4A6J | pdb_00004a6j

Structural model of ParM filament based on CryoEM map

PDB DOI: https://doi.org/10.2210/pdb4A6J/pdb
EM Map EMD-1980: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-11-04 Released: 2012-11-21
Deposition Author(s): Gayathri, P., Fujii, T., Moller-Jensen, J., Van Den Ent, F., Namba, K., Lowe, J.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 7.20 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

A Bipolar Spindle of Antiparallel Parm Filaments Drives Bacterial Plasmid Segregation.

Gayathri, P., Fujii, T., Moller-Jensen, J., Van Den Ent, F., Namba, K., Lowe, J.

(2012) Science 338: 1334

PubMed: 23112295 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.1229091
Primary Citation Related Structures:
4A61, 4A62, 4A6J

PubMed 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 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.

Organizational Affiliation

Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.

Macromolecule Content

Total Structure Weight: 363.35 kDa
Atom Count: 25,490
Modeled Residue Count: 3,200
Deposited Residue Count: 3,200
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PLASMID SEGREGATION PROTEIN PARM	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	320	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P11904 (Escherichia coli) Explore P11904 Go to UniProtKB: P11904
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11904
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain Y [auth H] SDF format, chain W [auth G] SDF format, chain U [auth F] SDF format, chain S [auth E] SDF format, chain Q [auth D] SDF format, chain O [auth C] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain CA [auth J] SDF format, chain AA [auth I] MOL2 format, chain Y [auth H] MOL2 format, chain W [auth G] MOL2 format, chain U [auth F] MOL2 format, chain S [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth C] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain CA [auth J] MOL2 format, chain AA [auth I] mmCIF format, chain Y [auth H] mmCIF format, chain W [auth G] mmCIF format, chain U [auth F] mmCIF format, chain S [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth C] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain CA [auth J] mmCIF format, chain AA [auth I]	AA [auth I] CA [auth J] K [auth A] M [auth B] O [auth C] AA [auth I], CA [auth J], K [auth A], M [auth B], O [auth C], Q [auth D], S [auth E], U [auth F], W [auth G], Y [auth H]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain AA [auth I] Focus chain CA [auth J] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H] Interactions & Density Focus chain AA [auth I] Focus chain CA [auth J] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Z [auth H] SDF format, chain X [auth G] SDF format, chain V [auth F] SDF format, chain T [auth E] SDF format, chain R [auth D] SDF format, chain P [auth C] SDF format, chain N [auth B] SDF format, chain L [auth A] SDF format, chain DA [auth J] SDF format, chain BA [auth I] MOL2 format, chain Z [auth H] MOL2 format, chain X [auth G] MOL2 format, chain V [auth F] MOL2 format, chain T [auth E] MOL2 format, chain R [auth D] MOL2 format, chain P [auth C] MOL2 format, chain N [auth B] MOL2 format, chain L [auth A] MOL2 format, chain DA [auth J] MOL2 format, chain BA [auth I] mmCIF format, chain Z [auth H] mmCIF format, chain X [auth G] mmCIF format, chain V [auth F] mmCIF format, chain T [auth E] mmCIF format, chain R [auth D] mmCIF format, chain P [auth C] mmCIF format, chain N [auth B] mmCIF format, chain L [auth A] mmCIF format, chain DA [auth J] mmCIF format, chain BA [auth I]	BA [auth I] DA [auth J] L [auth A] N [auth B] P [auth C] BA [auth I], DA [auth J], L [auth A], N [auth B], P [auth C], R [auth D], T [auth E], V [auth F], X [auth G], Z [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth I] Focus chain DA [auth J] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H] Interactions & Density Focus chain BA [auth I] Focus chain DA [auth J] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 7.20 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	SPIDER

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-11-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-11-21
Type: Initial release
Version 1.1: 2012-12-19
Changes: Database references
Version 1.2: 2017-08-23
Changes: Data collection
Version 1.3: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Refinement description