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- PDB-6riq: MinCD filament from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6riq
TitleMinCD filament from Pseudomonas aeruginosa
Components
  • MinC
  • Site-determining protein
KeywordsPROTEIN FIBRIL / Bacterial cell division
Function / homology
Function and homology information


regulation of cell septum assembly / negative regulation of cell division / division septum assembly / regulation of cell division / cytoplasmic side of plasma membrane / cell morphogenesis / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
Septum formation inhibitor MinC, N-terminal / ATP binding protein MinD / Septum formation inhibitor MinC, N-terminal domain / Septum formation inhibitor MinC, C-terminal / Septum formation inhibitor MinC / Septum formation inhibitor MinC, C-terminal domain superfamily / Septum formation inhibitor MinC, C-terminal domain / CobQ/CobB/MinD/ParA nucleotide binding domain / ATP binding protein MinD/FleN / Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal ...Septum formation inhibitor MinC, N-terminal / ATP binding protein MinD / Septum formation inhibitor MinC, N-terminal domain / Septum formation inhibitor MinC, C-terminal / Septum formation inhibitor MinC / Septum formation inhibitor MinC, C-terminal domain superfamily / Septum formation inhibitor MinC, C-terminal domain / CobQ/CobB/MinD/ParA nucleotide binding domain / ATP binding protein MinD/FleN / Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal / CobQ/CobB/MinD/ParA nucleotide binding domain / : / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Septum site-determining protein MinD / : / Septum site-determining protein MinD / Probable septum site-determining protein MinC
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSzewczak-Harris, A. / Wagstaff, J. / Lowe, J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust202754/Z/16/Z United Kingdom
Medical Research Council (United Kingdom)U105184326 United Kingdom
CitationJournal: FEBS Lett / Year: 2019
Title: Cryo-EM structure of the MinCD copolymeric filament from Pseudomonas aeruginosa at 3.1 Å resolution.
Authors: Andrzej Szewczak-Harris / James Wagstaff / Jan Löwe /
Abstract: Positioning of the division site in many bacterial species relies on the MinCDE system, which prevents the cytokinetic Z-ring from assembling anywhere but the mid-cell, through an oscillatory ...Positioning of the division site in many bacterial species relies on the MinCDE system, which prevents the cytokinetic Z-ring from assembling anywhere but the mid-cell, through an oscillatory diffusion-reaction mechanism. MinD dimers bind to membranes and, via their partner MinC, inhibit the polymerization of cell division protein FtsZ into the Z-ring. MinC and MinD form polymeric assemblies in solution and on cell membranes. Here, we report the high-resolution cryo-EM structure of the copolymeric filaments of Pseudomonas aeruginosa MinCD. The filaments consist of three protofilaments made of alternating MinC and MinD dimers. The MinCD protofilaments are almost completely straight and assemble as single protofilaments on lipid membranes, which we also visualized by cryo-EM.
History
DepositionApr 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.0Jun 19, 2019Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 19, 2019Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 19, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 19, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jun 19, 2019Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 19, 2019Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 19, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 19, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / em_image_scans
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.1Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: database_2 / em_admin / Data content type: EM metadata / EM metadata / EM metadata
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update
Revision 1.3Oct 1, 2025Group: Advisory / Data collection / Derived calculations
Category: em_admin / pdbx_validate_close_contact ...em_admin / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _em_admin.last_update
Revision 1.2Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: MinC
B: MinC
C: Site-determining protein
D: Site-determining protein
E: MinC
F: MinC
G: Site-determining protein
H: MinC
I: MinC
J: Site-determining protein
K: Site-determining protein
L: MinC
M: Site-determining protein
N: Site-determining protein
O: MinC
P: MinC
Q: Site-determining protein
R: Site-determining protein
S: MinC
T: MinC
U: Site-determining protein
V: Site-determining protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)498,78344
Polymers492,93722
Non-polymers5,84622
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, this study
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area55640 Å2
ΔGint-168 kcal/mol
Surface area133440 Å2
MethodPISA

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Components

#1: Protein
MinC


Mass: 15107.273 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2R4B4N7, UniProt: Q9HYZ7*PLUS
#2: Protein
Site-determining protein


Mass: 29705.143 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: minD, minD_2, ALP65_02808, C0044_24365, C8257_09550, CAZ10_22480, CGU42_07990, DZ940_07140, DZ962_16115, EFK68_22340, EGV95_09885, EGY23_16190, IPC1135_03845, NCTC13719_01733, PAERUG_E15_London_ ...Gene: minD, minD_2, ALP65_02808, C0044_24365, C8257_09550, CAZ10_22480, CGU42_07990, DZ940_07140, DZ962_16115, EFK68_22340, EGV95_09885, EGY23_16190, IPC1135_03845, NCTC13719_01733, PAERUG_E15_London_28_01_14_02879, RW109_RW109_02577
Production host: Escherichia coli (E. coli) / References: UniProt: A0A071KWM5, UniProt: Q9HYZ6*PLUS
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: MinCD Filament / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 38 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 3050

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 116.265 ° / Axial rise/subunit: 24.998 Å / Axial symmetry: C1
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 118659 / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: RECIPROCAL

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