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- EMDB-4897: MinCD filament from Pseudomonas aeruginosa -

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Basic information

Entry
Database: EMDB / ID: EMD-4897
TitleMinCD filament from Pseudomonas aeruginosa
Map dataPseudomonas aeruginosa MinCD filament
Sample
  • Complex: MinCD Filament
    • Protein or peptide: MinC
    • Protein or peptide: Site-determining protein
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Function / homology
Function and homology information


regulation of cell septum assembly / negative regulation of cell division / division septum assembly / regulation of cell division / cell morphogenesis / cytoplasmic side of plasma membrane / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Septum site-determining protein MinD / : / Septum site-determining protein MinD / Probable septum site-determining protein MinC
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSzewczak-Harris A / Wagstaff J / Lowe J
Funding support United Kingdom, 2 items
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, 2019-
Header (metadata) releaseMay 1, 2019-
Map releaseJun 19, 2019-
UpdateAug 21, 2019-
Current statusAug 21, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.032
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.032
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6riq
  • Surface level: 0.032
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4897.png

Downloads & links

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Map

FileDownload / File: emd_4897.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPseudomonas aeruginosa MinCD filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 396.96 Å		0.83 Å/pix.
x 480 pix.
= 396.96 Å		0.83 Å/pix.
x 480 pix.
= 396.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.032 / Movie #1: 0.032
Minimum - Maximum-0.1694421 - 0.24450353
Average (Standard dev.)-0.000018941068 (±0.0053541567)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 396.96002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8270.8270.827
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z396.960396.960396.960
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ858858858
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.1690.245-0.000

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Supplemental data

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Sample components

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Entire : MinCD Filament

EntireName: MinCD Filament
Components
  • Complex: MinCD Filament
    • Protein or peptide: MinC
    • Protein or peptide: Site-determining protein
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: MinCD Filament

SupramoleculeName: MinCD Filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: MinC

MacromoleculeName: MinC / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 15.107273 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KDSAPRKPAE EPSPSVGEAR PEPAKAEEKP AEPVSRPTKV VKTPVRGGMQ IYAAGGDLIV LAAVSPGAEL LADGNIHVYG PMRGRALAG VKGDATARIF CQQLAAELVS IAGNYKVAED LRRSPQWGKA VHVSLSGDVL NITRL

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Macromolecule #2: Site-determining protein

MacromoleculeName: Site-determining protein / type: protein_or_peptide / ID: 2 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 29.705143 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAKILVVTSG KGGVGKTTTS AAIGTGLALR GFKTVIVDFD VGLRNLDLIM GCERRVVYDF VNVVNGEATL TQALIKDKRL ENLHVLAAS QTRDKDALTK EGVEKVMAEL RKDFEYIICD SPAGIEKGAH LAMYFADEAI VVTNPEVSSV RDSDRMLGLL A SKSQRAEK ...String:
MAKILVVTSG KGGVGKTTTS AAIGTGLALR GFKTVIVDFD VGLRNLDLIM GCERRVVYDF VNVVNGEATL TQALIKDKRL ENLHVLAAS QTRDKDALTK EGVEKVMAEL RKDFEYIICD SPAGIEKGAH LAMYFADEAI VVTNPEVSSV RDSDRMLGLL A SKSQRAEK GEEPIKEHLL LTRYNPERVT KGEMLSVDDV EEILAIRLLG VIPESQAVLK ASNQGVPVIL DEQSDAGQAY SD AVDRLLG KEIPHRFLDV QKKGFLQRLF GGRE

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 11 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 11 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number real images: 3050 / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 24.998 Å
Applied symmetry - Helical parameters - Δ&Phi: 116.265 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 118659
Startup modelType of model: OTHER / Details: RELION 3
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL
Output model

PDB-6riq:
MinCD filament from Pseudomonas aeruginosa

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