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- PDB-7b9s: Structure of the mycobacterial ESX-5 Type VII Secretion System he... -

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Entry
Database: PDB / ID: 7b9s
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, repeat 1 domain / 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, repeat 1 domain / Type VII secretion system EccB / Type VII secretion system EccB, repeat 3 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: 3.4 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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  • Deposited structure unit
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  • EMDB-12105
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Structure viewerMolecule:
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Assembly

Deposited unit
E: EccE5
X: EccD5
C: EccC5
D: EccD5
B: EccB5
H: EccE5
I: EccD5
F: EccC5
G: EccD5
A: EccB5
M: EccE5
N: EccD5
K: EccC5
L: EccD5
J: EccB5
R: EccE5
S: EccD5
P: EccC5
Q: EccD5
O: EccB5
Y: EccE5
Z: EccD5
V: EccC5
W: EccD5
T: EccB5
4: EccE5
5: EccD5
2: EccC5
3: EccD5
1: EccB5


Theoretical massNumber of molelcules
Total (without water)2,144,64330
Polymers2,144,64330
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "O"
d_2ens_1chain "A"
d_3ens_1chain "B"
d_4ens_1chain "T"
d_5ens_1chain "J"
d_6ens_1chain "T"
d_1ens_2chain "K"
d_2ens_2chain "C"
d_3ens_2chain "F"
d_4ens_2chain "M"
d_5ens_2chain "P"
d_6ens_2chain "V"
d_1ens_3chain "R"
d_2ens_3chain "4"
d_3ens_3chain "H"
d_4ens_3chain "M"
d_5ens_3chain "E"
d_6ens_3chain "Y"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYSERT1 - 63
d_21ens_1GLYSERJ1 - 63
d_31ens_1GLYSERE1 - 63
d_41ens_1GLYSERY1 - 63
d_51ens_1GLYSERO1 - 63
d_61ens_1GLYSERT1 - 63
d_11ens_2ALALEUM1 - 396
d_21ens_2ALALEUC1 - 396
d_31ens_2ALALEUH1 - 396
d_41ens_2ALALEUM1 - 396
d_51ens_2ALALEUR1 - 396
d_61ens_2ALALEUW1 - 396
d_11ens_3ASPHISP1 - 165
d_21ens_3ASPHISZ1 - 165
d_31ens_3ASPHISF1 - 165
d_41ens_3ASPHISK1 - 165
d_51ens_3ASPHISA1 - 165
d_61ens_3ASPHISU1 - 165

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.999890041277, -0.0143164018042, -0.0038660049249), (0.0144431472698, -0.999281765218, -0.0350335439226), (-0.00336167393428, -0.0350855289574, 0.999378659371)267.521709602, 289.300151743, 3.70755751168
2given(0.498799439196, -0.866528905014, -0.0180769531063), (0.866709950931, 0.498773327448, 0.00624730205909), (0.00360283423841, -0.0187836259033, 0.999817080762)192.654345804, -43.2208319789, 1.42028041192
3given(-0.485188547295, -0.874164394665, -0.0207047017321), (0.874407452513, -0.485103296456, -0.00929509320692), (-0.00191847953577, -0.0226142182666, 0.999742425112)324.655432343, 99.4384312244, 2.22065250847
4given(0.497387415599, 0.867526839524, 0.00171508277706), (-0.867510931539, 0.497363756783, 0.00735371328543), (0.00552652363208, -0.00514549750369, 0.99997149029)-58.522443618, 187.416668939, -0.172626390114
5given(-0.507816499799, 0.861422001125, 0.00863356876002), (-0.861464943321, -0.507799465917, -0.00422538086712), (0.000744285563221, -0.00958323494477, 0.999953802756)75.2077370257, 332.418255116, 0.860682759029
6given(-0.500865524179, -0.865525108909, -0.000111970279531), (0.865524708127, -0.500865409485, 0.000906202526337), (-0.000840423080208, 0.000356972559856, 0.99999958313)324.430040873, 101.764997994, 0.0298932883768
7given(0.499924113885, 0.866067896716, -0.00150951429542), (-0.866069200852, 0.499923630373, -0.000709316457192), (0.000140325654478, 0.00166194824083, 0.999998609117)-58.5645282596, 187.402456231, -0.314696862356
8given(-0.499624338265, 0.86624179186, -0.000823801177224), (-0.866241892484, -0.499623164792, 0.00129495510904), (0.000710154082708, 0.00136060218022, 0.999998822221)74.1718531714, 331.639996283, -0.336283100232
9given(0.499521357036, -0.866301539651, 0.000237198507526), (0.866301562482, 0.499521373604, 1.24275140404E-5), (-0.000129251698843, 0.00019927762901, 0.999999971791)191.633065296, -42.7581863502, -0.0322714383786
10given(-0.999999925065, 0.000385346328172, 3.71328652021E-5), (-0.0003852896138, -0.999998777515, 0.00151542746651), (3.77167842175E-5, 0.00151541304604, 0.99999885105)265.675165249, 288.856952573, -0.287446833795
11given(0.498633646176, 0.86680842899, -0.00276302971018), (-0.866812817467, 0.498631701432, -0.00140207073214), (0.000162407476829, 0.00309414920919, 0.999995199921)-58.2250862785, 187.686142427, -0.252594502023
12given(0.499725807856, -0.866118680066, 0.0106089114674), (0.865940377491, 0.499838243939, 0.0175781832566), (-0.0205275325581, 0.000402412972272, 0.999789207019)191.138530303, -43.8884008072, 2.99902320983
13given(-0.498323886762, -0.866938916766, -0.00949834082208), (0.866950917511, -0.498376249927, 0.00414971506929), (-0.0083312969665, -0.00616669314825, 0.99994627925)324.891734333, 101.303160815, 1.36133391879
14given(-0.999988462054, 0.000312630559637, -0.00479353947055), (-0.00030525821857, -0.999998769718, -0.00153862892792), (-0.00479401459557, -0.00153714790798, 0.99998732722)265.965484942, 289.117693133, 0.656102253374
15given(-0.498470375287, 0.866901806736, 0.00292274527285), (-0.866906079384, -0.498463023698, -0.00290921517288), (-0.00106512344335, -0.00398390322454, 0.999991496977)73.7454053434, 332.014498995, 0.17244656887

