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

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Basic information

Entry
Database: PDB / ID: 6umm
TitleA complete structure of the ESX-3 translocon complex
Components
  • ESX-3 secretion system ATPase EccB3
  • ESX-3 secretion system protein EccC3
  • ESX-3 secretion system protein EccD3
  • ESX-3 secretion system protein EccE3
KeywordsTRANSPORT PROTEIN / ESX / secretion system / type VII secretion system / mycobacteria / complex / membrane protein
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides / hydrolase activity / ATP hydrolysis activity / DNA binding / extracellular region / 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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Roll / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
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 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsPoweleit, N. / Rosenberg, O.S.
Funding support United States, 5items
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, 2019Deposition site: RCSB / Processing site: RCSB
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Structure visualization

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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ESX-3 secretion system protein EccE3
B: ESX-3 secretion system protein EccD3
C: ESX-3 secretion system protein EccD3
D: ESX-3 secretion system ATPase EccB3
E: ESX-3 secretion system protein EccC3
F: ESX-3 secretion system protein EccE3
G: ESX-3 secretion system protein EccD3
H: ESX-3 secretion system protein EccD3
I: ESX-3 secretion system ATPase EccB3
J: ESX-3 secretion system protein EccC3


Theoretical massNumber of molelcules
Total (without water)362,88510
Polymers362,88510
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ESX-3 secretion system protein EccE3 / ESX conserved component E3 / Type VII secretion system protein EccE3 / T7SS protein EccE3


Mass: 30813.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QQ48
#2: Protein
ESX-3 secretion system protein EccD3 / ESX conserved component D3 / Type VII secretion system protein EccD3 / T7SS protein EccD3


Mass: 48292.480 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QQ46
#3: Protein ESX-3 secretion system ATPase EccB3 / ESX conserved component B3 / Type VII secretion system protein EccB3 / T7SS protein EccB3


Mass: 9145.638 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
References: UniProt: A0QQ39, Hydrolases; Acting on acid anhydrides
#4: Protein ESX-3 secretion system protein EccC3 / ESX conserved component C3 / Type VII secretion system protein EccC3 / T7SS protein EccC3


Mass: 44898.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QQ40
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ESX-3 translocon complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.66 MDa / Experimental value: NO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Buffer solutionpH: 8
Details: Solutions were made fresh and filter-sterilized before use.
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris-HCLC4H11NO31
2150 mMsodium chlorideNaCl1
30.1 %GDNC56H92O251
SpecimenConc.: 5.52 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 73.5 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 7337

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameCategory
2SerialEMimage acquisition
4CTFFINDCTF correction
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 778149
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90479 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00624149
ELECTRON MICROSCOPYf_angle_d0.70833117
ELECTRON MICROSCOPYf_dihedral_angle_d13.9414455
ELECTRON MICROSCOPYf_chiral_restr0.0434059
ELECTRON MICROSCOPYf_plane_restr0.0054239

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