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- PDB-5zc9: Crystal structure of the human eIF4A1-ATP analog-RocA-polypurine ... -

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Basic information

Entry
Database: PDB / ID: 5zc9
TitleCrystal structure of the human eIF4A1-ATP analog-RocA-polypurine RNA complex
Components
  • Eukaryotic initiation factor 4A-I
  • RNA (5'-R(*AP*GP*AP*GP*AP*GP*AP*GP*AP*G)-3')
KeywordsTRANSLATION/RNA / INITIATION FACTOR / DEAD-BOX / HELICASE / PROTEIN-RNA COMPLEX / ATPase / ROCAGLAMIDE A / ANTICANCER COMPOUND / TRANSLATION / TRANSLATION-RNA complex
Function / homologyDEAD/DEAH box helicase domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / DEAD-box subfamily ATP-dependent helicases signature. / Helicase conserved C-terminal domain / DEAD/DEAH box helicase / Eukaryotic initiation factor 4A / P-loop containing nucleoside triphosphate hydrolase / RNA helicase, DEAD-box type, Q motif / Helicase superfamily 1/2, ATP-binding domain / Helicase, C-terminal ...DEAD/DEAH box helicase domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / DEAD-box subfamily ATP-dependent helicases signature. / Helicase conserved C-terminal domain / DEAD/DEAH box helicase / Eukaryotic initiation factor 4A / P-loop containing nucleoside triphosphate hydrolase / RNA helicase, DEAD-box type, Q motif / Helicase superfamily 1/2, ATP-binding domain / Helicase, C-terminal / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / ISG15 antiviral mechanism / L13a-mediated translational silencing of Ceruloplasmin expression / Deadenylation of mRNA / Translation initiation complex formation / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / translation factor activity, RNA binding / RNA cap binding / eukaryotic translation initiation factor 4F complex / ATP-dependent RNA helicase activity / translational initiation / translation initiation factor activity / helicase activity / double-stranded RNA binding / RNA helicase / mRNA binding / viral process / RNA binding / extracellular exosome / membrane / ATP binding / cytosol / cytoplasm / Eukaryotic initiation factor 4A-I
Function and homology information
Specimen sourceHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2 Å resolution
AuthorsIwasaki, W. / Takahashi, M. / Sakamoto, A. / Iwasaki, S. / Ito, T.
CitationJournal: Mol. Cell / Year: 2019
Title: The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA.
Authors: Iwasaki, S. / Iwasaki, W. / Takahashi, M. / Sakamoto, A. / Watanabe, C. / Shichino, Y. / Floor, S.N. / Fujiwara, K. / Mito, M. / Dodo, K. / Sodeoka, M. / Imataka, H. / Honma, T. / Fukuzawa, K. / Ito, T. / Ingolia, N.T.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 16, 2018 / Release: Jan 16, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 16, 2019Structure modelrepositoryInitial release
1.1Mar 13, 2019Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic initiation factor 4A-I
B: RNA (5'-R(*AP*GP*AP*GP*AP*GP*AP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2655
Polyers48,2292
Non-polymers1,0363
Water4,432246
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)3070
ΔGint (kcal/M)-25
Surface area (Å2)17640
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)68.508, 100.263, 155.422
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI 2 2 2

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Components

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Protein/peptide / RNA chain , 2 types, 2 molecules AB

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


Mass: 44901.445 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4A1, DDX2A, EIF4A / Production host: Escherichia coli (E. coli) / References: UniProt: P60842, RNA helicase
#2: RNA chain RNA (5'-R(*AP*GP*AP*GP*AP*GP*AP*GP*AP*G)-3')


Mass: 3327.100 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 249 molecules

#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Formula: C10H17N6O12P3 / Comment: AMP-PNP (energy-carrying molecule analogue) *YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#5: Chemical ChemComp-RCG / (1R,2R,3S,3aR,8bS)-6,8-dimethoxy-3a-(4-methoxyphenyl)-N,N-dimethyl-1,8b-bis(oxidanyl)-3-phenyl-2,3-dihydro-1H-cyclopenta[b][1]benzofuran-2-carboxamide / Rocaglamide, Rocaglamide A


Mass: 505.559 Da / Num. of mol.: 1 / Formula: C29H31NO7 / Rocaglamide
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Formula: H2O / Water

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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: 2.77 / Density percent sol: 55.55 %
Crystal growTemp: 293 K / Method: vapor diffusion, sitting drop
Details: 80mM HEPES (pH7.5), 1120mM tri-sodium citrate, 100mM ammonium sulfate, 20mM Bis-Tris (pH 6.0), 0.2% (w/v) polyethylene glycol 3350, 40mM lithium chloride

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Collection date: Jan 24, 2018
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 29.65 Å2 / D resolution high: 2 Å / D resolution low: 45.733 Å / Number obs: 36536 / NetI over sigmaI: 11.52 / Redundancy: 6.6 % / Percent possible obs: 99.78
Reflection shellHighest resolution: 2 Å / Lowest resolution: 2.072 Å / MeanI over sigI obs: 1.6 / Number unique obs: 3603 / Redundancy: 6.6 % / Percent possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZU6
Overall SU ML: 0.27 / Cross valid method: FREE R-VALUE / Sigma F: 1.35 / Overall phase error: 26.1
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å
Least-squares processR factor R free: 0.2305 / R factor R work: 0.1929 / R factor obs: 0.1949 / Highest resolution: 2 Å / Lowest resolution: 45.733 Å / Number reflection R free: 1843 / Number reflection obs: 36502 / Percent reflection R free: 5.05 / Percent reflection obs: 99.8
Refine hist #LASTHighest resolution: 2 Å / Lowest resolution: 45.733 Å
Number of atoms included #LASTProtein: 3021 / Nucleic acid: 222 / Ligand: 69 / Solvent: 246 / Total: 3558
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043390
X-RAY DIFFRACTIONf_angle_d0.6934642
X-RAY DIFFRACTIONf_dihedral_angle_d18.7462044
X-RAY DIFFRACTIONf_chiral_restr0.046538
X-RAY DIFFRACTIONf_plane_restr0.003548
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
2.00010.34080.29532.0542131264499.00
2.05420.27490.27442.11461112634100.00
2.11460.34180.25832.18291362622100.00
2.18290.30500.23822.26091342651100.00
2.26090.27660.22492.35141412650100.00
2.35140.26360.22212.45841492636100.00
2.45840.26710.22292.58801442645100.00
2.58800.28920.21532.75011412663100.00
2.75010.26940.21662.96241472644100.00
2.96240.25150.20193.26051332690100.00
3.26050.20850.17293.73211672650100.00
3.73210.16630.14214.70131482712100.00
4.70130.17980.158945.74451612818100.00

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