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- PDB-9dts: Crystal structure of the human eIF4A1/AMPPNP/amidino-rocaglate/po... -

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Basic information

Entry
Database: PDB / ID: 9dts
TitleCrystal structure of the human eIF4A1/AMPPNP/amidino-rocaglate/polypurine RNA complex
Components
  • Eukaryotic initiation factor 4A-I
  • RNA (5'-R(P*AP*GP*AP*GP*AP*GP*AP*G)-3')
KeywordsTRANSLATION / HYDROLASE/RNA / RNA helicase / DEAD box helicase / rocaglate / protein-RNA complex / HYDROLASE-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 / nuclear stress granule / 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 ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / nuclear stress granule / 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 / translation initiation factor activity / translational initiation / helicase activity / ISG15 antiviral mechanism / cytoplasmic stress granule / double-stranded RNA binding / RNA helicase activity / RNA helicase / mRNA binding / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / RNA binding / extracellular exosome / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
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 domain / DEAD/DEAH box helicase / 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 domain / DEAD/DEAH box helicase / 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 / RNA / Eukaryotic initiation factor 4A-I
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsConley, J.F. / Allen, K.N.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118173 United States
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)U01 TR002625 United States
CitationJournal: Acs Omega / Year: 2025
Title: Structural Basis for the Improved RNA Clamping of Amidino-Rocaglates to eIF4A1.
Authors: Conley, J.F. / Brown, L.E. / McNeely, J.H. / Pelletier, J. / Porco Jr., J.A. / Allen, K.N.
History
DepositionOct 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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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: Eukaryotic initiation factor 4A-I
C: Eukaryotic initiation factor 4A-I
D: Eukaryotic initiation factor 4A-I
W: RNA (5'-R(P*AP*GP*AP*GP*AP*GP*AP*G)-3')
X: RNA (5'-R(P*AP*GP*AP*GP*AP*GP*AP*G)-3')
Y: RNA (5'-R(P*AP*GP*AP*GP*AP*GP*AP*G)-3')
Z: RNA (5'-R(P*AP*GP*AP*GP*AP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,59620
Polymers190,2358
Non-polymers4,36012
Water16,195899
1
A: Eukaryotic initiation factor 4A-I
W: RNA (5'-R(P*AP*GP*AP*GP*AP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6495
Polymers47,5592
Non-polymers1,0903
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-24 kcal/mol
Surface area18410 Å2
MethodPISA
2
B: Eukaryotic initiation factor 4A-I
X: RNA (5'-R(P*AP*GP*AP*GP*AP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6495
Polymers47,5592
Non-polymers1,0903
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-26 kcal/mol
Surface area18100 Å2
MethodPISA
3
C: Eukaryotic initiation factor 4A-I
Y: RNA (5'-R(P*AP*GP*AP*GP*AP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6495
Polymers47,5592
Non-polymers1,0903
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-21 kcal/mol
Surface area18110 Å2
MethodPISA
4
D: Eukaryotic initiation factor 4A-I
Z: RNA (5'-R(P*AP*GP*AP*GP*AP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6495
Polymers47,5592
Non-polymers1,0903
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-25 kcal/mol
Surface area18210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.110, 87.314, 93.159
Angle α, β, γ (deg.)95.220, 105.290, 108.350
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein / RNA chain , 2 types, 8 molecules ABCDWXYZ

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


Mass: 44231.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Cleavage product of SUMO-fusion protein / 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(P*AP*GP*AP*GP*AP*GP*AP*G)-3')


Mass: 3327.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 911 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-A1BB1 / (3aR,4R,5S,5aR,10bR)-3a-hydroxy-N,8,10-trimethoxy-5a-(4-methoxyphenyl)-N,2-dimethyl-5-phenyl-3a,4,5,5a-tetrahydro-1H-[1]benzofuro[3',2':1,5]cyclopenta[1,2-d]imidazole-4-carboxamide


Mass: 559.610 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H33N3O7 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 899 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 8
Details: 0.2 M ammonium acetate, 8% PEG20000, 10% Hampton Silver Bullet Reagent B5 (0.33% w/v 2,7-naphthalenedisulfonic acid disodium salt, 0.33% w/v azelaic acid, 0.33% w/v trans-cinnamic acid, 0.02 ...Details: 0.2 M ammonium acetate, 8% PEG20000, 10% Hampton Silver Bullet Reagent B5 (0.33% w/v 2,7-naphthalenedisulfonic acid disodium salt, 0.33% w/v azelaic acid, 0.33% w/v trans-cinnamic acid, 0.02 M HEPES sodium pH 6.8)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 1.689→81.362 Å / Num. obs: 201775 / % possible obs: 96 % / Redundancy: 3 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.061 / Rrim(I) all: 0.11 / Net I/σ(I): 5.61
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 2.7 % / Rmerge(I) obs: 1.18 / Num. unique obs: 19049 / CC1/2: 0.368 / CC star: 0.773 / Rpim(I) all: 0.84 / Rrim(I) all: 1.45 / % possible all: 91.16

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Processing

Software
NameVersionClassification
autoPROC1.0.5data processing
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→40.68 Å / SU ML: 0.2261 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.027
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2402 1999 0.99 %
Rwork0.2029 199758 -
obs0.2033 201757 95.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.02 Å2
Refinement stepCycle: LAST / Resolution: 1.69→40.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12035 720 292 899 13946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012213437
X-RAY DIFFRACTIONf_angle_d1.267818377
X-RAY DIFFRACTIONf_chiral_restr0.06742110
X-RAY DIFFRACTIONf_plane_restr0.01932204
X-RAY DIFFRACTIONf_dihedral_angle_d10.6092164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.730.34991290.35213353X-RAY DIFFRACTION89.87
1.73-1.780.33871540.320114009X-RAY DIFFRACTION94.72
1.78-1.830.35191300.292214333X-RAY DIFFRACTION96.07
1.83-1.890.2861420.269914311X-RAY DIFFRACTION96.27
1.89-1.960.27031510.245214323X-RAY DIFFRACTION96.4
1.96-2.030.27191500.227714318X-RAY DIFFRACTION96.62
2.03-2.130.24771290.210314438X-RAY DIFFRACTION96.47
2.13-2.240.2671580.206914292X-RAY DIFFRACTION96.53
2.24-2.380.25871360.194514402X-RAY DIFFRACTION96.77
2.38-2.560.24041360.193214348X-RAY DIFFRACTION96.66
2.56-2.820.25461440.201614446X-RAY DIFFRACTION96.92
2.82-3.230.21581490.20214383X-RAY DIFFRACTION96.88
3.23-4.070.21021430.177414273X-RAY DIFFRACTION96.06
4.07-40.680.22511480.185814529X-RAY DIFFRACTION97.62

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