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- PDB-9avr: Human eIF4A-1 in complex with AMP-PNP, RNA, and the inhibitor sil... -

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Basic information

Entry
Database: PDB / ID: 9avr
TitleHuman eIF4A-1 in complex with AMP-PNP, RNA, and the inhibitor silvestrol
Components
  • Eukaryotic initiation factor 4A-I
  • RNA oligonucleotide (AG)5
KeywordsRNA BINDING PROTEIN / Eukaryotic initiation factor 4A-1 / silvestrol inhibitor / anti-cancer / RNA binding / drug
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 / helicase activity / translational initiation / 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 / 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 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 / IODIDE ION / RNA / Eukaryotic initiation factor 4A-I
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsBhatt, G.B. / Naineni, S.K. / Cencic, R.C. / Jiramongkolsiri, E.J. / Huang, S.H. / Pelletier, J.P. / Nagar, B.N.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Protein-RNA interactions mediated by silvestrol-insight into a unique molecular clamp.
Authors: Naineni, S.K. / Bhatt, G. / Jiramongkolsiri, E. / Robert, F. / Cencic, R. / Huang, S. / Nagar, B. / Pelletier, J.
History
DepositionMar 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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 oligonucleotide (AG)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9747
Polymers49,5352
Non-polymers1,4395
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-26 kcal/mol
Surface area17400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.480, 84.295, 88.412
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,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 / eIF-4A-I / eIF4A-I / ATP-dependent RNA helicase eIF4A-1


Mass: 46207.824 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 oligonucleotide (AG)5


Mass: 3327.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 321 molecules

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


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / 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-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#6: Chemical ChemComp-A1AG8 / silvestrol / methyl (1R,2R,3S,3aR,8bS)-6-({(2S,3R,6R)-6-[(1R)-1,2-dihydroxyethyl]-3-methoxy-1,4-dioxan-2-yl}oxy)-1,8b-dihydroxy-8-methoxy-3a-(4-methoxyphenyl)-3-phenyl-2,3,3a,8b-tetrahydro-1H-benzo[b]cyclopenta[d]furan-2-carboxylate


Mass: 654.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H38O13 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium iodide, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.953 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 33958 / % possible obs: 98 % / Redundancy: 6.5 % / Biso Wilson estimate: 20.24 Å2 / CC1/2: 0.956 / Net I/σ(I): 0.3221
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 752 / CC1/2: 0.456

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Processing

Software
NameVersionClassification
PHENIX1.18_3861refinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→44.21 Å / SU ML: 0.1893 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.4538
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1967 4024 9.72 %
Rwork0.147 37379 -
obs0.1519 30812 95.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.35 Å2
Refinement stepCycle: LAST / Resolution: 1.91→44.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2983 177 81 316 3557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01543316
X-RAY DIFFRACTIONf_angle_d1.46574531
X-RAY DIFFRACTIONf_chiral_restr0.0812527
X-RAY DIFFRACTIONf_plane_restr0.008538
X-RAY DIFFRACTIONf_dihedral_angle_d15.78231263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-2.120.24141060.1919907X-RAY DIFFRACTION45
2.12-2.160.2998960.197924X-RAY DIFFRACTION44.76
2.16-2.20.2484950.1941903X-RAY DIFFRACTION44.24
2.2-2.230.2395980.183917X-RAY DIFFRACTION45.35
2.24-2.280.22031090.1603966X-RAY DIFFRACTION46.86
2.28-2.320.24851000.16871075X-RAY DIFFRACTION50.89
2.32-2.380.21211260.17671120X-RAY DIFFRACTION55.13
2.38-2.430.22611370.16781145X-RAY DIFFRACTION57.23
2.43-2.490.25361310.16731254X-RAY DIFFRACTION61.01
2.49-2.560.22181580.16061311X-RAY DIFFRACTION64.15
2.56-2.630.23931500.15411432X-RAY DIFFRACTION70
2.63-2.720.22911470.15711599X-RAY DIFFRACTION76.98
2.72-2.820.21031950.14441648X-RAY DIFFRACTION80.94
2.82-2.930.22611900.14871751X-RAY DIFFRACTION84.69
2.93-3.060.18011870.13921768X-RAY DIFFRACTION87
3.06-3.220.18611950.14211793X-RAY DIFFRACTION87.62
3.22-3.430.17081940.13241840X-RAY DIFFRACTION89.96
3.43-3.690.18312150.13081948X-RAY DIFFRACTION95.04
3.69-4.060.1672090.12191899X-RAY DIFFRACTION92.78
4.06-4.650.1492130.11811962X-RAY DIFFRACTION95.27
4.65-5.850.19032160.13782033X-RAY DIFFRACTION99.65
5.86-44.210.18122160.15112034X-RAY DIFFRACTION99.29
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)
10.517564332719-0.0366941115322-0.6174370799621.15572777018-0.735448427991.32542732869-0.0313670060290.1562221573950.110639389416-0.232713991860.1446109297790.22475910325-0.133972065137-0.688145650182-0.06289441032040.2159316132780.093769294221-0.03559531889790.2857718639670.03457302167350.161675355948-21.92627809394.583312786070.0946629010926
22.100935516620.1181852241831.086020616381.33154990236-0.3270470704391.56371938339-0.04160777699740.2498181306080.112092330038-0.04848844271830.000856303143255-0.16986065993-0.1828657030460.07073491143220.03410794487280.1491566251190.018826021990.01104362510790.0829188410213-0.01034666931210.123959667524-2.276568296594.086986409785.88982871544
31.294006615560.2101729097050.1321509934252.0832731588-0.5822512967851.135830395260.01894607232190.0185152020443-0.141112421814-0.0351244228420.004430051241560.0702511545220.0291853117626-0.111559369725-0.004523599816910.1230937558250.0355509914445-0.02508234040650.146672272765-0.03403504558580.116027680142-12.2197512629-15.745239823114.8885646754
42.935431221260.139854537578-0.2980468543143.00685269892-0.1678455077233.09579500483-0.003948492259750.00818560270438-0.2177282954970.07386901746650.06406937807530.1946054556860.164455252191-0.303252245373-0.0487162608640.1081723093690.0110906643111-0.02003428290820.1139189689990.0008357364039690.159651597281-18.6113518786-18.588253277616.3302748592
56.725862344361.20781852579-1.555447734115.78982996455-0.08393943594742.98989870040.102941906765-0.6589143474170.2139760596780.33861935242-0.28031441135-0.0799219396960.1726130688050.261524775030.113742452450.1236147195870.0245963672259-0.02731414913190.0742585529874-0.02834147899720.1461978430463.43730207891-8.1896512397518.8600273441
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 30 through 81 )AA30 - 811 - 52
22chain 'A' and (resid 82 through 202 )AA82 - 20253 - 173
33chain 'A' and (resid 203 through 320 )AA203 - 320174 - 291
44chain 'A' and (resid 321 through 402 )AA321 - 402292 - 373
55chain 'B' and (resid 1 through 8 )BB1 - 8

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