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- PDB-8a3v: Crystal structure of the Vibrio cholerae replicative helicase (Vc... -

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Basic information

Entry
Database: PDB / ID: 8a3v
TitleCrystal structure of the Vibrio cholerae replicative helicase (VcDnaB) in complex with its loader protein (VcDciA)
Components
  • DUF721 domain-containing protein
  • Replicative DNA helicase
KeywordsREPLICATION / DNA Replication / Replicative Helicase / Helicase Loader / DnaB-DciA complex
Function / homology
Function and homology information


DNA 5'-3' helicase / primosome complex / DNA replication, synthesis of primer / DNA helicase activity / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding
Similarity search - Function
Protein of unknown function DUF721/UPF0232 / Dna[CI] antecedent, DciA / DNA helicase, DnaB type / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / DnaB-like helicase C terminal domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. ...Protein of unknown function DUF721/UPF0232 / Dna[CI] antecedent, DciA / DNA helicase, DnaB type / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / DnaB-like helicase C terminal domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Replicative DNA helicase / DUF721 domain-containing protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWalbott, H. / Quevillon-Cheruel, S. / Cargemel, C.
Funding support France, 1items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05 France
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: The LH-DH module of bacterial replicative helicases is the common binding site for DciA and other helicase loaders.
Authors: Cargemel, C. / Marsin, S. / Noiray, M. / Legrand, P. / Bounoua, H. / Li de la Sierra-Gallay, I. / Walbott, H. / Quevillon-Cheruel, S.
History
DepositionJun 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Replicative DNA helicase
B: Replicative DNA helicase
C: DUF721 domain-containing protein
D: DUF721 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,5858
Polymers142,6824
Non-polymers9034
Water00
1
A: Replicative DNA helicase
B: Replicative DNA helicase
C: DUF721 domain-containing protein
hetero molecules

A: Replicative DNA helicase
B: Replicative DNA helicase
C: DUF721 domain-containing protein
hetero molecules

A: Replicative DNA helicase
B: Replicative DNA helicase
C: DUF721 domain-containing protein
hetero molecules

D: DUF721 domain-containing protein

D: DUF721 domain-containing protein

D: DUF721 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)430,75424
Polymers428,04512
Non-polymers2,70912
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_555y+2/3,x+1/3,-z+1/31
crystal symmetry operation11_555x-y+2/3,-y+1/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area46590 Å2
ΔGint-250 kcal/mol
Surface area173830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.515, 186.515, 252.839
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Replicative DNA helicase


Mass: 52937.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: dnaB, BC353_11625, C9J66_17780, ERS013165_03687, ERS013200_03939, ERS013206_03692, F0315_03560, FLM02_14585, HPY05_12185
Plasmid: pET21
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A085R2T8, DNA helicase
#2: Protein DUF721 domain-containing protein / Protein of uncharacterized function (DUF721)


Mass: 18403.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: D6U24_04005, ERS013186_02533, ERS013198_03405, ERS013202_01773, ERS013207_01848, F0M16_07320
Plasmid: pET29
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0H5ZA06
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.2 Å3/Da / Density % sol: 61.53 % / Description: Rhombohedral
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: 0.1M Sodium Acetate 0.9M Potassium/Sodium Tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.984 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 29, 2020 / Details: KB Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.9→48.26 Å / Num. obs: 21186 / % possible obs: 94.1 % / Redundancy: 17.4 % / Biso Wilson estimate: 102.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.046 / Rrim(I) all: 0.201 / Net I/σ(I): 13.4
Reflection shell

Num. unique obs: 1000 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.9-3.1219.92.361.60.5440.5412.42171.7
9.97-48.2616.30.03561.310.0090.036100

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (20-MAY-2020)refinement
Aimless0.7.4data scaling
STARANISO2.3.24data scaling
PDB_EXTRACT4data extraction
XDSVERSION Mar 17, 2020data reduction
MOLREPVers 11.7.03; 13.07.2020phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T66

