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- PDB-7pmm: DEAD-box helicase DbpA in the active conformation bound to a ss/d... -

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Basic information

Entry
Database: PDB / ID: 7pmm
TitleDEAD-box helicase DbpA in the active conformation bound to a ss/dsRNA junction and ADP/BeF3
Components
  • ATP-dependent RNA helicase DbpA
  • RNA (45mer) containing HP92 of the 23S rRNA
KeywordsRNA BINDING PROTEIN / DEAD-box helicase / RNA / ribosome biogenesis / ATPase
Function / homology
Function and homology information


DNA/RNA helicase activity / 3'-5' RNA helicase activity / ADP binding / ribosome biogenesis / RNA helicase activity / rRNA binding / RNA helicase / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
ATP-dependent RNA helicase DbpA / DEAD box helicase DbpA/CsdA, RNA-binding domain / DbpA RNA binding domain / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain ...ATP-dependent RNA helicase DbpA / DEAD box helicase DbpA/CsdA, RNA-binding domain / DbpA RNA binding domain / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / 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 / Nucleotide-binding alpha-beta plait domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / PHOSPHATE ION / PYROPHOSPHATE 2- / RNA / RNA (> 10) / ATP-dependent RNA helicase DbpA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWurm, J.P.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)WU 988/1-1 Germany
CitationJournal: Rna / Year: 2023
Title: Structural basis for RNA-duplex unwinding by the DEAD-box helicase DbpA.
Authors: Wurm, J.P.
History
DepositionSep 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2May 1, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DbpA
B: ATP-dependent RNA helicase DbpA
C: RNA (45mer) containing HP92 of the 23S rRNA
D: RNA (45mer) containing HP92 of the 23S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,23812
Polymers126,9324
Non-polymers1,3068
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10820 Å2
ΔGint-117 kcal/mol
Surface area47600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.690, 169.690, 111.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

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Protein / RNA chain , 2 types, 4 molecules ABCD

#1: Protein ATP-dependent RNA helicase DbpA


Mass: 49358.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: dbpA, b1343, JW1337 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P21693, RNA helicase
#2: RNA chain RNA (45mer) containing HP92 of the 23S rRNA


Mass: 14107.352 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 16 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.24 Å3/Da / Density % sol: 61.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 0.2 M di-Sodium tartate, 20 %(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→48.39 Å / Num. obs: 33298 / % possible obs: 99.92 % / Redundancy: 36.15 % / Biso Wilson estimate: 95.07 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1208 / Rpim(I) all: 0.02 / Rrim(I) all: 0.1225 / Net I/σ(I): 24.34
Reflection shellResolution: 3→3.107 Å / Rmerge(I) obs: 1.043 / Mean I/σ(I) obs: 3.11 / Num. unique obs: 3268 / CC1/2: 0.913 / CC star: 0.977 / Rpim(I) all: 0.27 / % possible all: 99.79

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874+SVNrefinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHENIX1.18.2_3874+SVNphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Deposition D_1292103740

Resolution: 3→48.39 Å / SU ML: 0.403 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.5829
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2246 1664 5 %
Rwork0.1971 31621 -
obs0.1985 33285 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 116.82 Å2
Refinement stepCycle: LAST / Resolution: 3→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6779 1836 64 8 8687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00358992
X-RAY DIFFRACTIONf_angle_d0.766512612
X-RAY DIFFRACTIONf_chiral_restr0.0531546
X-RAY DIFFRACTIONf_plane_restr0.00441306
X-RAY DIFFRACTIONf_dihedral_angle_d17.09753581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.090.33351370.29532599X-RAY DIFFRACTION99.96
3.09-3.190.32731360.27312587X-RAY DIFFRACTION100
3.19-3.30.26731360.2492585X-RAY DIFFRACTION100
3.3-3.430.27851360.23492587X-RAY DIFFRACTION100
3.43-3.590.28531370.22772602X-RAY DIFFRACTION100
3.59-3.780.27131370.21422604X-RAY DIFFRACTION100
3.78-4.020.25191380.20042622X-RAY DIFFRACTION99.89
4.02-4.330.18711380.18582627X-RAY DIFFRACTION99.96
4.33-4.760.19941390.16172629X-RAY DIFFRACTION100
4.76-5.450.2021390.18282653X-RAY DIFFRACTION100
5.45-6.860.22651430.22482699X-RAY DIFFRACTION100
6.86-48.390.19961480.17232827X-RAY DIFFRACTION99.83
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)
14.03461323637-4.477263951780.9590499138742.286924160450.285478462733-0.7912547472910.04937470046851.640258227320.689059025038-0.192322658433-0.656751095695-0.369824210563-1.1076316036-0.03002299912720.6743758014681.896575670970.2526963126630.06380430928811.497807082710.05495685212741.2654072875243.791817217-63.689867906325.6394566477
20.913979879375-2.18616190031-1.203563904214.11026917240.727374939659-0.420586559688-0.4877312437440.102453331631-0.09951679224271.511596145550.2383307175010.134176125692-0.0124744102827-0.3507754185950.3571547320681.486135656750.3819111169570.1517411184771.351773501550.2048788247111.3752946228326.9498767428-73.453284338655.2488473101
31.10591195278-0.188743612317-0.3894998309651.31103168774-0.00691622310792.80117087041-0.132144594160.09102742985820.0322334987174-0.06931021558010.0676473586360.138939649585-0.556458646662-0.2446938840320.05698701348290.702707157161-0.0992989245098-0.1037023438880.5338241608870.02538048399420.68828766081659.2989087094-89.803054667137.0687121537
42.162859468850.358780926816-0.334380638771.690277257280.1861930473841.79984316950.06336386670020.167468504345-0.465067237908-0.269188505491-0.0707053412270.1910793427530.546065453061-0.125317271317-0.02470116070221.057558259980.219744676782-0.02329129097830.7038028048920.02994458912890.87542979204910.9022718757-47.206607096445.9286728931
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'C' and resid 0 through 44)CK0 - 44
22(chain 'D' and resid 0 through 44)DL0 - 44
33(chain 'A' and resid 1 through 457)AA1 - 4571 - 457
44(chain 'B' and resid 0 through 456)BF0 - 4561 - 439

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