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- EMDB-20820: A complete structure of the ESX-3 translocon complex -

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Basic information

Entry
Database: EMDB / ID: EMD-20820
TitleA complete structure of the ESX-3 translocon complex
Map dataConsensus map used to generate all focused refinements. Unsharpened
Sample
  • Complex: ESX-3 translocon complex
    • Protein or peptide: ESX-3 secretion system protein EccE3
    • Protein or peptide: ESX-3 secretion system protein EccD3
    • Protein or peptide: ESX-3 secretion system ATPase EccB3
    • Protein or peptide: ESX-3 secretion system protein EccC3
KeywordsESX / secretion system / type VII secretion system / mycobacteria / complex / membrane protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides / hydrolase activity / ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane
Similarity search - Function
: / Type VII secretion system protein EccE / Putative type VII ESX secretion system translocon, EccE / Type VII secretion system membrane protein EccD / YukD-like / WXG100 protein secretion system (Wss), protein YukD / EccCa-like, Actinobacteria / EccCb-like, Actinobacteria / Type VII secretion system EccB / Type VII secretion system EccB, repeat 3 domain ...: / Type VII secretion system protein EccE / Putative type VII ESX secretion system translocon, EccE / Type VII secretion system membrane protein EccD / YukD-like / WXG100 protein secretion system (Wss), protein YukD / EccCa-like, Actinobacteria / EccCb-like, Actinobacteria / Type VII secretion system EccB / Type VII secretion system EccB, repeat 3 domain / Type VII secretion system EccB, repeat 1 domain / Type VII secretion system ESX-1, transport TM domain B / : / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ESX-3 secretion system ATPase EccB3 / ESX-3 secretion system protein EccC3 / ESX-3 secretion system protein EccD3 / ESX-3 secretion system protein EccE3
Similarity search - Component
Biological speciesMycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsPoweleit N / Rosenberg OS
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1RO1AI128214 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1U19AI135990-01 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)PO1AI095208 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5T32AI060537 United States
National Institutes of Health/Office of the Director1S10OD021741 United States
CitationJournal: Elife / Year: 2019
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
DepositionOct 9, 2019-
Header (metadata) releaseOct 23, 2019-
Map releaseOct 23, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.004
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.004
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6umm
  • Surface level: 0.004
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6umm
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20820.png

Downloads & links

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Map

FileDownload / File: emd_20820.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus map used to generate all focused refinements. Unsharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 440 pix.
= 360.8 Å		0.82 Å/pix.
x 440 pix.
= 360.8 Å		0.82 Å/pix.
x 440 pix.
= 360.8 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004 / Movie #1: 0.004
Minimum - Maximum0.0 - 1.0
Average (Standard dev.)0.007542188 (±0.081103444)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 288.63998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z360.800360.800360.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.0060.0230.000

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Supplemental data

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Mask #1

Fileemd_20820_msk_1.map
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Mask #2

Fileemd_20820_msk_2.map
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Mask #3

Fileemd_20820_msk_3.map
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Mask #4

Fileemd_20820_msk_4.map
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Mask #5

Fileemd_20820_msk_5.map
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Additional map: Focused refinement of the EccC ATPase 1, 2,...

Fileemd_20820_additional_1.map
AnnotationFocused refinement of the EccC ATPase 1, 2, and 3 domains. Unsharpened
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Additional map: Half1 of right protomer focused refinement.

Fileemd_20820_additional_10.map
AnnotationHalf1 of right protomer focused refinement.
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Additional map: Half2 of left protomer focused refinement

Fileemd_20820_additional_11.map
AnnotationHalf2 of left protomer focused refinement
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Additional map: Half1 of left protomer focused refinement

Fileemd_20820_additional_12.map
AnnotationHalf1 of left protomer focused refinement
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Additional map: Focused refinement of right protomer. Unsharpened

Fileemd_20820_additional_13.map
AnnotationFocused refinement of right protomer. Unsharpened
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Additional map: Focused refinement of symmetry expanded protomer. Unsharpened

Fileemd_20820_additional_2.map
AnnotationFocused refinement of symmetry expanded protomer. Unsharpened
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Additional map: Half2 of periplasmic focused refinement

Fileemd_20820_additional_3.map
AnnotationHalf2 of periplasmic focused refinement
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Additional map: Half1 of periplasmic focused refinement

Fileemd_20820_additional_4.map
AnnotationHalf1 of periplasmic focused refinement
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Additional map: Focused refinement of left protomer. Unsharpened

Fileemd_20820_additional_5.map
AnnotationFocused refinement of left protomer. Unsharpened
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Additional map: Focused refinement of periplasmic domain. Unsharpened

Fileemd_20820_additional_6.map
AnnotationFocused refinement of periplasmic domain. Unsharpened
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Additional map: Half2 of symmetry expanded protomer

Fileemd_20820_additional_7.map
AnnotationHalf2 of symmetry expanded protomer
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Additional map: Half1 of symmetry expanded protomer

Fileemd_20820_additional_8.map
AnnotationHalf1 of symmetry expanded protomer
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Additional map: Half2 of right protomer focused refinement

Fileemd_20820_additional_9.map
AnnotationHalf2 of right protomer focused refinement
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Half map: Half2 of consensus map

Fileemd_20820_half_map_1.map
AnnotationHalf2 of consensus map
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Half map: Half1 of consensus map

Fileemd_20820_half_map_2.map
AnnotationHalf1 of consensus map
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Sample components

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Entire : ESX-3 translocon complex

EntireName: ESX-3 translocon complex
Components
  • Complex: ESX-3 translocon complex
    • Protein or peptide: ESX-3 secretion system protein EccE3
    • Protein or peptide: ESX-3 secretion system protein EccD3
    • Protein or peptide: ESX-3 secretion system ATPase EccB3
    • Protein or peptide: ESX-3 secretion system protein EccC3

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Supramolecule #1: ESX-3 translocon complex

SupramoleculeName: ESX-3 translocon complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 660 KDa

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Macromolecule #1: ESX-3 secretion system protein EccE3

MacromoleculeName: ESX-3 secretion system protein EccE3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 30.813355 KDa
SequenceString: 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

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Macromolecule #2: ESX-3 secretion system protein EccD3

MacromoleculeName: ESX-3 secretion system protein EccD3 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 48.29248 KDa
SequenceString: 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

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Macromolecule #3: ESX-3 secretion system ATPase EccB3

MacromoleculeName: 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
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 9.145638 KDa
SequenceString:
FSSRTPVNEN PDGVQYRRGF VTRHQVSGWR FVMRRIASGV ALHDTRMLVD PLRTQSRAVL TGALILVTGL VGCFIFSLFR P

UniProtKB: ESX-3 secretion system ATPase EccB3

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Macromolecule #4: ESX-3 secretion system protein EccC3

MacromoleculeName: ESX-3 secretion system protein EccC3 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 44.898371 KDa
SequenceString: 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

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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

Concentration5.52 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris-HCL
150.0 mMNaClsodium chloride
0.1 %C56H92O25GDN

Details: Solutions were made fresh and filter-sterilized before use.
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen 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

Particle selectionNumber selected: 778149
Startup modelType of model: INSILICO MODEL / In silico model: Initially generated by SDG
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 90479
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 4 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6umm:
A complete structure of the ESX-3 translocon complex

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