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- PDB-6xki: Crystal structure of eIF4A-I in complex with RNA bound to des-MeP... -

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Basic information

Entry
Database: PDB / ID: 6xki
TitleCrystal structure of eIF4A-I in complex with RNA bound to des-MePateA, a pateamine A analog
Components
  • Eukaryotic initiation factor 4A-I
  • RNA (5'-R(*AP*GP*AP*GP*AP*GP*AP*GP*AP*G)-3')
KeywordsTRANSLATION/RNA/INHIBITOR / Inhibitor / RNA / Translation initiation / TRANSLATION / TRANSLATION-RNA-INHIBITOR 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 / Deadenylation of mRNA / Translation initiation complex formation / Ribosomal scanning and start codon recognition / ISG15 antiviral mechanism / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / eukaryotic translation initiation factor 4F complex / cytoplasmic translational initiation / translational initiation ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Deadenylation of mRNA / Translation initiation complex formation / Ribosomal scanning and start codon recognition / ISG15 antiviral mechanism / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / eukaryotic translation initiation factor 4F complex / cytoplasmic translational initiation / translational initiation / translation initiation factor activity / double-stranded RNA binding / RNA helicase activity / RNA helicase / ATP hydrolysis activity / ATP binding / 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-V6D / RNA / Eukaryotic initiation factor 4A-I
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsLiang, J. / Naineni, S.K. / Pelletier, J. / Nagar, B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-133535 Canada
CitationJournal: Cell Chem Biol / Year: 2021
Title: Functional mimicry revealed by the crystal structure of an eIF4A:RNA complex bound to the interfacial inhibitor, desmethyl pateamine A.
Authors: Naineni, S.K. / Liang, J. / Hull, K. / Cencic, R. / Zhu, M. / Northcote, P. / Teesdale-Spittle, P. / Romo, D. / Nagar, B. / Pelletier, J.
History
DepositionJun 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 30, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 18, 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: 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)48,7405
Polymers47,6682
Non-polymers1,0723
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-23 kcal/mol
Surface area17610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.785, 99.942, 153.663
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein / RNA chain , 2 types, 2 molecules AB

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


Mass: 44340.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Eif4a1, Ddx2a, Eif4a / Production host: Escherichia coli (E. coli) / References: UniProt: P60843, 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, 29 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-V6D / (3S,6Z,8E,11S,15R)-15-amino-3-[(1E,3E,5E)-7-(dimethylamino)-2,5-dimethylhepta-1,3,5-trien-1-yl]-9,11-dimethyl-4,12-dioxa-20-thia-21-azabicyclo[16.2.1]henicosa-1(21),6,8,18-tetraene-5,13-dione / des-methyl Pateamine A


Mass: 541.745 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H43N3O4S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.76 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: 0.1 M MES pH 6.7, 1.9 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.87→50 Å / Num. obs: 11588 / % possible obs: 96.6 % / Redundancy: 11.4 % / Biso Wilson estimate: 50.56 Å2 / CC1/2: 0.984 / Net I/σ(I): 12.25
Reflection shellResolution: 2.87→2.95 Å / Num. unique obs: 453 / CC1/2: 0.811

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Processing

Software
NameVersionClassification
PHENIX1.18_3861refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZC9