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Components

#1: Protein
EccE5


Mass: 44469.617 Da / Num. of mol.: 6
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.: 12
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.: 6
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.: 6
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: Hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, EccD5-1, EccD5-2, EccE
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 2.142 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 mMNaClSodium chloride1
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 FIELDBright-field microscopy / 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
IDNameVersionCategory
1cryoSPARC2.14particle selection
2SerialEMimage acquisition
4cryoSPARC2.14CTF correction
7Coot0.9-premodel fitting
8ISOLDE1.1.0model fitting
9UCSF Chimera1.14model fitting
11cryoSPARC2.14initial Euler assignment
12cryoSPARC2.14final Euler assignment
14cryoSPARC2.143D reconstruction
21PHENIX1.18.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121974 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Details: Model was initially fitted using ChimeraX and then completed manually using Coot and ISOLDE.
Atomic model buildingPDB-ID: 7B9F

7b9f


Accession code: 7B9F / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 154.5 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006473728
ELECTRON MICROSCOPYf_angle_d1.0254100824
ELECTRON MICROSCOPYf_chiral_restr0.060712048
ELECTRON MICROSCOPYf_plane_restr0.007812648
ELECTRON MICROSCOPYf_dihedral_angle_d16.870126106
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2TELECTRON MICROSCOPYNCS constraints0.000701791195521
ens_1d_3TELECTRON MICROSCOPYNCS constraints0.000707416431641
ens_1d_4TELECTRON MICROSCOPYNCS constraints0.000694177145372
ens_1d_5TELECTRON MICROSCOPYNCS constraints0.000706406123251
ens_1d_6TELECTRON MICROSCOPYNCS constraints0.000701241636674
ens_2d_2MELECTRON MICROSCOPYNCS constraints0.000709464289852
ens_2d_3MELECTRON MICROSCOPYNCS constraints0.000702595161572
ens_2d_4MELECTRON MICROSCOPYNCS constraints0.000707671007957
ens_2d_5MELECTRON MICROSCOPYNCS constraints0.000713127691764
ens_2d_6MELECTRON MICROSCOPYNCS constraints0.000703327313669
ens_3d_2PELECTRON MICROSCOPYNCS constraints0.000701807648981
ens_3d_3PELECTRON MICROSCOPYNCS constraints0.000710024787917
ens_3d_4PELECTRON MICROSCOPYNCS constraints0.000703159853849
ens_3d_5PELECTRON MICROSCOPYNCS constraints0.000708853415282
ens_3d_6PELECTRON MICROSCOPYNCS constraints0.000709872599618

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