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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 / 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 / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / cytoplasmic translational initiation / 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 / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / cytoplasmic translational initiation / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-RCG / RNA / Eukaryotic initiation factor 4A-I
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
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, ...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.
History
DepositionFeb 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Polymers48,2292
Non-polymers1,0363
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-25 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
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-MI222

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Components

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Protein / RNA chain , 2 types, 2 molecules AB

#1: Protein 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 method: isolated from a genetically manipulated source
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 method: obtained synthetically / 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 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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 / Rocaglamide


Mass: 505.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H31NO7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.77 Å3/Da / Density % sol: 55.55 %
Crystal growTemperature: 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 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→45.733 Å / Num. obs: 36536 / % possible obs: 99.78 % / Redundancy: 6.6 % / Biso Wilson estimate: 29.65 Å2 / Net I/σ(I): 11.52
Reflection shellResolution: 2→2.072 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3603 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZU6

2zu6


Resolution: 2→45.733 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1
RfactorNum. reflection% reflection
Rfree0.2305 1843 5.05 %
Rwork0.1929 --
obs0.1949 36502 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→45.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 222 69 246 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
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.05420.34081310.29532644X-RAY DIFFRACTION99
2.0542-2.11460.27491110.27442634X-RAY DIFFRACTION100
2.1146-2.18290.34181360.25832622X-RAY DIFFRACTION100
2.1829-2.26090.3051340.23822651X-RAY DIFFRACTION100
2.2609-2.35140.27661410.22492650X-RAY DIFFRACTION100
2.3514-2.45840.26361490.22212636X-RAY DIFFRACTION100
2.4584-2.5880.26711440.22292645X-RAY DIFFRACTION100
2.588-2.75010.28921410.21532663X-RAY DIFFRACTION100
2.7501-2.96240.26941470.21662644X-RAY DIFFRACTION100
2.9624-3.26050.25151330.20192690X-RAY DIFFRACTION100
3.2605-3.73210.20851670.17292650X-RAY DIFFRACTION100
3.7321-4.70130.16631480.14212712X-RAY DIFFRACTION100
4.7013-45.74450.17981610.15892818X-RAY DIFFRACTION100

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