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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20820 | ||||||||||||||||||
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Title | A complete structure of the ESX-3 translocon complex | ||||||||||||||||||
![]() | Consensus map used to generate all focused refinements. Unsharpened | ||||||||||||||||||
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![]() | ESX / secretion system / type VII secretion system / mycobacteria / complex / membrane protein / TRANSPORT PROTEIN | ||||||||||||||||||
Function / homology | ![]() Hydrolases; Acting on acid anhydrides / hydrolase activity / ATP hydrolysis activity / DNA binding / extracellular region / ATP binding / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||||||||
![]() | Poweleit N / Rosenberg OS | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The structure of the endogenous ESX-3 secretion system. Authors: Nicole Poweleit / Nadine Czudnochowski / Rachel Nakagawa / Donovan D Trinidad / Kenan C Murphy / Christopher M Sassetti / Oren S Rosenberg / ![]() Abstract: The ESX (or Type VII) secretion systems are protein export systems in mycobacteria and many Gram-positive bacteria that mediate a broad range of functions including virulence, conjugation, and ...The ESX (or Type VII) secretion systems are protein export systems in mycobacteria and many Gram-positive bacteria that mediate a broad range of functions including virulence, conjugation, and metabolic regulation. These systems translocate folded dimers of WXG100-superfamily protein substrates across the cytoplasmic membrane. We report the cryo-electron microscopy structure of an ESX-3 system, purified using an epitope tag inserted with recombineering into the chromosome of the model organism . The structure reveals a stacked architecture that extends above and below the inner membrane of the bacterium. The ESX-3 protomer complex is assembled from a single copy of the EccB, EccC, and EccE and two copies of the EccD protein. In the structure, the protomers form a stable dimer that is consistent with assembly into a larger oligomer. The ESX-3 structure provides a framework for further study of these important bacterial transporters. | ||||||||||||||||||
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
-Related structure data
Related structure data | ![]() 6ummMC 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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Annotation | Consensus map used to generate all focused refinements. Unsharpened | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
+Mask #1
+Mask #2
+Mask #3
+Mask #4
+Mask #5
+Additional map: Focused refinement of the EccC ATPase 1, 2,...
+Additional map: Half1 of right protomer focused refinement.
+Additional map: Half2 of left protomer focused refinement
+Additional map: Half1 of left protomer focused refinement
+Additional map: Focused refinement of right protomer. Unsharpened
+Additional map: Focused refinement of symmetry expanded protomer. Unsharpened
+Additional map: Half2 of periplasmic focused refinement
+Additional map: Half1 of periplasmic focused refinement
+Additional map: Focused refinement of left protomer. Unsharpened
+Additional map: Focused refinement of periplasmic domain. Unsharpened
+Additional map: Half2 of symmetry expanded protomer
+Additional map: Half1 of symmetry expanded protomer
+Additional map: Half2 of right protomer focused refinement
+Half map: Half2 of consensus map
+Half map: Half1 of consensus map
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Sample components
-Entire : ESX-3 translocon complex
Entire | Name: ESX-3 translocon complex |
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Components |
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-Supramolecule #1: ESX-3 translocon complex
