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- PDB-6sgx: Structure of protomer 1 of the ESX-3 core complex -

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Basic information

Entry
Database: PDB / ID: 6sgx
TitleStructure of protomer 1 of the ESX-3 core complex
Components
  • ESX-3 secretion system EccB3
  • ESX-3 secretion system protein EccC3
  • ESX-3 secretion system protein EccD3
  • ESX-3 secretion system protein EccE3
KeywordsMEMBRANE PROTEIN / Type VII Secretion System ESX-3 secretion system T7SS ESX-3 Mycobacterium smegmatis
Function / homology
Function and homology information


Hydrolases, Acting on acid anhydrides / hydrolase activity / DNA binding / integral component of membrane / ATP binding / plasma membrane
EccCb-like, Actinobacteria / Type VII secretion system EccB, repeat 3 domain / FtsK domain profile. / Putative type VII ESX secretion system translocon, EccE / WXG100 protein secretion system (Wss), protein YukD / Type VII secretion system ESX-1, transport TM domain B / FtsK domain / AAA+ ATPase domain / Type VII secretion system membrane protein EccD / Type VII secretion system EccB ...EccCb-like, Actinobacteria / Type VII secretion system EccB, repeat 3 domain / FtsK domain profile. / Putative type VII ESX secretion system translocon, EccE / WXG100 protein secretion system (Wss), protein YukD / Type VII secretion system ESX-1, transport TM domain B / FtsK domain / AAA+ ATPase domain / Type VII secretion system membrane protein EccD / Type VII secretion system EccB / Type VII secretion system protein EccE / EccCa-like, Actinobacteria / FtsK/SpoIIIE family / YukD-like / P-loop containing nucleoside triphosphate hydrolase
ESX-3 secretion system ATPase EccB3 / ESX-3 secretion system protein EccC3 / ESX-3 secretion system protein EccD3 / ESX-3 secretion system protein EccE3
Biological speciesMycobacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsFamelis, N. / Rivera-Calzada, A. / Llorca, O. / Geibel, S.
Funding support Spain, Germany, 5items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesSAF2017-82632-P o-funded by the European Regional Development Fund Spain
European Regional Development FundY2018/BIO4747 co-funded by the Autonomous Region of Madrid Spain
European Regional Development FundP2018/NMT4443 co-funded by Autonomous Region of Madrid Spain
European UnionHorizon 2020, iNEXT (PID2907) , Grant number 653706 Spain
Bavarian State Ministry of Science and the Arts Funding OrganisationN-BM-2013-246 Germany
CitationJournal: Nature / Year: 2019
Title: Architecture of the ESX-3/Type VII secretion system
Authors: Famelis, N. / Rivera-Calzada, A. / Degliesposti, G. / Wingender, M. / Mietrach, N. / Skehel, J.M. / Fernandez-Leiro, R. / Bottcher, B. / Schlosser, A. / Llorca, O. / Geibel, S.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: ESX-3 secretion system 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


Theoretical massNumber of molelcules
Total (without water)178,5705
Polymers178,5705
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area18810 Å2
ΔGint-131 kcal/mol
Surface area72810 Å2
MethodPISA

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Components

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


Mass: 8875.269 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Gene: eccB3, MSMEG_0616, MSMEI_0600
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QQ39, Hydrolases, Acting on acid anhydrides
#2: Protein/peptide ESX-3 secretion system protein EccD3 / ESX conserved component D3 / Type VII secretion system protein EccD3 / T7SS protein EccD3


Mass: 47114.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Gene: eccD3, snm, MSMEG_0623, MSMEI_0607
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QQ46
#3: Protein/peptide ESX-3 secretion system protein EccC3 / ESX conserved component C3 / Type VII secretion system protein EccC3 / T7SS protein EccC3


Mass: 44653.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Gene: eccC3, MSMEG_0617, MSMEI_0601
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QQ40
#4: Protein/peptide 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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Gene: eccE3, MSMEG_0626, MSMEI_0609
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
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: Protomer1 of the ESX-3 core complex / Type: COMPLEX
Details: ESX-3 core complex The sample consists of four protein components, EccB3:EccC3:EccD3:EccE3 in a 1:1:2:1 stoichiometry Molecular weight of the complex without the amphipol micelle: 0.65 MDa
Entity ID: 1, 2, 3, 4 / Source: RECOMBINANT
Molecular weightValue: 0.65 MDa / Experimental value: YES
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Source (recombinant)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Plasmid: pMyNT
Buffer solutionpH: 8 / Details: 30 mM Hepes pH 8.0, 150 mM NaCl
SpecimenConc.: 0.3 mg/ml / Details: bound to Amphipol A8-35 / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K / Details: Blotting time: 3s Blotting force: -10

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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: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 1600 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 11903
Details: Images acquired as 55 frames movies at a calibrated magnification of 1.0635 Angs/px

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1RELIONparticle selection
2EPUimage acquisition
4GctfCTF correction
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
19PHENIX1.15.2-3472model refinementReal-space refinement
Image processingDetails: Images were collected in counting mode
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2066007
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126308
Details: In order to get the best possible resolution for protomer 1, the extra density not corresponding to this protomer was subtracted and masked out during the refinement.
Symmetry type: POINT
Atomic model buildingB value: 29.4 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Map correlation coefficient
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.00611436
f_angle_d1.00415655
f_dihedral_angle_d12.3386850
f_chiral_restr0.0591951
f_plane_restr0.0081974

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