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- PDB-6lar: Structure of ESX-3 complex -

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Basic information

Entry
Database: PDB / ID: 6lar
TitleStructure of ESX-3 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
KeywordsMEMBRANE 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 speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang, S.H. / Zhou, K.X. / Li, J. / Rao, Z.H.
CitationJournal: To Be Published
Title: cryo-em structure of esx-3
Authors: Wang, S.H. / Zhou, K.X. / Li, J. / Rao, Z.H.
History
DepositionNov 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-0862
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)466,79410
Polymers466,79410
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area37430 Å2
ΔGint-259 kcal/mol
Surface area150870 Å2

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Components

#1: Protein ESX-3 secretion system ATPase EccB3 / ESX conserved component B3 / Type VII secretion system protein EccB3 / T7SS protein EccB3


Mass: 53684.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2 155 / Gene: eccB3 / Production host: Escherichia coli (E. coli)
References: UniProt: A0QQ39, Hydrolases; Acting on acid anhydrides
#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 genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2 155 / Gene: eccD3 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QQ46
#3: Protein ESX-3 secretion system protein EccC3 / ESX conserved component C3 / Type VII secretion system protein EccC3 / T7SS protein EccC3


Mass: 49900.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2 155 / Gene: eccC3 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QQ40
#4: Protein ESX-3 secretion system protein EccE3 / ESX conserved component E3 / Type VII secretion system protein EccE3 / T7SS protein EccE3


Mass: 33226.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2 155 / Gene: eccE3 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QQ48

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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 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.FormulaBuffer-ID
120 mMHEPES1
2100 mMNaCl1
SpecimenConc.: 5 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: 281 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: SPOT SCAN
Electron lensMode: OTHER / Nominal magnification: 29000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 4823
Image scansWidth: 5760 / Height: 4092

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Processing

EM softwareName: SerialEM / Category: image acquisition
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 215839 / Symmetry type: POINT

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