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- PDB-5e7j: Crystal structure of the active catalytic core of the human DEAD-... -

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Basic information

Entry
Database: PDB / ID: 5e7j
TitleCrystal structure of the active catalytic core of the human DEAD-box protein DDX3 bound to AMP
ComponentsATP-dependent RNA helicase DDX3X
KeywordsHYDROLASE / DEAD-box protein / RNA helicase / RecA fold
Function / homology
Function and homology information


positive regulation of protein acetylation / CTPase activity / positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / positive regulation of translation in response to endoplasmic reticulum stress / protein localization to cytoplasmic stress granule / RNA strand annealing activity / NLRP3 inflammasome complex / eukaryotic initiation factor 4E binding / positive regulation of chemokine (C-C motif) ligand 5 production ...positive regulation of protein acetylation / CTPase activity / positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / positive regulation of translation in response to endoplasmic reticulum stress / protein localization to cytoplasmic stress granule / RNA strand annealing activity / NLRP3 inflammasome complex / eukaryotic initiation factor 4E binding / positive regulation of chemokine (C-C motif) ligand 5 production / RNA secondary structure unwinding / gamete generation / positive regulation of protein K63-linked ubiquitination / cellular response to arsenic-containing substance / poly(A) binding / gamma-tubulin binding / cellular response to osmotic stress / P granule / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of NLRP3 inflammasome complex assembly / : / transcription factor binding / cell leading edge / lipid homeostasis / positive regulation of interferon-alpha production / positive regulation of type I interferon production / ribosomal small subunit binding / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of protein-containing complex assembly / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of translational initiation / positive regulation of viral genome replication / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / signaling adaptor activity / stress granule assembly / positive regulation of protein autophosphorylation / translation initiation factor binding / DNA helicase activity / positive regulation of interferon-beta production / intrinsic apoptotic signaling pathway / protein serine/threonine kinase activator activity / : / ribonucleoside triphosphate phosphatase activity / cytosolic ribosome assembly / positive regulation of translation / chromosome segregation / translational initiation / response to virus / positive regulation of protein serine/threonine kinase activity / negative regulation of cell growth / cellular response to virus / mRNA 5'-UTR binding / Wnt signaling pathway / cytoplasmic stress granule / RNA stem-loop binding / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of canonical Wnt signaling pathway / lamellipodium / positive regulation of cell growth / secretory granule lumen / ficolin-1-rich granule lumen / RNA helicase activity / negative regulation of translation / cell differentiation / intracellular signal transduction / RNA helicase / cadherin binding / positive regulation of apoptotic process / negative regulation of gene expression / innate immune response / GTPase activity / mRNA binding / centrosome / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / ATP-dependent RNA helicase DDX3X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.23 Å
AuthorsFloor, S.N. / Condon, K.J. / Doudna, J.A.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Autoinhibitory Interdomain Interactions and Subfamily-specific Extensions Redefine the Catalytic Core of the Human DEAD-box Protein DDX3.
Authors: Floor, S.N. / Condon, K.J. / Sharma, D. / Jankowsky, E. / Doudna, J.A.
History
DepositionOct 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Feb 10, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DDX3X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4392
Polymers51,0921
Non-polymers3471
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-4 kcal/mol
Surface area20530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.350, 89.910, 107.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ATP-dependent RNA helicase DDX3X / DEAD box protein 3 / X-chromosomal / DEAD box / X isoform / Helicase-like protein 2 / HLP2


Mass: 51092.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX3X, DBX, DDX3 / Plasmid: pHMGWA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: O00571, RNA helicase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM

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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: 2.43 Å3/Da / Density % sol: 49.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 3000, sodium citrate / PH range: 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 2.23→69.007 Å / Num. obs: 24117 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 29.8 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.078 / Χ2: 0.952 / Net I/σ(I): 16.99 / Num. measured all: 96049
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.23-2.290.9380.4832.822999181211740.59664.8
2.29-2.350.8610.4512.945836177416560.5393.3
2.35-2.420.9070.4083.757184172317130.46699.4
2.42-2.490.9240.3454.47051168116770.39599.8
2.49-2.570.9470.2825.466881164416380.32299.6
2.57-2.660.9690.2466.186460155815490.28299.4
2.66-2.770.9690.2047.426189152715140.23499.1
2.77-2.880.9790.1599.16183147614750.18199.9
2.88-3.010.9880.12411.585878140213980.14199.7
3.01-3.150.9930.09414.245651134913490.108100
3.15-3.320.9950.07119.155419130613030.08199.8
3.32-3.520.9970.05523.424803121412000.06398.8
3.52-3.770.9980.04528.584571115011360.05298.8
3.77-4.070.9990.03632.754187108510590.04297.6
4.07-4.460.9990.02840.79402510049940.03299
4.46-4.980.9990.02543.9636589249160.02999.1
4.98-5.760.9990.02839.8731958088040.03399.5
5.76-7.050.9990.02839.9625986926830.03398.7
7.05-9.9710.01952.6821525655580.02298.8
9.970.9990.01660.7611293293210.01997.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementResolution: 2.23→69.007 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2637 1200 5 %
Rwork0.2298 22805 -
obs0.2316 24005 95.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.84 Å2 / Biso mean: 37.4013 Å2 / Biso min: 16.92 Å2
Refinement stepCycle: final / Resolution: 2.23→69.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3423 0 23 0 3446
Biso mean--42.53 --
Num. residues----433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033514
X-RAY DIFFRACTIONf_angle_d0.794749
X-RAY DIFFRACTIONf_chiral_restr0.027525
X-RAY DIFFRACTIONf_plane_restr0.003617
X-RAY DIFFRACTIONf_dihedral_angle_d13.5491337
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2292-2.31850.4476950.43941814190970
2.3185-2.4240.29921330.28642528266198
2.424-2.55180.30531370.282926012738100
2.5518-2.71170.30411370.27532605274299
2.7117-2.9210.26051360.262625892725100
2.921-3.2150.34911390.255226362775100
3.215-3.68020.25351380.22132620275899
3.6802-4.63650.22771380.18692632277098
4.6365-69.04020.2091470.18092780292799

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