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- PDB-5bq5: Crystal structure of the IstB AAA+ domain bound to ADP-BeF3 -

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Basic information

Entry
Database: PDB / ID: 5bq5
TitleCrystal structure of the IstB AAA+ domain bound to ADP-BeF3
ComponentsInsertion sequence IS5376 putative ATP-binding protein
KeywordsATP-binding protein / AAA+ / ATPase / transposition / DNA binding
Function / homology
Function and homology information


DNA replication / ATP hydrolysis activity / ATP binding
Similarity search - Function
: / DNA replication protein DnaC/insertion sequence putative ATP-binding protein / IstB-like ATP-binding protein / IstB-like ATP binding protein / ClpA/B family / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...: / DNA replication protein DnaC/insertion sequence putative ATP-binding protein / IstB-like ATP-binding protein / IstB-like ATP binding protein / ClpA/B family / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / Insertion sequence IS5376 putative ATP-binding protein
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsArias-Palomo, E. / Berger, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071747 United States
CitationJournal: Cell / Year: 2015
Title: An Atypical AAA+ ATPase Assembly Controls Efficient Transposition through DNA Remodeling and Transposase Recruitment.
Authors: Ernesto Arias-Palomo / James M Berger /
Abstract: Transposons are ubiquitous genetic elements that drive genome rearrangements, evolution, and the spread of infectious disease and drug-resistance. Many transposons, such as Mu, Tn7, and IS21, require ...Transposons are ubiquitous genetic elements that drive genome rearrangements, evolution, and the spread of infectious disease and drug-resistance. Many transposons, such as Mu, Tn7, and IS21, require regulatory AAA+ ATPases for function. We use X-ray crystallography and cryo-electron microscopy to show that the ATPase subunit of IS21, IstB, assembles into a clamshell-shaped decamer that sandwiches DNA between two helical pentamers of ATP-associated AAA+ domains, sharply bending the duplex into a 180° U-turn. Biochemical studies corroborate key features of the structure and further show that the IS21 transposase, IstA, recognizes the IstB•DNA complex and promotes its disassembly by stimulating ATP hydrolysis. Collectively, these studies reveal a distinct manner of higher-order assembly and client engagement by a AAA+ ATPase and suggest a mechanistic model where IstB binding and subsequent DNA bending primes a selected insertion site for efficient transposition.
History
DepositionMay 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insertion sequence IS5376 putative ATP-binding protein
B: Insertion sequence IS5376 putative ATP-binding protein
C: Insertion sequence IS5376 putative ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,46212
Polymers65,9103
Non-polymers1,5539
Water9,548530
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A: Insertion sequence IS5376 putative ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4874
Polymers21,9701
Non-polymers5183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Insertion sequence IS5376 putative ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4874
Polymers21,9701
Non-polymers5183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Insertion sequence IS5376 putative ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4874
Polymers21,9701
Non-polymers5183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.806, 133.806, 70.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA67 - 246
211chain BB62 - 248
311chain CC67 - 246

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Components

#1: Protein Insertion sequence IS5376 putative ATP-binding protein / IstB


Mass: 21969.957 Da / Num. of mol.: 3 / Fragment: UNP residues 63-248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q45619
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: BeF3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 100 mM BIS-TRIS propane pH 6.5, 300 mM ammonium sulfate and 18.5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.97955 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97955 Å / Relative weight: 1
ReflectionResolution: 2.1→43.798 Å / Num. obs: 42394 / % possible obs: 100 % / Redundancy: 15.3 % / Biso Wilson estimate: 31.79 Å2 / Rpim(I) all: 0.044 / Rrim(I) all: 0.173 / Rsym value: 0.15 / Net I/av σ(I): 4.939 / Net I/σ(I): 18.9 / Num. measured all: 648053
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.1-2.2115.31.6050.59417161510.4351.6051.9100
2.21-2.3515.30.9830.88980658520.2670.9833.2100
2.35-2.5115.40.6581.28373054480.1790.6584.8100
2.51-2.7115.40.4191.87891351350.1140.4197.5100
2.71-2.9715.40.2632.97214946920.0730.26311.7100
2.97-3.3215.40.1425.36535242540.040.14220.3100
3.32-3.8315.30.07210.25788037800.0210.07236.4100
3.83-4.715.10.04316.14837532000.0150.04355.4100
4.7-6.6414.90.0416.73689424790.0170.0457.4100
6.64-48.67514.80.02720.82078314030.0130.02776.799.5

