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- PDB-5e7m: Crystal structure of the active catalytic core of the human DEAD-... -

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Basic information

Entry
Database: PDB / ID: 5e7m
TitleCrystal structure of the active catalytic core of the human DEAD-box protein DDX3 bound to AMPPNP
ComponentsATP-dependent RNA helicase DDX3X
KeywordsHYDROLASE / DEAD-box protein / RNA helicase / RecA fold
Function / homology
Function and homology information


positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / CTPase activity / positive regulation of translation in response to endoplasmic reticulum stress / gamete generation / eukaryotic initiation factor 4E binding / RNA strand annealing activity / protein localization to cytoplasmic stress granule / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of mitochondrial translation ...positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / CTPase activity / positive regulation of translation in response to endoplasmic reticulum stress / gamete generation / eukaryotic initiation factor 4E binding / RNA strand annealing activity / protein localization to cytoplasmic stress granule / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of mitochondrial translation / cellular response to arsenic-containing substance / NLRP3 inflammasome complex / positive regulation of protein K63-linked ubiquitination / poly(A) binding / canonical inflammasome complex / gamma-tubulin binding / P granule / negative regulation of non-canonical NF-kappaB signal transduction / transcription factor binding / cellular response to osmotic stress / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of intrinsic apoptotic signaling pathway / ribosomal small subunit binding / cytoplasmic pattern recognition receptor signaling pathway / Wnt signaling pathway / RNA stem-loop binding / cell leading edge / lipid homeostasis / positive regulation of interferon-alpha production / positive regulation of NLRP3 inflammasome complex assembly / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of translational initiation / negative regulation of protein-containing complex assembly / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of viral genome replication / Dengue virus activates/modulates innate and adaptive immune responses / intrinsic apoptotic signaling pathway / positive regulation of type I interferon production / signaling adaptor activity / positive regulation of interferon-beta production / translation initiation factor binding / protein serine/threonine kinase activator activity / stress granule assembly / chromosome segregation / cytosolic ribosome assembly / cellular response to virus / positive regulation of translation / translational initiation / negative regulation of cell growth / positive regulation of non-canonical NF-kappaB signal transduction / response to virus / cytoplasmic stress granule / mRNA 5'-UTR binding / positive regulation of canonical Wnt signaling pathway / positive regulation of cell growth / lamellipodium / cell differentiation / ribonucleoside triphosphate phosphatase activity / secretory granule lumen / ficolin-1-rich granule lumen / innate immune response / DNA helicase activity / RNA helicase activity / intracellular signal transduction / negative regulation of translation / positive regulation of apoptotic process / RNA helicase / cadherin binding / negative regulation of gene expression / mRNA binding / centrosome / positive regulation of gene expression / GTPase activity / negative regulation of apoptotic process / Neutrophil degranulation / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / extracellular exosome / nucleoplasm / ATP binding / extracellular region / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / 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. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / ATP-dependent RNA helicase DDX3X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.304 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 1.2Dec 16, 2015Group: Other
Revision 1.3Feb 10, 2016Group: Database references
Revision 1.4Mar 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)51,5982
Polymers51,0921
Non-polymers5061
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-1 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.930, 100.280, 107.260
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 / Fragment: DEAD-box domains
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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.91 Å3/Da / Density % sol: 57.7 %
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: 2.304→47.5 Å / Num. obs: 25668 / % possible obs: 97.15 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 75.41 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.127 / Rrim(I) all: 0.135 / Χ2: 1.026 / Net I/σ(I): 10.8 / Num. measured all: 198462
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.304-2.3867.60.03714.820.13135741926186727.41974.66
2.36-2.420.1738.2280.2414622188418748.81799.5
2.42-2.490.2655.80.3614259183818356.21799.8
2.49-2.570.4192.8330.7313923179417933.03699.9
2.57-2.660.6222.1910.9813263170317032.348100
2.66-2.750.7221.6041.3612931167516751.72100
2.75-2.850.8271.1451.912663163216321.227100
2.85-2.970.9240.7162.9612075155215510.76899.9
2.97-3.10.9640.4674.4711598149614960.501100
3.1-3.250.9820.2817.111183145314530.301100
3.25-3.430.9910.18810.0610401135613560.202100
3.43-3.640.9950.13314.199972131013100.143100
3.64-3.890.9970.08920.139138123312330.096100
3.89-4.20.9980.06424.278450114911490.069100
4.2-4.60.9980.04732.77446105510550.051100
4.6-5.140.9980.04335.2165259559550.047100
5.14-5.940.9990.04434.6658948718710.048100
5.94-7.270.9990.03837.5550827377370.042100
7.27-10.290.9990.0342.9837795905850.03399.2
10.290.9990.0339.9916843543130.03388.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementResolution: 2.304→47.497 Å / FOM work R set: 0.632 / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.284 1281 4.99 %
Rwork0.2247 24373 -
obs0.2276 25654 97.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 290.59 Å2 / Biso mean: 100.35 Å2 / Biso min: 48.56 Å2
Refinement stepCycle: final / Resolution: 2.304→47.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 31 5 3390
Biso mean--118.05 102.92 -
Num. residues----424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013449
X-RAY DIFFRACTIONf_angle_d1.4024664
X-RAY DIFFRACTIONf_chiral_restr0.052520
X-RAY DIFFRACTIONf_plane_restr0.007604
X-RAY DIFFRACTIONf_dihedral_angle_d15.9481317
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 (%)
2.304-2.39620.55651090.55242101221077
2.3962-2.50530.53141410.49392699284098
2.5053-2.63740.46111440.39527452889100
2.6374-2.80260.32941460.333127542900100
2.8026-3.01890.33191450.292727532898100
3.0189-3.32270.35641460.250427742920100
3.3227-3.80330.27121470.225327992946100
3.8033-4.79110.25411480.184528212969100
4.7911-47.50710.2371550.18242927308299

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