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- PDB-4a6j: Structural model of ParM filament based on CryoEM map -

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Basic information

Entry
Database: PDB / ID: 4a6j
TitleStructural model of ParM filament based on CryoEM map
ComponentsPLASMID SEGREGATION PROTEIN PARM
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


plasmid partitioning / identical protein binding
Similarity search - Function
Plasmid segregation protein ParM/StbA / : / Plasmid segregation protein ParM, N-terminal / Plasmid segregation protein ParM, C-terminal / ParM-like / ATPase, nucleotide binding domain
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Plasmid segregation protein ParM
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsGayathri, P. / Fujii, T. / Moller-Jensen, J. / Van Den Ent, F. / Namba, K. / Lowe, J.
CitationJournal: Science / Year: 2012
Title: A bipolar spindle of antiparallel ParM filaments drives bacterial plasmid segregation.
Authors: P Gayathri / T Fujii / J Møller-Jensen / F van den Ent / K Namba / J Löwe /
Abstract: To ensure their stable inheritance by daughter cells during cell division, bacterial low-copy-number plasmids make simple DNA segregating machines that use an elongating protein filament between ...To ensure their stable inheritance by daughter cells during cell division, bacterial low-copy-number plasmids make simple DNA segregating machines that use an elongating protein filament between sister plasmids. In the ParMRC system of the Escherichia coli R1 plasmid, ParM, an actinlike protein, forms the spindle between ParRC complexes on sister plasmids. By using a combination of structural work and total internal reflection fluorescence microscopy, we show that ParRC bound and could accelerate growth at only one end of polar ParM filaments, mechanistically resembling eukaryotic formins. The architecture of ParM filaments enabled two ParRC-bound filaments to associate in an antiparallel orientation, forming a bipolar spindle. The spindle elongated as a bundle of at least two antiparallel filaments, thereby pushing two plasmid clusters toward the poles.
History
DepositionNov 4, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-1980
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)363,34930
Polymers358,04410
Non-polymers5,30520
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
PLASMID SEGREGATION PROTEIN PARM / PARM / PARA LOCUS 36 KDA PROTEIN / PROTEIN STBA


Mass: 35804.375 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11904
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: PARM FILAMENT / Type: COMPLEX
Buffer solutionName: 30 MM TRIS-HCL, 25 MM KCL, 2 MM MGCL2, 1 MM DTT, 5MM AMPPNP
pH: 7.5
Details: 30 MM TRIS-HCL, 25 MM KCL, 2 MM MGCL2, 1 MM DTT, 5MM AMPPNP
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: LIQUID ETHENE

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC / Date: Aug 17, 2009
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 91463 X / Cs: 1.6 mm
Specimen holderTemperature: 50 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k)
Image scansNum. digital images: 207
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2SPIDER3D reconstruction
CTF correctionDetails: CTFFIND3 EACH PARTICLE
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 7.2 Å / Actual pixel size: 1.64 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMD-1980. (DEPOSITION ID: 10363).
Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY
Atomic model buildingPDB-ID: 4A62

4a62


Accession code: 4A62 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 7.2 Å
Refinement stepCycle: LAST / Highest resolution: 7.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25140 0 320 0 25460

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