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- PDB-7b9f: Structure of the mycobacterial ESX-5 Type VII Secretion System he... -

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Basic information

Entry
Database: PDB / ID: 7b9f
TitleStructure of the mycobacterial ESX-5 Type VII Secretion System hexameric pore complex
Components
  • EccB5
  • EccC5
  • EccD5
  • EccE5
KeywordsTRANSPORT PROTEIN / Mycobacterial ESX-5 Type VII Secretion System
Function / homology
Function and homology information


hydrolase activity / ATP hydrolysis activity / DNA binding / ATP binding / membrane / 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 EccB, repeat 1 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
Secretion protein Snm4 / Type VII secretion protein EccE / Type VII secretion protein EccB / FtsK domain-containing protein
Similarity search - Component
Biological speciesMycobacterium xenopi RIVM700367 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsChojnowski, G. / Ritter, C. / Beckham, K.S.H. / Mullapudi, E. / Rettel, M. / Savitski, M.M. / Mortensen, S.A. / Ziemianowicz, D. / Kosinski, J. / Wilmanns, M.
CitationJournal: Sci Adv / Year: 2021
Title: Structure of the mycobacterial ESX-5 type VII secretion system pore complex.
Authors: Katherine S H Beckham / Christina Ritter / Grzegorz Chojnowski / Daniel S Ziemianowicz / Edukondalu Mullapudi / Mandy Rettel / Mikhail M Savitski / Simon A Mortensen / Jan Kosinski / Matthias Wilmanns /
Abstract: The ESX-5 type VII secretion system is a membrane-spanning protein complex key to the virulence of mycobacterial pathogens. However, the overall architecture of the fully assembled translocation ...The ESX-5 type VII secretion system is a membrane-spanning protein complex key to the virulence of mycobacterial pathogens. However, the overall architecture of the fully assembled translocation machinery and the composition of the central secretion pore have remained unknown. Here, we present the high-resolution structure of the 2.1-megadalton ESX-5 core complex. Our structure captured a dynamic, secretion-competent conformation of the pore within a well-defined transmembrane section, sandwiched between two flexible protein layers at the cytosolic entrance and the periplasmic exit. We propose that this flexibility endows the ESX-5 machinery with large conformational plasticity required to accommodate targeted protein secretion. Compared to known secretion systems, a highly dynamic state of the pore may represent a fundamental principle of bacterial secretion machineries.
History
DepositionDec 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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  • Superimposition on EM map
  • EMDB-12103
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Structure viewerMolecule:
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Assembly

Deposited unit
E: EccE5
X: EccD5
C: EccC5
D: EccD5
B: EccB5


Theoretical massNumber of molelcules
Total (without water)357,4405
Polymers357,4405
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: focused-refinement map of a hexameric complex protomer
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area20550 Å2
ΔGint-150 kcal/mol
Surface area69750 Å2
MethodPISA

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Components

#1: Protein EccE5


Mass: 44469.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium xenopi RIVM700367 (bacteria)
Gene: MXEN_09224
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: I0RST0
#2: Protein EccD5


Mass: 53399.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium xenopi RIVM700367 (bacteria)
Gene: MXEN_09214
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: I0RSS8
#3: Protein EccC5


Mass: 152946.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium xenopi RIVM700367 (bacteria)
Gene: MXEN_04114
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: I0RZI0
#4: Protein EccB5


Mass: 53226.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium xenopi RIVM700367 (bacteria)
Gene: MXEN_04109
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: I0RZH9

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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: Protomeric unit of the hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, EccD5-1, EccD5-2, EccE
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.357 MDa / Experimental value: NO
Source (natural)Organism: Mycobacterium xenopi RIVM700367 (bacteria) / Cellular location: membrane
Source (recombinant)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameBuffer-ID
120 mMTris pH 8.01
2150 mMNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 283 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 / Nominal magnification: 130000 X / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 49.34 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 27873

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
EM software
IDNameVersionCategoryDetails
1cryoSPARC2.14particle selection
2SerialEMimage acquisition
4cryoSPARC2.14CTF correction
7ARP/wARP8.1model fittingwebservice
8Coot0.9-premodel fitting
9ISOLDE1.1.0model fitting
11cryoSPARC2.14initial Euler assignment
12cryoSPARC2.14final Euler assignment
14cryoSPARC2.143D reconstruction
21PHENIX1.18.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 731844 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Details: Initial model was build into the map using ARP/wARP 8.1 web-service.
Atomic model buildingPDB-ID: 7B7J

7b7j


Accession code: 7B7J / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 128.07 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007711530
ELECTRON MICROSCOPYf_angle_d0.980615771
ELECTRON MICROSCOPYf_chiral_restr0.05991891
ELECTRON MICROSCOPYf_plane_restr0.00681983
ELECTRON MICROSCOPYf_dihedral_angle_d15.94911603

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