Supramolecule | Name: ESX-3 translocon complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() Strain: ATCC 700084 / mc(2)155 |
Molecular weight | Theoretical: 660 KDa |
-Macromolecule #1: ESX-3 secretion system protein EccE3
Macromolecule | Name: ESX-3 secretion system protein EccE3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC 700084 / mc(2)155 |
Molecular weight | Theoretical: 30.813355 KDa |
Sequence | String: MTARIALASL FVVAAVLAQP WQTTTQRWVL GVSIAAVIVL LAWWKGMFLT TRIGRALAMV RRNRAEDTVE TDAHRATVVL RVDPAAPAQ LPVVVGYLDR YGITCDKVRI THRDAGGTRR SWISLTVDAV DNLAALQARS ARIPLQDTTE VVGRRLADHL R EQGWTVTV ...String: MTARIALASL FVVAAVLAQP WQTTTQRWVL GVSIAAVIVL LAWWKGMFLT TRIGRALAMV RRNRAEDTVE TDAHRATVVL RVDPAAPAQ LPVVVGYLDR YGITCDKVRI THRDAGGTRR SWISLTVDAV DNLAALQARS ARIPLQDTTE VVGRRLADHL R EQGWTVTV VEGVDTPLPV SGKETWRGVA DDAGVVAAYR VKVDDRLDEV LAEIGHLPAE ETWTALEFTG SPAEPLLTVC AA VRTSDRP AAKAPLAGLT PARGRHRPAL AALNPLSTER LDGTAVPL UniProtKB: ESX-3 secretion system protein EccE3 |
-Macromolecule #2: ESX-3 secretion system protein EccD3
Macromolecule | Name: ESX-3 secretion system protein EccD3 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC 700084 / mc(2)155 |
Molecular weight | Theoretical: 48.29248 KDa |
Sequence | String: MSENTVMPIV RVAVLAAGDD GGRLTEMALP SELPLREILP AVQRIVQPAR ENDGAADPAA APNPVRLSLA PIGGAPFSLD ATLDTVGVV DGDLLALQAV PSGPPAPRIV EDIADAAVIF SEARRRQWGP THIARGAALA LIGLILVGTG LSVAHRVITG D LLGQFIVS ...String: MSENTVMPIV RVAVLAAGDD GGRLTEMALP SELPLREILP AVQRIVQPAR ENDGAADPAA APNPVRLSLA PIGGAPFSLD ATLDTVGVV DGDLLALQAV PSGPPAPRIV EDIADAAVIF SEARRRQWGP THIARGAALA LIGLILVGTG LSVAHRVITG D LLGQFIVS GIALATVIAA LAVRNRSAVL ATSLAVTALV PVAAAFALGV PGDFGAPNVL LAAAGVAAWS LISMAGSPDD RG IAVFTAT AVTGVGVLLV AGAASLWVIS SDVIGCALVL LGLIVTVQAA QLSAMWARFP LPVIPAPGDP TPAARPLSVL ADL PRRVRV SQAHQTGVIA AGVLLGVAGS VALVSSANAS PWAWYIVVAA AAGAALRARV WDSAACKAWL LGHSYLLAVA LLVA FVIGD RYQAALWALA ALAVLVLVWI VAALNPKIAS PDTYSLPMRR MVGFLATGLD ASLIPVMALL VGLFSLVLDR UniProtKB: ESX-3 secretion system protein EccD3 |
-Macromolecule #3: ESX-3 secretion system ATPase EccB3
Macromolecule | Name: ESX-3 secretion system ATPase EccB3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on acid anhydrides |
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Source (natural) | Organism: ![]() Strain: ATCC 700084 / mc(2)155 |
Molecular weight | Theoretical: 9.145638 KDa |
Sequence | String: FSSRTPVNEN PDGVQYRRGF VTRHQVSGWR FVMRRIASGV ALHDTRMLVD PLRTQSRAVL TGALILVTGL VGCFIFSLFR P UniProtKB: ESX-3 secretion system ATPase EccB3 |
-Macromolecule #4: ESX-3 secretion system protein EccC3
Macromolecule | Name: ESX-3 secretion system protein EccC3 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC 700084 / mc(2)155 |
Molecular weight | Theoretical: 44.898371 KDa |
Sequence | String: MSRLIFEHQR RLTPPTTRKG TITIEPPPQL PRVVPPSLLR RVLPFLIVIL IVGMIVALFA TGMRLISPTM LFFPFVLLLA ATALYRGGD NKMRTEEVDA ERADYLRYLS VVRDNVRAHA AEQRAALEWS HPEPEVLATI PGTRRQWERD PRDRDFLVLR A GRHDVPLD ...String: MSRLIFEHQR RLTPPTTRKG TITIEPPPQL PRVVPPSLLR RVLPFLIVIL IVGMIVALFA TGMRLISPTM LFFPFVLLLA ATALYRGGD NKMRTEEVDA ERADYLRYLS VVRDNVRAHA AEQRAALEWS HPEPEVLATI PGTRRQWERD PRDRDFLVLR A GRHDVPLD AALKVKDTAD EIDLEPVAHS ALRGLLDVQR TVRDAPTGLD VAKLARITVI GEADEARAAI RAWIAQAVTW HD PTMLGVA LAAPDLESGD WSWLKWLPHV DVPNEADGVG PARYLTTSTA ELRERLAPAL ADRPLFPAES GAALKHLLVV LDD PDADPD DIARKPGLTG VTVIHRTTEL PNREQYPDPE RPILRVADGR IERWQVGGWQ PCVDVADAMS AAEAAHIARR LSRW DSN UniProtKB: ESX-3 secretion system protein EccC3 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 5.52 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
Details: Solutions were made fresh and filter-sterilized before use. | ||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 7337 / Average electron dose: 73.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-6umm: |