6t66


Resolution: 2.9→40.8 Å / Cor.coef. Fo:Fc: 0.87 / Cor.coef. Fo:Fc free: 0.874 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.676
RfactorNum. reflection% reflectionSelection details
Rfree0.2901 1229 6.05 %RANDOM
Rwork0.2791 ---
obs0.2798 20312 54 %-
Displacement parametersBiso mean: 125.28 Å2
Baniso -1Baniso -2Baniso -3
1-6.0139 Å20 Å20 Å2
2--6.0139 Å20 Å2
3----12.0278 Å2
Refine analyzeLuzzati coordinate error obs: 0.77 Å
Refinement stepCycle: LAST / Resolution: 2.9→40.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9311 0 56 0 9367
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0059491HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.7212833HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3497SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1662HARMONIC5
X-RAY DIFFRACTIONt_it9491HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.17
X-RAY DIFFRACTIONt_other_torsion14.5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1274SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7236SEMIHARMONIC4
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.5902 -9.83 %
Rwork0.4683 367 -
all0.4802 407 -
obs--14.25 %
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)
15.7951.45523.975710.8359-1.065300.22680.77990.7435-0.3086-0.0454-0.19920.7435-0.1992-0.1814-0.43560.076-0.2076-0.17230.0556-0.30472.313576.1433-18.2849
25.7951.45521.065310.83593.975700.2446-0.5078-0.7435-0.5078-0.4260.19920.7435-0.19920.1814-0.43560.076-0.0556-0.1723-0.20760.30449.754840.2159-20.1253
34.5994-5.0559-3.97573.71611.06538.3155-0.2268-0.7799-0.74350.30860.04540.19920.7435-0.19920.18140.28360.18720.0556-0.28360.20760.30453.340378.560215.8692
410.8359-1.45521.06535.7953.975700.13610.30860.7435-0.77990.4082-0.1992-0.1992-0.7435-0.54420.28360.1872-0.0556-0.2836-0.20760.30451.280830.94714.8159
55.7951.45521.065310.83593.97578.31550.13610.3086-0.1992-0.77990.4082-0.7435-0.74350.1992-0.54420.28360.18720.0556-0.28360.20760.30460.504753.18420.7322
610.8359-1.45521.06535.7953.975700.1361-0.77990.74350.30860.4082-0.1992-0.74350.1992-0.54420.28360.1872-0.0556-0.2836-0.20760.30476.599825.496322.436
75.7951.45521.065310.83593.97578.3155-0.13610.77990.7435-0.3086-0.4082-0.19920.7435-0.19920.54420.4356-0.0760.05560.17230.20760.30464.59949.002456.1549
85.7951.4552-3.975710.83591.06538.3155-0.390.63330.19920.1312-0.15430.7435-0.1992-0.74350.54420.17230.076-0.20760.43560.05560.30460.094421.307942.9575
910.8359-1.45521.06535.7953.97578.3155-0.17190.59390.1361-0.4946-0.22920.7070.7435-0.19920.40110.17230.0760.20760.4356-0.05560.30436.645328.369617.3484
1010.8359-1.45523.97575.795-1.06538.31550.6981-0.03650.1992-0.0365-0.51670.7435-0.1992-0.7435-0.18140.17230.076-0.05560.4356-0.20760.30429.251349.915532.1151
115.7951.45521.065310.83593.97578.3155-0.1895-0.2161-0.0730.12060.73370.5863-0.74350.1992-0.54420.4356-0.076-0.05560.1723-0.20760.3049.498842.269143.1415
1210.8359-1.45523.97575.795-1.06538.3155-0.22680.3086-0.1992-0.77990.0454-0.7435-0.74350.19920.1814-0.43560.076-0.2076-0.17230.0556-0.304-9.041959.651263.4266
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|174 }
2X-RAY DIFFRACTION2{ B|1 - B|174 }
3X-RAY DIFFRACTION3{ A|175 - A|207 }
4X-RAY DIFFRACTION4{ B|175 - B|207 }
5X-RAY DIFFRACTION5{ A|208 - A|600 }
6X-RAY DIFFRACTION6{ B|208 - B|600 }
7X-RAY DIFFRACTION7{ C|1 - C|101 }
8X-RAY DIFFRACTION8{ C|102 - C|115 }
9X-RAY DIFFRACTION9{ C|116 - C|160 }
10X-RAY DIFFRACTION10{ D|1 - D|101 }
11X-RAY DIFFRACTION11{ D|102 - D|115 }
12X-RAY DIFFRACTION12{ D|116 - D|160 }

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