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- PDB-7npf: Vibrio cholerae ParA2-ATPyS-DNA filament -

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Basic information

Entry
Database: PDB / ID: 7npf
TitleVibrio cholerae ParA2-ATPyS-DNA filament
Components
  • (DNA (49-MER)) x 2
  • AAA family ATPase
KeywordsDNA BINDING PROTEIN / ATPase / Chromosome segregation / Bacterial cell division / filament
Function / homologyAAA domain / AAA domain / P-loop containing nucleoside triphosphate hydrolase / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / Chromosome partitioning protein ParA
Function and homology information
Biological speciesVibrio cholerae (bacteria)
Neoarius leptaspis (salmon catfish)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsParker, A.V. / Bergeron, J.R.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Not funded United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: The structure of the bacterial DNA segregation ATPase filament reveals the conformational plasticity of ParA upon DNA binding.
Authors: Alexandra V Parker / Daniel Mann / Svetomir B Tzokov / Ling C Hwang / Julien R C Bergeron /
Abstract: The efficient segregation of replicated genetic material is an essential step for cell division. Bacterial cells use several evolutionarily-distinct genome segregation systems, the most common of ...The efficient segregation of replicated genetic material is an essential step for cell division. Bacterial cells use several evolutionarily-distinct genome segregation systems, the most common of which is the type I Par system. It consists of an adapter protein, ParB, that binds to the DNA cargo via interaction with the parS DNA sequence; and an ATPase, ParA, that binds nonspecific DNA and mediates cargo transport. However, the molecular details of how this system functions are not well understood. Here, we report the cryo-EM structure of the Vibrio cholerae ParA2 filament bound to DNA, as well as the crystal structures of this protein in various nucleotide states. These structures show that ParA forms a left-handed filament on DNA, stabilized by nucleotide binding, and that ParA undergoes profound structural rearrangements upon DNA binding and filament assembly. Collectively, our data suggest the structural basis for ParA's cooperative binding to DNA and the formation of high ParA density regions on the nucleoid.
History
DepositionFeb 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 2.0Oct 20, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / em_admin ...atom_site / em_admin / em_entity_assembly / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / entity_src_nat / pdbx_database_proc / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_seq_map_depositor_info / pdbx_struct_conn_angle / pdbx_struct_ref_seq_depositor_info / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_polymer_linkage / struct_asym / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.label_entity_id / _atom_site.label_seq_id ..._atom_site.label_entity_id / _atom_site.label_seq_id / _em_admin.last_update / _em_entity_assembly.entity_id_list / _entity_src_nat.entity_id / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_seq_map_depositor_info.entity_id / _pdbx_seq_map_depositor_info.one_letter_code_mod / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_ref_seq_depositor_info.entity_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_asym.entity_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: AAA family ATPase
B: AAA family ATPase
C: AAA family ATPase
D: AAA family ATPase
E: AAA family ATPase
F: AAA family ATPase
G: AAA family ATPase
H: AAA family ATPase
I: DNA (49-MER)
J: DNA (49-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)406,07126
Polymers401,69010
Non-polymers4,38016
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area47010 Å2
ΔGint-341 kcal/mol
Surface area141950 Å2
MethodPISA

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Components

#1: Protein
AAA family ATPase / Chromosome partitioning protein ParA / ParA family protein / Plasmid partition protein A


Mass: 46440.969 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: parA, BC353_10845, C9J66_03480, D6U24_01990, ERS013138_01197, ERS013166_00021, ERS013186_00500, ERS013193_00027, ERS013198_00323, ERS013199_01186, ERS013200_00295, ERS013202_00851, ERS013206_ ...Gene: parA, BC353_10845, C9J66_03480, D6U24_01990, ERS013138_01197, ERS013166_00021, ERS013186_00500, ERS013193_00027, ERS013198_00323, ERS013199_01186, ERS013200_00295, ERS013202_00851, ERS013206_01885, EYB64_07940, F0315_18570, FLM02_03395, FXF03_20770, HPY05_13545
Production host: Escherichia coli (E. coli) / References: UniProt: A0A085S0Z4
#2: DNA chain DNA (49-MER)


Mass: 15302.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neoarius leptaspis (salmon catfish)
#3: DNA chain DNA (49-MER)


Mass: 14860.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neoarius leptaspis (salmon catfish)
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
Has ligand of interestY

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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: ParA2-ATPgS-DNA / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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
Image recordingElectron dose: 52.02 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -80.57 ° / Axial rise/subunit: 28.68 Å / Axial symmetry: C1
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 182997 / Symmetry type: HELICAL
Atomic model buildingProtocol: OTHER

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