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- PDB-9i9g: Crystal structure of human eIF4A1 C-terminal domain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 9i9g
TitleCrystal structure of human eIF4A1 C-terminal domain in complex with hippuristanol
ComponentsEukaryotic initiation factor 4A-I
KeywordsTRANSLATION / INITIATION FACTOR / DEAD-BOX / HELICASE / ATPASE
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 / nuclear stress granule / 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 ...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 / nuclear stress granule / 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 / 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
: / Eukaryotic initiation factor 4A-I
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTurnbull, A.P. / Schmidt, T. / Bushell, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: To Be Published
Title: The mechanism of selective eIF4A1-dependent translation
Authors: Schmidt, T. / Turnbull, A.P. / Bushell, M.
History
DepositionFeb 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release

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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)20,3212
Polymers19,8591
Non-polymers4631
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9010 Å2
Unit cell
Length a, b, c (Å)31.199, 32.974, 37.781
Angle α, β, γ (deg.)77.093, 74.669, 81.044
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 19858.535 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: Chemical ChemComp-A1I1L / Hippuristanol / (1S,2S,3'S,4S,6R,7R,8R,9S,11S,12S,13S,16R,18S)-2',2',3',7,9,13-hexamethylspiro[5-oxapentacyclo[10.8.0.0^2,9.0^4,8.0^13,18]icosane-6,5'-oxolane]-7,11,16-triol


Mass: 462.662 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H46O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
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: 1.83 Å3/Da / Density % sol: 32.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20 % (w/v) PEG 6000, 0.2 M sodium chloride, 0.1 M sodium acetate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.7→35.76 Å / Num. obs: 15055 / % possible obs: 97 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rrim(I) all: 0.06 / Net I/σ(I): 14.2
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 714 / CC1/2: 0.967 / Rrim(I) all: 0.173

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→35.002 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.096 / SU ML: 0.071 / Cross valid method: FREE R-VALUE / ESU R: 0.116 / ESU R Free: 0.11
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1896 771 5.123 %
Rwork0.1489 14278 -
all0.151 --
obs-15049 97.003 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.507 Å2
Baniso -1Baniso -2Baniso -3
1-0.202 Å20.055 Å2-0.114 Å2
2---0.583 Å20.29 Å2
3---0.381 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1354 0 33 167 1554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121447
X-RAY DIFFRACTIONr_bond_other_d0.0030.0161389
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.6931981
X-RAY DIFFRACTIONr_angle_other_deg0.7321.6253179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8415176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.466516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.40610254
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.6051074
X-RAY DIFFRACTIONr_chiral_restr0.090.2236
X-RAY DIFFRACTIONr_chiral_restr_other1.1250.214
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021697
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02347
X-RAY DIFFRACTIONr_nbd_refined0.2180.2307
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.21359
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2721
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2829
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2650.2107
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.190.222
X-RAY DIFFRACTIONr_nbd_other0.190.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.232
X-RAY DIFFRACTIONr_mcbond_it1.531.412678
X-RAY DIFFRACTIONr_mcbond_other1.5291.411679
X-RAY DIFFRACTIONr_mcangle_it2.3712.532847
X-RAY DIFFRACTIONr_mcangle_other2.372.531848
X-RAY DIFFRACTIONr_scbond_it2.6441.717769
X-RAY DIFFRACTIONr_scbond_other2.6421.716770
X-RAY DIFFRACTIONr_scangle_it4.0772.9951129
X-RAY DIFFRACTIONr_scangle_other4.0752.9931130
X-RAY DIFFRACTIONr_lrange_it5.75524.0841732
X-RAY DIFFRACTIONr_lrange_other5.75424.0751733
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.7-1.7440.168610.16910160.16911780.9820.98391.42610.159
1.744-1.7920.227610.1639970.16710970.9730.98496.44490.155
1.792-1.8440.23530.16610040.1711030.9690.98495.82960.159
1.844-1.90.204530.1559550.15810440.9750.98596.55170.152
1.9-1.9620.229540.1599230.16210170.9670.98596.06690.155
1.962-2.0310.216430.1519130.1549880.9760.98796.76110.149
2.031-2.1070.219450.1518970.1559690.9730.98697.21360.151
2.107-2.1930.208400.1448400.1479050.9740.98897.23760.147
2.193-2.290.208450.1467990.1498670.9690.98897.34720.149
2.29-2.4010.178420.1457760.1478410.9780.98797.26520.151
2.401-2.5310.186440.1417550.1438140.9790.98898.15720.148
2.531-2.6830.205330.146960.1437440.9750.98997.98390.146
2.683-2.8670.167420.1496610.157140.9840.98798.45940.159
2.867-3.0950.158310.1436260.1446700.9830.98898.05970.155
3.095-3.3880.178340.1495630.1516030.9790.98799.0050.165
3.388-3.7830.141310.1465240.1455600.9880.98899.10710.161
3.783-4.360.152150.1274630.1284820.9850.9999.17010.148
4.36-5.320.189130.1393980.1414130.980.9999.51570.166
5.32-7.4380.186200.1932980.1923190.9860.98299.68650.219
7.438-35.0020.279110.1611740.1681850.9660.9811000.183

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