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- PDB-6cz5: Crystal structure of small molecule AMP-acrylamide covalently bou... -

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Basic information

Entry
Database: PDB / ID: 6cz5
TitleCrystal structure of small molecule AMP-acrylamide covalently bound to DDX3 S228C
ComponentsATP-dependent RNA helicase DDX3X
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Inhibitor / DEAD-box protein / HYDROLASE-HYDROLASE INHIBITOR complex
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 / NLRP3 inflammasome complex / 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 / RNA stem-loop binding / cell leading edge / lipid homeostasis / positive regulation of interferon-alpha production / positive regulation of translational initiation / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / ribosomal small subunit binding / transcription factor binding / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of type I interferon production / positive regulation of G1/S transition of mitotic cell cycle / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / negative regulation of intrinsic apoptotic signaling pathway / signaling adaptor activity / translation initiation factor binding / stress granule assembly / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of protein autophosphorylation / translational initiation / DNA helicase activity / positive regulation of interferon-beta production / ribonucleoside triphosphate phosphatase activity / protein serine/threonine kinase activator activity / intrinsic apoptotic signaling pathway / positive regulation of translation / cytosolic ribosome assembly / chromosome segregation / response to virus / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of protein serine/threonine kinase activity / mRNA 5'-UTR binding / negative regulation of cell growth / cellular response to virus / Wnt signaling pathway / cytoplasmic stress granule / 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 / cell differentiation / negative regulation of translation / RNA helicase activity / RNA helicase / intracellular signal transduction / cadherin binding / positive regulation of apoptotic process / mRNA binding / innate immune response / GTPase activity / 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 / 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 / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-FPJ / ATP-dependent RNA helicase DDX3X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsBarkovich, K.J. / Moore, M.K. / Hu, Q. / Shokat, K.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)F30 CA203522 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)RO1 CA190409 United States
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Chemical genetic inhibition of DEAD-box proteins using covalent complementarity.
Authors: Barkovich, K.J. / Moore, M.K. / Hu, Q. / Shokat, K.M.
History
DepositionApr 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.name
Revision 1.2Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.3Oct 10, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,5132
Polymers54,1101
Non-polymers4021
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.960, 101.090, 105.690
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: 54110.250 Da / Num. of mol.: 1 / Fragment: UNP residues 132-607 / Mutation: S228C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX3X, DBX, DDX3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O00571, RNA helicase
#2: Chemical ChemComp-FPJ / 5'-O-[(R)-hydroxy(propanoylamino)phosphoryl]adenosine


Mass: 402.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N6O7P / Feature type: SUBJECT OF INVESTIGATION

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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: 2.88 Å3/Da / Density % sol: 57.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 100 mM sodium citrate, 8% PEG3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→73.054 Å / Num. obs: 12100 / % possible obs: 100 % / Redundancy: 5.4 % / Biso Wilson estimate: 87.39 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.057 / Rrim(I) all: 0.135 / Net I/σ(I): 8.5
Reflection shellResolution: 3→3.16 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.089 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.766 / Rpim(I) all: 0.5 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5E7J

5e7j


Resolution: 3→73.054 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.96
RfactorNum. reflection% reflection
Rfree0.2667 566 4.68 %
Rwork0.2219 --
obs0.2242 12082 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 167.14 Å2 / Biso mean: 87.5497 Å2 / Biso min: 41.17 Å2
Refinement stepCycle: final / Resolution: 3→73.054 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3378 0 27 0 3405
Biso mean--107.2 --
Num. residues----427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023471
X-RAY DIFFRACTIONf_angle_d0.5234692
X-RAY DIFFRACTIONf_chiral_restr0.041521
X-RAY DIFFRACTIONf_plane_restr0.004610
X-RAY DIFFRACTIONf_dihedral_angle_d10.6292122
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.0002-3.30210.35261410.321128082949
3.3021-3.77990.33291250.252328352960
3.7799-4.76220.25151430.203628743017
4.7622-73.07510.23921570.201429993156

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