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- PDB-3ews: Human DEAD-box RNA-helicase DDX19 in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 3ews
TitleHuman DEAD-box RNA-helicase DDX19 in complex with ADP
ComponentsATP-dependent RNA helicase DDX19B
KeywordsHYDROLASE / RNA HELICASE / DEAD / ADP / Structural Genomics / Structural Genomics Consortium / SGC / rRNA / ATP-binding / Nucleotide-binding / RNA-binding / mRNA / Alternative splicing / Cytoplasm / Helicase / Membrane / mRNA transport / Nuclear pore complex / Nucleus / Protein transport / Translocation / Transport
Function / homology
Function and homology information


poly(A)+ mRNA export from nucleus / mRNA export from nucleus / nuclear pore / helicase activity / cytoplasmic stress granule / nuclear envelope / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity ...poly(A)+ mRNA export from nucleus / mRNA export from nucleus / nuclear pore / helicase activity / cytoplasmic stress granule / nuclear envelope / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / RNA binding / extracellular exosome / nucleoplasm / ATP binding / membrane / 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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent RNA helicase DDX19B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLehtio, l. / Karlberg, t. / Andersson, j. / Arrowsmith, c.h. / Berglund, h. / Bountra, c. / Collins, r. / Dahlgren, l.g. / Edwards, a.m. / Flodin, s. ...Lehtio, l. / Karlberg, t. / Andersson, j. / Arrowsmith, c.h. / Berglund, h. / Bountra, c. / Collins, r. / Dahlgren, l.g. / Edwards, a.m. / Flodin, s. / Flores, a. / Graslund, s. / Hammarstrom, m. / Johansson, a. / Johansson, i. / Kotenyova, t. / Moche, m. / Nilsson, m.e. / Nordlund, p. / Nyman, t. / Olesen, k. / Persson, c. / Sagemark, j. / Thorsell, a.g. / Tresaugues, l. / Van den berg, s. / Weigelt, j. / Welin, m. / Wikstrom, m. / Wisniewska, m. / Schueler, h. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2009
Title: The DEXD/H-box RNA Helicase DDX19 Is Regulated by an {alpha}-Helical Switch.
Authors: Collins, R. / Karlberg, T. / Lehtio, L. / Schutz, P. / van den Berg, S. / Dahlgren, L.G. / Hammarstrom, M. / Weigelt, J. / Schuler, H.
History
DepositionOct 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DDX19B
B: ATP-dependent RNA helicase DDX19B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8484
Polymers100,9942
Non-polymers8542
Water46826
1
A: ATP-dependent RNA helicase DDX19B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9242
Polymers50,4971
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ATP-dependent RNA helicase DDX19B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9242
Polymers50,4971
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.580, 47.610, 124.690
Angle α, β, γ (deg.)90.00, 95.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATP-dependent RNA helicase DDX19B / DEAD box protein 19B / DEAD box RNA helicase DEAD5


Mass: 50496.910 Da / Num. of mol.: 2
Fragment: Helicase ATP-binding domain, Helicase C-terminal domain, UNP residues 54-475
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DBP5, DDX19, DDX19B / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)R3 pRARE
References: UniProt: Q9UMR2, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M ammonium acetate, 0.1M Bis-Tris, 17% PEG-10000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: Rayonics MX-225 / Detector: CCD / Date: Dec 21, 2007 / Details: mirrors
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 26518 / Num. obs: 26518 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 52.72 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 14.51
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 4.27 / Num. unique all: 2752 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→19.859 Å / SU ML: 0.42 / Isotropic thermal model: Isotropic + TLS / Cross valid method: THROUGHOUT / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2597 1326 5 %random
Rwork0.1882 ---
all0.1918 26516 --
obs0.1918 26516 99.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.45 Å2 / ksol: 0.321 e/Å3
Refinement stepCycle: LAST / Resolution: 2.7→19.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6428 0 54 26 6508
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg0.786
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_dihedral_angle_d17.157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.80790.31211460.22772784X-RAY DIFFRACTION100
2.8079-2.93530.32841450.22012748X-RAY DIFFRACTION99
2.9353-3.08950.31291450.21412761X-RAY DIFFRACTION99
3.0895-3.28220.3051470.20982791X-RAY DIFFRACTION100
3.2822-3.53430.27581460.19472775X-RAY DIFFRACTION100
3.5343-3.88760.24781470.19012794X-RAY DIFFRACTION99
3.8876-4.44470.2731480.16172809X-RAY DIFFRACTION100
4.4447-5.57920.20111490.14912836X-RAY DIFFRACTION100
5.5792-19.85920.20141530.16742892X-RAY DIFFRACTION99
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)
12.4091-0.97220.19152.23670.13192.6330.1386-0.15920.0968-0.0411-0.139-0.1064-0.05730.2630.01750.14210.0077-0.01010.1809-0.03080.121530.7407-0.702547.9156
23.1662-0.5458-1.6746-0.60560.07892.1191-0.1569-0.59860.2277-0.2520.10940.08680.15270.45620.03940.41330.02390.0495-0.0503-0.02210.35541.4272-1.706812.8255
32.93970.0889-3.6250.60190.75185.74420.36151.33190.1663-0.12530.01150.0528-0.406-2.3042-0.29850.27740.2231-0.00540.83870.12570.20483.57751.925115.4675
43.29660.8131-2.2431.06910.24162.44610.1764-0.3391-0.08920.0667-0.0777-0.10620.0174-0.3937-0.05160.15370.0562-0.03260.5807-0.02250.2647-8.9035-2.761949.6729
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 53:300
2X-RAY DIFFRACTION2chain A and resid 301:472
3X-RAY DIFFRACTION3chain B and resid 54:300
4X-RAY DIFFRACTION4chain B and resid 301:471

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