral gate dynamics are influenced by substrate, we studied the interaction of the SAM complex with a β-signal peptide mimic, darobactin A. Darobactin A binds to the SAM complex with nanomolar affinity and inhibits the import and assembly of mitochondrial β-barrel proteins in vitro. Lastly, we solved a 3.0 Å cryo-EM structure of the Thermothelomyces thermophilus SAM complex bound to darobactin A, which reveals that darobactin A stabilizes the Sam50 lateral gate similar to the open conformation by binding to strand β1, therefore blocking β-barrel biogenesis.
History
DepositionFeb 28, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_49496.png

Downloads & links

-
Map

FileDownload / File: emd_49496.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationnon-sharpened map SAM complex bound to darobactin A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0394
Minimum - Maximum-0.071454614 - 0.2114961
Average (Standard dev.)0.000053081407 (±0.0044770753)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half-map B SAM complex bound to darobactin A

Fileemd_49496_half_map_1.map
Annotationhalf-map B SAM complex bound to darobactin A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half-map A SAM complex bound to darobactin A

Fileemd_49496_half_map_2.map
Annotationhalf-map A SAM complex bound to darobactin A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Thermothelomyces thermophilus SAM complex bound to darobactin A

EntireName: Thermothelomyces thermophilus SAM complex bound to darobactin A
Components
  • Complex: Thermothelomyces thermophilus SAM complex bound to darobactin A
    • Protein or peptide: Sam35
    • Protein or peptide: Sam50
    • Protein or peptide: Sam37
    • Protein or peptide: darobactin A
  • Ligand: ERGOSTEROL

-
Supramolecule #1: Thermothelomyces thermophilus SAM complex bound to darobactin A

SupramoleculeName: Thermothelomyces thermophilus SAM complex bound to darobactin A
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Thermothelomyces thermophilus (fungus)

-
Macromolecule #1: Sam35

MacromoleculeName: Sam35 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermothelomyces thermophilus (fungus)
Molecular weightTheoretical: 36.88268 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae W303 (yeast)
SequenceString: MSASIPSAAP SWRKMQIPRP LQRLFDYFPL RIYEPNELPE RSQQLTSGDL PTLYVFSTDS DARLGLPSFN PGCLKWQTLL RLANLDFRI LPSTNHSSPT GSLPFLLPPR TSPTASPAPI PASGLLSFAR KNPWRPGKAA DLDLGHLDAD LPPRAQAYLA L ITHSLRNA ...String:
MSASIPSAAP SWRKMQIPRP LQRLFDYFPL RIYEPNELPE RSQQLTSGDL PTLYVFSTDS DARLGLPSFN PGCLKWQTLL RLANLDFRI LPSTNHSSPT GSLPFLLPPR TSPTASPAPI PASGLLSFAR KNPWRPGKAA DLDLGHLDAD LPPRAQAYLA L ITHSLRNA WLCALYLDPT HDALLRRLYV DPASSSRAVR AALLHQLRRA AAEQVATASS GGGKIVSLAP VDSADGIDEE AV YRSARDA LDALASLLRE SETAWFFGTE RPGSFDAALF SYTHLMVEYM SEEEDTESAK GRVSLGRMVK EAGNGELAEH RER MLGVAW PEWDGYRR

UniProtKB: Thioredoxin-like fold domain-containing protein

-
Macromolecule #2: Sam50

MacromoleculeName: Sam50 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermothelomyces thermophilus (fungus)
Molecular weightTheoretical: 53.468043 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae W303 (yeast)
SequenceString: MSASSLGFGG SNAVDKVNAT TTPGTVATPN SGPTKMLDEH ILTPASISTL EVHGATNTRR SLLDQIFKPV LEDTAAAGTT LGQVLDRVG AATKKLARFD IFKEEGFGVF LSEAAPPQSA PPTDRTDLDI SIRVKEKSRL VFSAGTDFGN AEGSAYTNAV V RNIFGGAE ...String:
MSASSLGFGG SNAVDKVNAT TTPGTVATPN SGPTKMLDEH ILTPASISTL EVHGATNTRR SLLDQIFKPV LEDTAAAGTT LGQVLDRVG AATKKLARFD IFKEEGFGVF LSEAAPPQSA PPTDRTDLDI SIRVKEKSRL VFSAGTDFGN AEGSAYTNAV V RNIFGGAE TLTVNASTGT RTRSAYNATF STPINGNPDL RLSVEALRSA TQKPWASHEE HLTGANLRLA WLTEKGDTHA LA YSSVWRQ LTGLAPTASP TVRADAGDSL KSSLTHTFTR DRRDNPMLPQ SGYLFRSVSE LAGWGPLNGD VSFAKTEVEA SGA LPVAIP GLAGKSGVSV GGGLRLGVLY PLPLGYSLTG AAQPSRINDR FQLGGPNDVR GFKIGGLGPH DGVDAVGGDV FAAG SVNAL LPLPRTGPDS PLRLQLYANA GRLVALNSKG TDKEGKEGLA MDSAAVFKGV KSAVGKLTNG IPSLAAGVGL VYAHP VARF ELNFSLPLVL RRGEEGRKGL QVGVGISFL

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

-
Macromolecule #3: Sam37

MacromoleculeName: Sam37 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermothelomyces thermophilus (fungus)
Molecular weightTheoretical: 49.327566 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae W303 (yeast)
SequenceString: MSSAWSHPQF EKGGGSGGGS GGSAWSHPQF EKGGAVQLHV WGPAFGLPSI DAECLAAIAY LAQTLGSADY QLIQSSPSAV PTQHLPTLY DSRTSTWIGG FTSITAHLHT HPPPTFQSAP QPTDGSSSTT TTTTTTTTAA SATADGTAYT AFLSAHAAPL L ALSLYVSS ...String:
MSSAWSHPQF EKGGGSGGGS GGSAWSHPQF EKGGAVQLHV WGPAFGLPSI DAECLAAIAY LAQTLGSADY QLIQSSPSAV PTQHLPTLY DSRTSTWIGG FTSITAHLHT HPPPTFQSAP QPTDGSSSTT TTTTTTTTAA SATADGTAYT AFLSAHAAPL L ALSLYVSS ANYGAATRPA YSAVLPLPLP WTEPPAVRAA MARRAAHLGL SSLDADAAAE RARAEERRAA ADGWVAVPPH AT AGRAAGG GGGGGGGGGK GGGVAAVLTP EQKSRIRLEE AAREVLDVLA EVDWAAGGGG RQVAAEVRCL AFGYLALMLL PDV PRPWLR EIMEGRYPAL CTFVRDFRAR VFPQGGKLLP WADGGAQASA SASASASAVA LRFVRAVMAE VPLVGEWWSR WWTA RKKRE VLASKGAKPA PSNDLLLLLG AGLGLTVVGA GVFFYRGLPP FGEAVQVWRK PVVGLSSFGA AGAMFSGALY GLD

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

-
Macromolecule #4: darobactin A

MacromoleculeName: darobactin A / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus khanii (bacteria)
Molecular weightTheoretical: 971.047 Da
SequenceString:
WN(UX8)SKSF

-
Macromolecule #5: ERGOSTEROL

MacromoleculeName: ERGOSTEROL / type: ligand / ID: 5 / Number of copies: 12 / Formula: ERG
Molecular weightTheoretical: 396.648 Da
Chemical component information

ChemComp-ERG:
ERGOSTEROL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 163391
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more