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- PDB-5ai7: ParM doublet model -

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Basic information

Entry
Database: PDB / ID: 5ai7
TitleParM doublet model
ComponentsPLASMID SEGREGATION PROTEIN PARM
KeywordsMOTOR PROTEIN / PARM / ACTIN-LIKE PROTEIN / DOUBLET / ANTIPARALLEL
Function / homologyPlasmid segregation protein ParM/StbA / : / Plasmid segregation protein ParM, N-terminal / Plasmid segregation protein ParM, C-terminal / ParM-like / plasmid partitioning / ATPase, nucleotide binding domain / identical protein binding / Plasmid segregation protein ParM
Function and homology information
Biological speciesESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM
Model type detailsCA ATOMS ONLY, CHAIN A, B, C, D, E, F, G, H, I, J, K, L, M, N
AuthorsBharat, T.A.M. / Murshudov, G.N. / Sachse, C. / Lowe, J.
CitationJournal: Nature / Year: 2015
Title: Structures of actin-like ParM filaments show architecture of plasmid-segregating spindles.
Authors: Tanmay A M Bharat / Garib N Murshudov / Carsten Sachse / Jan Löwe /
Abstract: Active segregation of Escherichia coli low-copy-number plasmid R1 involves formation of a bipolar spindle made of left-handed double-helical actin-like ParM filaments. ParR links the filaments with ...Active segregation of Escherichia coli low-copy-number plasmid R1 involves formation of a bipolar spindle made of left-handed double-helical actin-like ParM filaments. ParR links the filaments with centromeric parC plasmid DNA, while facilitating the addition of subunits to ParM filaments. Growing ParMRC spindles push sister plasmids to the cell poles. Here, using modern electron cryomicroscopy methods, we investigate the structures and arrangements of ParM filaments in vitro and in cells, revealing at near-atomic resolution how subunits and filaments come together to produce the simplest known mitotic machinery. To understand the mechanism of dynamic instability, we determine structures of ParM filaments in different nucleotide states. The structure of filaments bound to the ATP analogue AMPPNP is determined at 4.3 Å resolution and refined. The ParM filament structure shows strong longitudinal interfaces and weaker lateral interactions. Also using electron cryomicroscopy, we reconstruct ParM doublets forming antiparallel spindles. Finally, with whole-cell electron cryotomography, we show that doublets are abundant in bacterial cells containing low-copy-number plasmids with the ParMRC locus, leading to an asynchronous model of R1 plasmid segregation.
History
DepositionFeb 12, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jul 15, 2015Group: Database references
Revision 1.3Aug 30, 2017Group: Data collection / Derived calculations
Category: em_image_scans / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Oct 3, 2018Group: Data collection
Category: diffrn_radiation / diffrn_radiation_wavelength / em_software
Item: _em_software.image_processing_id
Revision 1.5Nov 6, 2019Group: Data collection / Database references / Category: pdbx_database_related

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Structure visualization

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Assembly

Deposited unit
A: PLASMID SEGREGATION PROTEIN PARM
B: PLASMID SEGREGATION PROTEIN PARM
C: PLASMID SEGREGATION PROTEIN PARM
D: PLASMID SEGREGATION PROTEIN PARM
E: PLASMID SEGREGATION PROTEIN PARM
F: PLASMID SEGREGATION PROTEIN PARM
G: PLASMID SEGREGATION PROTEIN PARM
H: PLASMID SEGREGATION PROTEIN PARM
I: PLASMID SEGREGATION PROTEIN PARM
J: PLASMID SEGREGATION PROTEIN PARM
K: PLASMID SEGREGATION PROTEIN PARM
L: PLASMID SEGREGATION PROTEIN PARM
M: PLASMID SEGREGATION PROTEIN PARM
N: PLASMID SEGREGATION PROTEIN PARM


Theoretical massNumber of molelcules
Total (without water)498,86514
Polymers498,86514
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

#1: Protein
PLASMID SEGREGATION PROTEIN PARM / PARA LOCUS 36 KDA PROTEIN / PROTEIN STBA / Coordinate model: Cα atoms only


Mass: 35633.223 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Details: THIS IS A MODEL OF THE PARM DOUBLET BASED ON CRYO-EM DATA. ONLY CARBON-ALPHAS HAVE BEEN DEPOSITED.
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI / References: UniProt: P11904

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: PARM ANTIPARALLEL DOUBLET / Type: COMPLEX
Buffer solutionName: 50 MM TRIS-HCL, 100 MM KCL, AND 1 MM MGCL2, 2% PEG 6000
pH: 7
Details: 50 MM TRIS-HCL, 100 MM KCL, AND 1 MM MGCL2, 2% PEG 6000
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationDetails: VIROBOT MARK IV (FEI)

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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 defocus max: 6000 nm / Nominal defocus min: 3000 nm / Cs: 2.7 mm
Image recordingElectron dose: 0.3 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM softwareName: SPRING / Category: 3D reconstruction / Details: SPRING (DESFOSSES AND SACHSE)
3D reconstructionMethod: CRYO-EM ALIGNMENT
Details: THIS IS A MODEL OF THE PARM ANTIPARALLEL ANTIPARALLEL DOUBLET BASED ON CRYOEM DATA. TWO COPIES OF THE PARM AMPPNP CRYO-EM FILAMENT STRUCTURE WERE PLACED IN AN ANTIPARALLEL ORIENTATION. ...Details: THIS IS A MODEL OF THE PARM ANTIPARALLEL ANTIPARALLEL DOUBLET BASED ON CRYOEM DATA. TWO COPIES OF THE PARM AMPPNP CRYO-EM FILAMENT STRUCTURE WERE PLACED IN AN ANTIPARALLEL ORIENTATION. ANTIPARALLEL ASSIGNMENT WAS DONE USING CRYO-EM ALIGNMENT. THIS IS A MODEL OF THE PARM ANTIPARALLEL DOUBLET CONSTRUCTED USING CRYO-EM DATA. ONLY C-ALPHAS HAVE BEEN DEPOSITED.
Symmetry type: HELICAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms4452 0 0 0 4452

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