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- PDB-7npd: Vibiro cholerae ParA2 -

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Basic information

Entry
Database: PDB / ID: 7npd
TitleVibiro cholerae ParA2
ComponentsWalker A-type ATPase
KeywordsDNA BINDING PROTEIN / ATPase / Chromosome segregation / Bacterial cell division / Hydrolase
Function / homologyParA helix turn helix domain / AAA domain / AAA domain / P-loop containing nucleoside triphosphate hydrolase / Chromosome partitioning protein ParA
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsParker, A.V. / Bergeron, J.R.C.
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 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc / refine_hist
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _refine_hist.d_res_high
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Walker A-type ATPase


Theoretical massNumber of molelcules
Total (without water)46,4411
Polymers46,4411
Non-polymers00
Water84747
1
A: Walker A-type ATPase

A: Walker A-type ATPase


Theoretical massNumber of molelcules
Total (without water)92,8822
Polymers92,8822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-y,-x,-z+1/31
Buried area4650 Å2
ΔGint-38 kcal/mol
Surface area32260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.247, 63.247, 214.373
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein Walker A-type ATPase / Chromosome (Plasmid) partitioning protein ParA / Chromosome partitioning protein ParA / ParA family ...Chromosome (Plasmid) partitioning protein ParA / Chromosome partitioning protein ParA / ParA family protein / Plasmid partition protein A / ParA2vc / ParA2 / AAA family ATPase


Mass: 46440.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: parA, BC353_10845, C9J66_03480, ERS013138_01197, ERS013166_00021, ERS013186_00500, ERS013193_00027, ERS013197_04093, ERS013198_00323, ERS013199_01186, ERS013200_00295, ERS013202_00851, ...Gene: parA, BC353_10845, C9J66_03480, ERS013138_01197, ERS013166_00021, ERS013186_00500, ERS013193_00027, ERS013197_04093, ERS013198_00323, ERS013199_01186, ERS013200_00295, ERS013202_00851, ERS013206_01885, F0315_18570, FLM02_03395, FXF03_20770, HPY05_13545
Production host: Escherichia coli (E. coli) / References: UniProt: A0A085S0Z4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M tri-Sodium citrate pH 5.5 20% w/v PEG 3000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.6→38.31 Å / Num. obs: 14628 / % possible obs: 91.02 % / Redundancy: 2 % / Rmerge(I) obs: 0.01654 / Net I/σ(I): 36.81
Reflection shellResolution: 2.6→2.694 Å / Rmerge(I) obs: 0.3752 / Num. unique obs: 689

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
xia2data scaling
PHASERphasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EZ7

3ez7


Resolution: 2.6→38.31 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 48.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3367 1469 10.04 %
Rwork0.2739 13159 -
obs0.2803 14628 75.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 173.59 Å2 / Biso mean: 80.999 Å2 / Biso min: 22.25 Å2
Refinement stepCycle: final / Resolution: 2.6→38.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2894 0 0 47 2941
Biso mean---65.49 -
Num. residues----387
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.710.4397880.438678887645
2.71-2.850.4911510.44271336148778
2.85-3.030.48811980.420217581956100
3.03-3.270.40441900.367817251915100
3.27-3.590.40591950.311917521947100
3.6-4.120.33091940.245917601954100
4.12-5.180.28822010.212117781979100
5.18-38.310.28912050.245218372042100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.0084-0.0031-0.0038-0.00050.00190.0035-0.0447-0.0624-0.13360.0702-0.0048-0.06130.14420.053700.643100.060.4893-0.23280.518-11.3458-11.808423.8788
20.0127-0.0175-0.00340.019-0.00760.01220.01160.2811-0.1508-0.0463-0.44730.1268-0.338-0.250300.3047-0.43980.0274-0.83150.6350.0997-8.854525.318714.4061
3-0.0042-0.00880.002-0.00290.0033-0.0004-0.066-0.0065-0.0005-0.051-0.02150.0040.00010.0113-00.51010.08730.04120.52230.11290.3888-1.49998.184710.6868
4-0.0055-0.0164-0.0157-0.0049-0.02010.0028-0.0506-0.1429-0.28410.3669-0.2059-0.2574-0.31030.19100.2986-0.83070.0952-0.69850.79520.1152-0.799117.398830.9706
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 33 )A4 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 179 )A34 - 179
3X-RAY DIFFRACTION3chain 'A' and (resid 180 through 203 )A180 - 203
4X-RAY DIFFRACTION4chain 'A' and (resid 204 through 406 )A204 - 406

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