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- PDB-2i4i: Crystal Structure of human DEAD-box RNA helicase DDX3X -

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Basic information

Entry
Database: PDB / ID: 2i4i
TitleCrystal Structure of human DEAD-box RNA helicase DDX3X
ComponentsATP-dependent RNA helicase DDX3X
KeywordsHYDROLASE / RNA / HELICASE / DEAD / STRUCTURAL GENOMICS / SGC / Structural Genomics Consortium
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 / eukaryotic initiation factor 4E binding / RNA strand annealing activity / positive regulation of chemokine (C-C motif) ligand 5 production / RNA secondary structure unwinding ...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 / eukaryotic initiation factor 4E binding / RNA strand annealing activity / positive regulation of chemokine (C-C motif) ligand 5 production / RNA secondary structure unwinding / gamete generation / positive regulation of protein K63-linked ubiquitination / NLRP3 inflammasome complex / 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 / cell leading edge / lipid homeostasis / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / transcription factor binding / ribosomal small subunit binding / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of type I interferon production / positive regulation of translational initiation / positive regulation of viral genome replication / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of interferon-alpha production / negative regulation of protein-containing complex assembly / signaling adaptor activity / stress granule assembly / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / DNA helicase activity / positive regulation of protein autophosphorylation / translation initiation factor binding / translational initiation / positive regulation of interferon-beta production / ribonucleoside triphosphate phosphatase activity / protein serine/threonine kinase activator activity / intrinsic apoptotic signaling pathway / cytosolic ribosome assembly / positive regulation of translation / chromosome segregation / response to virus / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / positive regulation of non-canonical NF-kappaB signal transduction / RNA stem-loop binding / positive regulation of canonical Wnt signaling pathway / lamellipodium / positive regulation of cell growth / secretory granule lumen / ficolin-1-rich granule lumen / RNA helicase activity / cell differentiation / negative regulation of translation / 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 / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
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 / 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-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 / 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 MONOPHOSPHATE / ATP-dependent RNA helicase DDX3X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHogbom, M. / Karlberg, T. / Arrowsmith, C. / Berglund, H. / Busam, R.D. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. ...Hogbom, M. / Karlberg, T. / Arrowsmith, C. / Berglund, H. / Busam, R.D. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. / Hallberg, B.M. / Hammarstrom, M. / Johansson, I. / Kotenyova, T. / Magnusdottir, A. / Nilsson-Ehle, P. / Nordlund, P. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / Uppenberg, J. / Van Den Berg, S. / Wallden, K. / Weigelt, J. / Welin, M. / Holmberg-Schiavone, L. / Structural Genomics Consortium (SGC)
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of Conserved Domains 1 and 2 of the Human DEAD-box Helicase DDX3X in Complex with the Mononucleotide AMP
Authors: Hogbom, M. / Collins, R. / van den Berg, S. / Jenvert, R.-M. / Karlberg, T. / Kotenyova, T. / Flores, A. / Karlsson Hedestam, G.B. / Holmberg Schiavone, L.H.
History
DepositionAug 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,4742
Polymers47,1271
Non-polymers3471
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.288, 67.288, 253.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 47126.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX3X / Plasmid: pNIC-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O00571, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 3.51 Å3/Da / Density % sol: 64.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: 1.75M Na formate, 0.1M Tris pH 7.5, 20mM ATPgS and MgCl2, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 22, 2006
RadiationMonochromator: Three sets of four different thickness of Aluminium or Carbon foils
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.2→14.91 Å / Num. all: 32841 / Num. obs: 32841 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 %
Reflection shellResolution: 2.2→2.26 Å / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DNAdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WRB for the DEAD domain and 2DB3 for the helicase domain

1wrb

2db3


Resolution: 2.2→14.91 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 8.982 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21822 1751 5.1 %RANDOM
Rwork0.18719 ---
all0.18719 33112 --
obs0.18873 32841 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.846 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20.96 Å20 Å2
2--1.91 Å20 Å2
3----2.87 Å2
Refinement stepCycle: LAST / Resolution: 2.2→14.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3243 0 23 199 3465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223328
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.9784493
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4565405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45123.396159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97915596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4851531
X-RAY DIFFRACTIONr_chiral_restr0.1130.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022508
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.21446
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22246
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2199
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0271.52099
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6523269
X-RAY DIFFRACTIONr_scbond_it2.65631388
X-RAY DIFFRACTIONr_scangle_it4.1664.51224
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 145 -
Rwork0.206 2321 -
obs--98.68 %
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)
12.55920.85841.09271.30030.96877.3301-0.0909-0.01250.0531-0.1211-0.08570.1991-0.0871-0.84850.1766-0.1278-0.119-0.0205-0.0505-0.0079-0.251215-11.78520.382
21.48180.3191-1.18491.6048-0.33473.0366-0.0654-0.0306-0.0548-0.27030.0404-0.1348-0.02130.24460.0249-0.0836-0.1516-0.0038-0.1568-0.0074-0.32332.859-9.00315.027
30.4768-0.01360.1624.15683.99075.6572-0.0154-0.159-0.0144-0.23410.2068-0.1118-0.16950.2167-0.1914-0.0325-0.11780.0757-0.0406-0.0085-0.2790.879-39.14133.052
42.1515-0.3504-1.92782.9311.29449.86940.1346-0.14690.1399-0.49760.2931-0.4313-1.16520.6649-0.42770.228-0.27270.1325-0.1081-0.0507-0.22836.067-39.17918.409
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA167 - 2492 - 84
2X-RAY DIFFRACTION2AA250 - 40485 - 239
3X-RAY DIFFRACTION3AA405 - 496240 - 331
4X-RAY DIFFRACTION4AA497 - 580332 - 415

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