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- PDB-8po8: Structure of Escherichia coli HrpA in complex with ADP and oligon... -

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Basic information

Entry
Database: PDB / ID: 8po8
TitleStructure of Escherichia coli HrpA in complex with ADP and oligonucleotide poly(dC)11 forming an i-motif
Components
  • ATP-dependent RNA helicase HrpA
  • DNA (5'-D(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')
KeywordsHYDROLASE / Helicase
Function / homology
Function and homology information


RNA modification / 3'-5' RNA helicase activity / helicase activity / RNA helicase activity / RNA helicase / ATP hydrolysis activity / RNA binding / ATP binding
Similarity search - Function
RNA helicase HrpA / RNA helicase HrpA, C-terminal / Domain of unknown function (DUF3418) / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation ...RNA helicase HrpA / RNA helicase HrpA, C-terminal / Domain of unknown function (DUF3418) / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / SUCCINIC ACID / DNA / DNA (> 10) / ATP-dependent RNA helicase HrpA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsXin, B.G. / Yuan, L.G. / Zhang, L.L. / Xie, S.M. / Liu, N.N. / Ai, X. / Li, H.H. / Rety, S. / Xi, X.G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870788 China
Other governmentZ101021903
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structural insights into the N-terminal APHB domain of HrpA: mediating canonical and i-motif recognition.
Authors: Xin, B.G. / Huang, L.Y. / Yuan, L.G. / Liu, N.N. / Li, H.H. / Ai, X. / Lei, D.S. / Hou, X.M. / Rety, S. / Xi, X.G.
History
DepositionJul 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent RNA helicase HrpA
B: ATP-dependent RNA helicase HrpA
C: DNA (5'-D(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')
D: DNA (5'-D(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,03910
Polymers178,9004
Non-polymers1,1396
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint-13 kcal/mol
Surface area54990 Å2
Unit cell
Length a, b, c (Å)80.260, 105.973, 177.552
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / DNA chain , 2 types, 4 molecules ABCD

#1: Protein ATP-dependent RNA helicase HrpA


Mass: 86313.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: hrpA, b1413, JW5905 / Plasmid: pET15b-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): C2566H / References: UniProt: P43329, RNA helicase
#2: DNA chain DNA (5'-D(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')