5zc9


Resolution: 2.87→45.58 Å / SU ML: 0.2798 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.2723
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2623 536 5.05 %
Rwork0.2217 10088 -
obs0.2238 10624 87.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.24 Å2
Refinement stepCycle: LAST / Resolution: 2.87→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 222 70 26 3340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323389
X-RAY DIFFRACTIONf_angle_d0.474632
X-RAY DIFFRACTIONf_chiral_restr0.0396536
X-RAY DIFFRACTIONf_plane_restr0.0022550
X-RAY DIFFRACTIONf_dihedral_angle_d11.42051311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.87-3.160.29291050.28821595X-RAY DIFFRACTION57.34
3.16-3.620.28591300.25042641X-RAY DIFFRACTION92.96
3.62-4.560.25211400.212871X-RAY DIFFRACTION99.97
4.56-45.580.25191610.20362981X-RAY DIFFRACTION99.87
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)
10.693992441240.5188536164350.2381973614620.5746902269440.214831245070.4858336335850.0273797871416-0.608259570569-0.1241628549650.803954753438-0.129144351309-0.3434893728320.3426264376040.008569980912880.0003502310885161.88434966093-0.198330652277-0.6429031301890.834437195532-0.1321706178580.633242274437-12.5686507104-29.2218334985-1.00221026439
20.7238027206290.8199224225810.820370418712.37786094575-0.5821944719422.53057176979-0.0460069635805-0.3626812091890.08611967230671.38384132872-0.175132878139-1.21824125355-0.4311748149250.788326337495-0.02849323643790.6625405089470.0156825945074-0.333080582230.441559496225-0.06000493453660.477796788994-14.8199647651-39.7255418635-16.0258301822
32.29698585494-0.418661506237-0.6577613109335.61923280433-0.05703056643072.207101975950.0439256169247-0.212705739936-0.05988913438421.069426283210.01874146753430.122483505875-0.0448482319987-0.231911446158-0.06666128029520.4150982576240.0131953643653-0.04570596829650.334284279288-0.01295744745520.219335111778-27.5197613801-42.4982315445-19.1648066307
40.9780868020740.448998899622-0.06940843126254.57800360636-1.878434782470.786519211607-0.0158949615341-0.3107127354980.6702866350370.771744160684-0.004682119198780.299820519836-0.00872333033727-0.220041379319-0.1788446644191.234318658180.2297729153840.3062951485660.706593886272-0.1105592942920.678807843649-31.9545448572-20.2682530392-17.5595181581
51.28871038532-0.454717307285-0.3687489290152.23111573003-0.7063764126941.63164306138-0.01782960829630.2708274071810.2516370678340.201696841172-0.023132444399-0.942204207069-0.1885443616640.256628290190.02047988776320.176929361787-0.0064244137881-0.05162879804930.4178407233990.02999857297460.696268070565-17.5291665483-17.7441327056-34.2059192378
61.52450129736-0.795467108624-2.24445605948.32526798815-0.7599789220063.809798525270.1973332456520.04898485474130.8103664053810.9584042019790.3304777240070.535895753501-0.526461452686-0.535819453535-0.3647291634540.5595409709750.1512982313910.1871649836210.4747798919130.02298443427420.793562026553-29.9058004176-14.7792387851-24.9228162853
73.52259174264-0.1617004504140.5582830693432.237424617871.252812485731.081760879270.114873408788-0.1060467684751.067492074460.8167330537420.314953073034-0.401893205511-0.1850484794210.246259394615-0.3643679131991.084569197770.1465933172570.2323473818750.6599825430630.04676181056680.975392408056-26.3936786802-4.9145808152-21.8201278345
80.627783418167-0.1629050432750.463083506131.54189460319-0.2090389557251.81025724951-0.1899107089880.2820506826170.0735839388801-0.03831763397410.08981816797471.02733419420.221421077974-0.5413918589860.0918095192429-0.862218683529-0.1450689059140.1667340085160.6564771533660.07834255689420.597630386923-26.3907512689-36.8300138588-36.1050600897
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 29 through 58 )AA29 - 581 - 30
22chain 'A' and (resid 59 through 167 )AA59 - 16731 - 139
33chain 'A' and (resid 168 through 226 )AA168 - 226140 - 198
44chain 'A' and (resid 227 through 255 )AA227 - 255199 - 227
55chain 'A' and (resid 256 through 353 )AA256 - 353228 - 325
66chain 'A' and (resid 354 through 390 )AA354 - 390326 - 362
77chain 'A' and (resid 391 through 406 )AA391 - 406363 - 378
88chain 'B' and (resid 1 through 10 )BD1 - 10

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