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- PDB-5lta: Crystal structure of the Prp43-ADP-BeF3-U7-RNA complex -

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Basic information

Entry
Database: PDB / ID: 5lta
TitleCrystal structure of the Prp43-ADP-BeF3-U7-RNA complex
Components
  • Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsProtein/RNA / RNA HELICASE / DEAH-BOX PROTEIN / DHX15 / Protein-RNA complex
Function / homology
Function and homology information


RNA helicase activity / nucleic acid binding / hydrolase activity / RNA helicase / ribonucleoprotein complex / ATP binding
Similarity search - Function
DHX15, DEXH-box helicase domain / : / 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 / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. ...DHX15, DEXH-box helicase domain / : / 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 / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / 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 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / CACODYLATE ION / RNA / RNA (> 10) / RNA helicase
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.621 Å
AuthorsTauchert, M.J. / Ficner, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB860 Germany
CitationJournal: Elife / Year: 2017
Title: Structural insights into the mechanism of the DEAH-box RNA helicase Prp43.
Authors: Tauchert, M.J. / Fourmann, J.B. / Luhrmann, R. / Ficner, R.
History
DepositionSep 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
E: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1506
Polymers86,4952
Non-polymers6554
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-37 kcal/mol
Surface area30890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.392, 106.392, 356.698
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein / RNA chain , 2 types, 2 molecules AE

#1: Protein Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43


Mass: 81641.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN WAS EXPRESSED WITH 2 ADDITIONAL N-TERMINAL AMINO ACIDS (MA) AND A C-TERMINAL STREP-TAG (WSHPQFEK)
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0005780 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: G0RY84, RNA helicase
#2: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 4853.695 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 56 molecules

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


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#6: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6AsO2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 3.55 Å3/Da / Density % sol: 65.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2.5 % (w/v) PGA-LM, 13 % (w/v) PEG 8000 and 100 mM Na Cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.82656 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656 Å / Relative weight: 1
ReflectionResolution: 2.62→48.56 Å / Num. obs: 36887 / % possible obs: 98.5 % / Redundancy: 5.14 % / Biso Wilson estimate: 65 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Net I/σ(I): 22.16
Reflection shellResolution: 2.62→2.7 Å / Redundancy: 5.34 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.85 / CC1/2: 0.652 / % possible all: 86.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5d0u

5d0u


Resolution: 2.621→48.558 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.45
RfactorNum. reflection% reflection
Rfree0.2295 1991 5.4 %
Rwork0.1971 --
obs0.1989 36884 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.621→48.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5605 144 37 52 5838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035982
X-RAY DIFFRACTIONf_angle_d0.7998150
X-RAY DIFFRACTIONf_dihedral_angle_d13.7732315
X-RAY DIFFRACTIONf_chiral_restr0.031922
X-RAY DIFFRACTIONf_plane_restr0.0031017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6211-2.68670.3061390.30782426X-RAY DIFFRACTION100
2.6867-2.75930.32451390.28122435X-RAY DIFFRACTION100
2.7593-2.84050.32351400.30072432X-RAY DIFFRACTION100
2.8405-2.93210.33361400.27662444X-RAY DIFFRACTION99
2.9321-3.03690.3521390.26092438X-RAY DIFFRACTION100
3.0369-3.15850.29361410.25062453X-RAY DIFFRACTION100
3.1585-3.30220.2981390.25372461X-RAY DIFFRACTION100
3.3022-3.47630.29071390.23882473X-RAY DIFFRACTION100
3.4763-3.6940.23721400.20712479X-RAY DIFFRACTION100
3.694-3.97910.21421430.17862482X-RAY DIFFRACTION100
3.9791-4.37930.1991420.16162509X-RAY DIFFRACTION100
4.3793-5.01240.18841440.15112524X-RAY DIFFRACTION100
5.0124-6.31290.19261480.18452589X-RAY DIFFRACTION100
6.3129-48.5660.18641580.16542748X-RAY DIFFRACTION99

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