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- PDB-8iju: ATP-dependent RNA helicase DDX39A (URH49delta41) -

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Basic information

Entry
Database: PDB / ID: 8iju
TitleATP-dependent RNA helicase DDX39A (URH49delta41)
ComponentsATP-dependent RNA helicase DDX39A
KeywordsRNA BINDING PROTEIN / ATP-dependent RNA helicase
Function / homology
Function and homology information


mRNA 3'-end processing / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA export from nucleus / RNA Polymerase II Transcription Termination / mRNA export from nucleus / mRNA splicing, via spliceosome / RNA helicase activity / RNA helicase / nuclear speck / ATP hydrolysis activity ...mRNA 3'-end processing / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA export from nucleus / RNA Polymerase II Transcription Termination / mRNA export from nucleus / mRNA splicing, via spliceosome / RNA helicase activity / RNA helicase / nuclear speck / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / cytoplasm
Similarity search - Function
RNA helicase, DEAD-box type, Q motif / 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 ...RNA helicase, DEAD-box type, Q motif / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / PHOSPHATE ION / ATP-dependent RNA helicase DDX39A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsMikami, B. / Fujita, K. / Masuda, S. / Kojima, M.
Funding support Japan, 7items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)26292053 Japan
Japan Society for the Promotion of Science (JSPS)17K19232 Japan
Japan Society for the Promotion of Science (JSPS)19K22280 Japan
Japan Society for the Promotion of Science (JSPS)19H02884 Japan
Japan Society for the Promotion of Science (JSPS)21K19078 Japan
Japan Society for the Promotion of Science (JSPS)22H02264 Japan
Japan Society for the Promotion of Science (JSPS)19K15807 Japan
CitationJournal: Nat Commun / Year: 2024
Title: Structural differences between the closely related RNA helicases, UAP56 and URH49, fashion distinct functional apo-complexes.
Authors: Fujita, K.I. / Ito, M. / Irie, M. / Harada, K. / Fujiwara, N. / Ikeda, Y. / Yoshioka, H. / Yamazaki, T. / Kojima, M. / Mikami, B. / Mayeda, A. / Masuda, S.
History
DepositionFeb 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DDX39A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,96622
Polymers45,5091
Non-polymers1,45721
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, monomer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-8 kcal/mol
Surface area17730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.974, 96.606, 59.755
Angle α, β, γ (deg.)90.000, 95.510, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein ATP-dependent RNA helicase DDX39A / DEAD box protein 39 / Nuclear RNA helicase URH49


Mass: 45508.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX39A, DDX39 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O00148, RNA helicase
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
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: 2.32 Å3/Da / Density % sol: 47.1 % / Description: rectangle
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 mM Na2PO4, 30 % (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 68537 / % possible obs: 98.5 % / Redundancy: 2.4 % / Biso Wilson estimate: 26.22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.058 / Net I/σ(I): 12.4
Reflection shellResolution: 1.82→1.93 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 2.09 / Num. unique obs: 10621 / CC1/2: 0.843 / Rrim(I) all: 0.481 / % possible all: 94.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→37.5 Å / SU ML: 0.2158 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.9307
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2219 1749 5 %
Rwork0.1843 33209 -
obs0.1862 34958 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.51 Å2
Refinement stepCycle: LAST / Resolution: 1.82→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3039 0 92 177 3308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073258
X-RAY DIFFRACTIONf_angle_d0.85864359
X-RAY DIFFRACTIONf_chiral_restr0.0565480
X-RAY DIFFRACTIONf_plane_restr0.0065562
X-RAY DIFFRACTIONf_dihedral_angle_d15.52891278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.880.31191310.26262492X-RAY DIFFRACTION90.54
1.88-1.940.31881490.23882816X-RAY DIFFRACTION99.63
1.94-2.010.28141450.23142760X-RAY DIFFRACTION99.97
2.01-2.090.25211470.21712793X-RAY DIFFRACTION99.97
2.09-2.180.23771460.2072773X-RAY DIFFRACTION100
2.18-2.30.2591470.20082794X-RAY DIFFRACTION99.97
2.3-2.440.24511460.20082765X-RAY DIFFRACTION100
2.44-2.630.24781460.19542789X-RAY DIFFRACTION99.97
2.63-2.890.23361480.19342805X-RAY DIFFRACTION100
2.89-3.310.24131470.18062786X-RAY DIFFRACTION100
3.31-4.170.18961480.1572813X-RAY DIFFRACTION99.93
4.17-37.50.17091490.16062823X-RAY DIFFRACTION99.56

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