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
PHENIX1.9-1692refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→43.798 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.07 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2034 2138 5.05 %
Rwork0.1821 78517 -
obs0.1832 41344 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.5 Å2 / Biso mean: 49.7823 Å2 / Biso min: 15.94 Å2
Refinement stepCycle: final / Resolution: 2.1→43.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4460 0 129 530 5119
Biso mean--28.27 47.52 -
Num. residues----547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054672
X-RAY DIFFRACTIONf_angle_d0.7896279
X-RAY DIFFRACTIONf_chiral_restr0.033699
X-RAY DIFFRACTIONf_plane_restr0.003784
X-RAY DIFFRACTIONf_dihedral_angle_d13.5791752
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3325X-RAY DIFFRACTION9.61TORSIONAL
12B3325X-RAY DIFFRACTION9.61TORSIONAL
13C3325X-RAY DIFFRACTION9.61TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1001-2.1240.34911340.311126612795100
2.124-2.1490.36131350.315126342769100
2.149-2.17520.27641320.291825652697100
2.1752-2.20270.26871520.279326282780100
2.2027-2.23170.26171360.256926322768100
2.2317-2.26230.28541470.270125892736100
2.2623-2.29460.27321650.244926632828100
2.2946-2.32880.28251390.25726092748100
2.3288-2.36520.2691430.246826162759100
2.3652-2.4040.24321190.233526242743100
2.404-2.44540.27241630.227126372800100
2.4454-2.48990.24611570.221225902747100
2.4899-2.53780.2271090.214926402749100
2.5378-2.58960.25241210.201726032724100
2.5896-2.64590.24241410.191326242765100
2.6459-2.70740.23971370.19626332770100
2.7074-2.77510.19121280.195426272755100
2.7751-2.85020.21171390.196526712810100
2.8502-2.9340.29241320.192925722704100
2.934-3.02870.21341350.185126492784100
3.0287-3.13690.18921390.186525962735100
3.1369-3.26250.19831730.171626052778100
3.2625-3.41090.18651290.162226042733100
3.4109-3.59060.17441550.154526082763100
3.5906-3.81550.16291430.15826052748100
3.8155-4.10990.16771420.13512605274799
4.1099-4.52310.13311340.1272588272299
4.5231-5.17670.15121160.13272642275899
5.1767-6.51860.17831490.17212582273199
6.5186-43.80780.16581280.16022615274399
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)
10.14840.1149-0.03651.3142-0.24241.31520.0464-0.05260.1059-0.1124-0.0177-0.0163-0.06760.07120.00040.1573-0.0001-0.00390.1989-0.00060.247422.620732.80139.0697
20.23020.4354-0.19481.014-0.37210.7549-0.17060.05860.3097-0.90390.30461.33440.3436-0.58960.33910.514-0.1184-0.26850.2711-0.01990.49799.812415.965826.546
30.3307-0.04420.17071.342-0.25330.64620.0213-0.1088-0.0898-0.1032-0.04150.18150.2052-0.0203-0.00020.24270.0055-0.01220.2031-0.02130.305418.667915.866938.6143
40.05190.0444-0.00720.0730.0240.07630.3744-0.00670.57670.2064-0.11250.2729-0.1816-0.02460.00080.2696-0.03820.10270.4185-0.0970.38256.061138.612854.343
50.82470.40010.07640.24660.34370.95940.2919-0.2305-0.42490.1119-0.1922-0.09090.1624-0.0730.00430.3376-0.0422-0.0080.31250.07380.2608-9.936539.469412.4327
60.20050.169-0.05870.258-0.21180.52120.2685-0.79760.75140.6422-0.32380.623-0.5638-0.47770.07250.6529-0.13360.02760.573-0.24580.4917-5.28759.162124.2742
70.87140.49990.00970.57740.51710.41560.0954-0.1450.3333-0.0058-0.1975-0.0143-0.19510.1935-00.3843-0.0525-0.01860.38550.00740.32131.39454.538313.1623
80.26330.4838-0.12880.8305-0.28210.146-0.1330.219-0.1291-0.01110.10210.2322-0.27230.082500.37580.08330.01780.3396-0.04340.2907-17.526345.8167-0.618
90.3357-0.04190.24910.24370.07450.19130.02360.1726-0.2484-0.32080.0337-0.12180.330.18790.01510.4459-0.05390.06560.4179-0.00280.248926.746144.216217.2
100.33030.0020.05670.1970.03150.04650.07960.3008-0.2929-0.0723-0.1694-0.6666-0.22630.5256-00.3879-0.07190.0040.45440.06410.476135.276752.819925.7276
110.2544-0.0386-0.08220.22980.00210.02770.02160.0629-0.26560.20940.0298-0.03870.0224-0.0484-00.35-0.04980.02350.29790.0240.285624.80751.073425.323
120.06920.0574-0.05030.1062-0.12280.13560.19-0.26410.17610.0817-0.0150.3733-0.1025-0.2881-0.00550.4326-0.02210.14570.42-0.03730.501111.013962.512732.1301
130.07910.05250.02840.03570.01710.01430.0203-0.4819-0.39040.2552-0.0633-0.0493-0.4878-0.19860.00190.91620.0260.22440.51-0.04770.4814.193665.485140.6303
140.29960.2541-0.23510.1992-0.1650.1608-0.0785-0.0153-0.10020.00460.08550.325-0.0662-0.38590.00010.3859-0.01710.02410.3486-0.00470.380615.718762.720225.8925
150.29450.2843-0.10450.86150.04930.0512-0.0080.05660.23070.1217-0.06110.244-0.2824-0.102-00.3745-0.0475-0.01420.30680.03040.293322.196568.714824.8737
160.2207-0.239-0.0380.374-0.08240.08080.10270.4343-0.2393-0.15820.1374-0.4020.04450.2039-0.0140.4134-0.06540.05230.35690.0090.202927.550156.460615.1486
170.0468-0.00290.01050.01130.01560.03880.2123-0.3036-0.3192-0.31920.16260.23490.14440.2314-0.00380.4353-0.0321-0.09730.4406-0.03780.360613.433940.80338.2522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 67 through 128 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 129 through 158 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 235 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 236 through 246 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 62 through 128 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 129 through 159 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 160 through 224 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 225 through 248 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 67 through 82 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 83 through 99 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 100 through 128 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 129 through 146 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 147 through 158 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 159 through 177 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 178 through 224 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 225 through 235 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 236 through 246 )C0

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