Mass: 3136.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 4 types, 137 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine 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: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 10% PEG 3350 4% Tacsimate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97777 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97777 Å / Relative weight: 1
ReflectionResolution: 2.52→90.997 Å / Num. obs: 48761 / % possible obs: 94 % / Redundancy: 6.6 % / Biso Wilson estimate: 47.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.044 / Rrim(I) all: 0.115 / Net I/σ(I): 12.3
Reflection shellResolution: 2.521→2.564 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.852 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2508 / CC1/2: 0.774 / Rpim(I) all: 0.356 / Rrim(I) all: 0.925 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSBUILT 20190315data reduction
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→63.98 Å / SU ML: 0.3631 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.7553
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2427 2392 4.91 %
Rwork0.2105 46330 -
obs0.212 48722 93.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.92 Å2
Refinement stepCycle: LAST / Resolution: 2.52→63.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9732 400 72 131 10335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003310397
X-RAY DIFFRACTIONf_angle_d0.746514131
X-RAY DIFFRACTIONf_chiral_restr0.05081613
X-RAY DIFFRACTIONf_plane_restr0.00431784
X-RAY DIFFRACTIONf_dihedral_angle_d18.72294083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.570.36931590.33652785X-RAY DIFFRACTION98.79
2.57-2.630.33341400.29662850X-RAY DIFFRACTION99.9
2.63-2.690.32541000.32241847X-RAY DIFFRACTION64.17
2.69-2.760.31051480.2712859X-RAY DIFFRACTION99.97
2.76-2.830.33271700.25082845X-RAY DIFFRACTION99.97
2.83-2.910.26011430.24992885X-RAY DIFFRACTION100
2.91-3.010.29671310.25962895X-RAY DIFFRACTION100
3.01-3.120.29791250.26912894X-RAY DIFFRACTION100
3.12-3.240.32731450.27652885X-RAY DIFFRACTION100
3.24-3.390.28781510.23712867X-RAY DIFFRACTION100
3.39-3.570.26391100.22862161X-RAY DIFFRACTION74.29
3.57-3.790.26931150.20752549X-RAY DIFFRACTION87.09
3.79-4.080.21571090.19512110X-RAY DIFFRACTION72.78
4.08-4.490.16981660.162900X-RAY DIFFRACTION100
4.49-5.140.17651640.16332930X-RAY DIFFRACTION100
5.14-6.480.24241740.20122957X-RAY DIFFRACTION100
6.48-63.980.19981420.15813111X-RAY DIFFRACTION99.09
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)
11.8100473245-0.6313938290062.323998631071.55684621188-3.161471458737.360461904590.0439744828775-0.1414393327470.1713148401340.3085035326920.4056056367770.311482319131-0.390882102149-0.168998801315-0.4648972615710.4564592962210.0340995722648-0.002741612002750.3198833450640.08432070812180.439445899626-19.818477868886.183555712751.7223322529
22.11023538857-0.656935963026-0.7237051244243.245541719130.4921372937682.33798335140.01368096684030.02441880329980.0562424433293-0.0739510484107-0.0105181078996-0.0530479341072-0.05528189649170.00300791698305-0.001533786812850.2573507134720.00964471664316-0.03145344837210.3338039861930.04653797116440.284394240586-4.9366675684961.04740041659.8118129395
33.604210794032.01792346128-0.6130572014462.81429185848-0.8104180001392.55877262318-0.129288979126-0.371005005605-0.2603276947040.3153026407590.1187368117850.534326559850.420491139319-0.4632706996750.01583484271160.3897993968730.02628938891160.08058196739320.4543633275480.07969512523620.5245068429070.62990383851132.268508823372.482506576
42.98904091418-1.510860604731.011044516912.51397357215-0.8796744904611.075960224670.2362724075230.432256366179-0.420726590893-0.386189589306-0.1657537934250.1569001318770.121121788610.0575954811175-0.06510835994370.314543888694-0.0350443604385-0.00815914179030.348816020375-0.03120659763020.298571829248-1.2199459747640.472679712250.6966715886
54.42391664775-0.2006362574930.6670845280174.71217460093-2.601314379223.629226553710.02331444107540.391086224552-0.89078646049-0.3762063610170.01515446828180.4448128808340.36313513147-0.0393890521816-0.01265390897920.421636437423-0.02380229420430.009214888826330.447955864267-0.23903875180.722840125656-21.599867005129.555438673250.8523444039
62.40511724373-0.5867138958111.383984824361.660492916191.303453587522.57931048516-0.1502667134241.170783021580.0454648063542-0.449609818986-0.1863557497560.2621071094150.2600844318120.05308327838740.2815983752891.15556405903-0.08250192264160.07200146080210.979269791173-0.0606532503750.625970036885-43.444824819459.230436442732.706392304
71.843402180270.634911885554-0.0830785676862.15385753931-0.2343086132932.223331736190.01786324243220.0649043248881-0.176786108602-0.07004554725550.0270897198315-0.158360525930.02201265584370.0910520417897-0.04499301416380.2116398207840.00263087460821-0.01126476691930.241245098519-0.007529797346850.241206808153-45.352289310152.039029094266.211262815
81.259956435040.5647243571340.3706614249563.46801421762-1.601868783872.545593949050.27138048243-0.234903535164-0.2056689089720.446798388732-0.203638546833-0.1819782641790.1285736998550.0444476878275-0.05592213331110.387562058523-0.048836451348-0.05399837785160.310098790926-0.004805621541890.312942695796-42.518629703755.143792366787.7946926272
97.066363008471.762466548341.860666953791.797983132041.454826652081.228108780160.06930521346430.5508283733461.181273633-0.2194842187470.08291692184050.627101672615-0.362102425781-0.0392132434143-0.1291585032620.5334552817150.01421222407040.02142207910490.3203303053610.1083268659630.54480878125-41.683909458382.093074115668.0136355179
102.33800836727-0.294390099721-0.4444088315013.486926651260.07546424993985.459034564190.13695954687-0.5817204037850.1468794453770.705018962089-0.0779014082566-0.414365734174-0.1054812104570.280889873742-0.08974928568340.487201775102-0.129220430639-0.09022065486350.433370131781-0.03643969451860.413540435839-26.159440099273.454855392592.0230194184
116.894268271544.776358563880.4227208103217.176266302940.4203869248245.919823024440.1995947187320.892792672299-1.13272246719-0.11619981516-0.252926966963-0.4832929064451.78283533913-1.12760756118-0.01123638281551.14436712287-0.272272873387-0.2799875462550.901377996183-0.05521330538721.34624555882-27.229777461171.219163454341.2832441975
124.615761372470.5618281940661.925916018884.0054467855-0.01434143592433.56055240995-0.256460973194-0.4929299341740.0378739674606-0.41814079597-0.02436958440030.213664372938-0.814407985539-1.157358910080.08230763176291.67995400775-0.109366768118-0.1832077041441.16234988116-0.02766580530211.28234032967-33.623019897170.986346920644.0940917549
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 67 )AA4 - 671 - 64
22chain 'A' and (resid 68 through 248 )AA68 - 24865 - 245
33chain 'A' and (resid 249 through 351 )AA249 - 351246 - 348
44chain 'A' and (resid 352 through 471 )AA352 - 471349 - 468
55chain 'A' and (resid 472 through 626 )AA472 - 626469 - 603
66chain 'B' and (resid 7 through 45 )BD7 - 451 - 39
77chain 'B' and (resid 46 through 287 )BD46 - 28740 - 275
88chain 'B' and (resid 288 through 443 )BD288 - 443276 - 431
99chain 'B' and (resid 444 through 487 )BD444 - 487432 - 472
1010chain 'B' and (resid 488 through 630 )BD488 - 630473 - 615
1111chain 'C' and (resid 1 through 11 )CG1 - 11
1212chain 'D' and (resid 2 through 11 )DH2 - 11

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