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- PDB-5zbz: Crystal structure of the DEAD domain of Human eIF4A with sanguinarine -

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Basic information

Entry
Database: PDB / ID: 5zbz
TitleCrystal structure of the DEAD domain of Human eIF4A with sanguinarine
ComponentsEukaryotic initiation factor 4A-I
KeywordsHYDROLASE / eukaryotic translation initiation factor 4A / sanguinarine / inhibitor / TRANSLATION
Function / homology
Function and homology information


Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / RNA cap binding / eukaryotic translation initiation factor 4F complex / cytoplasmic translational initiation / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / translation factor activity, RNA binding / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / Ribosomal scanning and start codon recognition / Translation initiation complex formation ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / RNA cap binding / eukaryotic translation initiation factor 4F complex / cytoplasmic translational initiation / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / translation factor activity, RNA binding / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / Ribosomal scanning and start codon recognition / Translation initiation complex formation / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / translational initiation / translation initiation factor activity / helicase activity / ISG15 antiviral mechanism / double-stranded RNA binding / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / RNA binding / extracellular exosome / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
ATP-dependent RNA helicase eIF4A, DEAD-box helicase domain / 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. ...ATP-dependent RNA helicase eIF4A, DEAD-box helicase domain / 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
MALONATE ION / Chem-SAU / Eukaryotic initiation factor 4A-I
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.30860259206 Å
AuthorsDing, Y. / Ding, L.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31470764 China
National Natural Science Foundation of China21572038 China
National Natural Science Foundation of China91527305 China
CitationJournal: Cell Chem Biol / Year: 2019
Title: Targeting the N Terminus of eIF4AI for Inhibition of Its Catalytic Recycling.
Authors: Jiang, C. / Tang, Y. / Ding, L. / Tan, R. / Li, X. / Lu, J. / Jiang, J. / Cui, Z. / Tang, Z. / Li, W. / Cao, Z. / Schneider-Poetsch, T. / Jiang, W. / Luo, C. / Ding, Y. / Liu, J. / Dang, Y.
History
DepositionFeb 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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

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Assembly

Deposited unit
A: Eukaryotic initiation factor 4A-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3603
Polymers24,9261
Non-polymers4342
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Elute in the same position.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint4 kcal/mol
Surface area10620 Å2
Unit cell
Length a, b, c (Å)73.471, 56.630, 66.324
Angle α, β, γ (deg.)90.000, 116.775, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11A-517-

HOH

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Components

#1: Protein Eukaryotic initiation factor 4A-I / eIF4A-I / ATP-dependent RNA helicase eIF4A-1


Mass: 24926.096 Da / Num. of mol.: 1 / Fragment: DEAD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4A1, DDX2A, EIF4A / Plasmid: pMBP (pMal-C2x derived)
Details (production host): N terminal MBP and poly-His tag, TEV cleavage site
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P60842, RNA helicase
#2: Chemical ChemComp-SAU / 13-methyl[1,3]benzodioxolo[5,6-c][1,3]dioxolo[4,5-i]phenanthridin-13-ium / Sanguinarine / Sanguinarine


Mass: 332.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H14NO4 / Comment: alkaloid*YM
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Sodium malonate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979253 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979253 Å / Relative weight: 1
ReflectionResolution: 1.309→36.49 Å / Num. obs: 53159 / % possible obs: 90.66 % / Redundancy: 2 % / Biso Wilson estimate: 18.1276228586 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.02669 / Rpim(I) all: 0.02669 / Rrim(I) all: 0.03775 / Net I/σ(I): 12.23
Reflection shellResolution: 1.309→1.355 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.3181 / Mean I/σ(I) obs: 2.21 / Num. unique obs: 5697 / CC1/2: 0.763 / Rpim(I) all: 0.3181 / Rrim(I) all: 0.4498 / % possible all: 97.52

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZU6
Resolution: 1.30860259206→36.4916112542 Å / SU ML: 0.147287544653 / Cross valid method: FREE R-VALUE / σ(F): 0.31589380531 / σ(I): 1996 / Phase error: 23.7075111376
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.210421443451 1999 3.76282352941 %
Rwork0.193698497124 51126 -
obs0.194325913427 53125 90.6709221553 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.529063773 Å2
Refinement stepCycle: LAST / Resolution: 1.30860259206→36.4916112542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 32 132 1896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009274156731341794
X-RAY DIFFRACTIONf_angle_d1.250774494232430
X-RAY DIFFRACTIONf_chiral_restr0.084464824928271
X-RAY DIFFRACTIONf_plane_restr0.00743692373154302
X-RAY DIFFRACTIONf_dihedral_angle_d16.6898421826675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3086-1.34130.3118323360991560.3024453493993988X-RAY DIFFRACTION99.2337164751
1.3413-1.37760.254141954387600.2926691394351523X-RAY DIFFRACTION86.7872807018
1.3776-1.41810.2945968339781260.2875304548773233X-RAY DIFFRACTION93.1244801774
1.4181-1.46390.2404312355281480.2643858155673783X-RAY DIFFRACTION94.7914154811
1.4639-1.51620.263525242431540.2199726790593970X-RAY DIFFRACTION99.3256262042
1.5162-1.57690.246445885741570.2102434760284004X-RAY DIFFRACTION99.2604961832
1.5769-1.64870.2161545412281560.2084300411714005X-RAY DIFFRACTION99.4978479197
1.6487-1.73560.234453927931560.2139349523073979X-RAY DIFFRACTION99.4707721915
1.7356-1.84440.2156456180961570.213391227863996X-RAY DIFFRACTION99.2116579073
1.8444-1.98680.2081565177811170.2057240512012997X-RAY DIFFRACTION74.5689655172
1.9868-2.18670.2139120346771570.1845092015184006X-RAY DIFFRACTION99.2371871275
2.1867-2.5030.1869139728011540.1781297470963970X-RAY DIFFRACTION98.6602870813
2.503-3.15330.1979986753671550.1867930437213946X-RAY DIFFRACTION96.7445152159
3.1533-36.50580.2030312692481460.1782396975793726X-RAY DIFFRACTION90.5307458499

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