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- PDB-5osx: Translation initiation factor 4E in complex with m7G(5'S)ppp(5'S)... -

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Basic information

Entry
Database: PDB / ID: 5osx
TitleTranslation initiation factor 4E in complex with m7G(5'S)ppp(5'S)G mRNA 5' cap analog
ComponentsEukaryotic translation initiation factor 4EEIF4E
KeywordsTRANSLATION / Protein-ligand complex / translation initiation factor / eIF4E / m7G(5'S)ppp(5'S)G / phosphorothiolate / mRNA 5' cap analog
Function / homology
Function and homology information


Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / 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 ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / 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 / mTORC1-mediated signalling / eukaryotic initiation factor 4G binding / regulation of translation at postsynapse, modulating synaptic transmission / chromatoid body / eukaryotic translation initiation factor 4F complex / mRNA cap binding / : / RNA 7-methylguanosine cap binding / nuclear export / RISC complex / postsynaptic cytosol / stem cell population maintenance / negative regulation of neuron differentiation / behavioral fear response / mRNA export from nucleus / translational initiation / translation initiation factor activity / cellular response to dexamethasone stimulus / positive regulation of mitotic cell cycle / P-body / G1/S transition of mitotic cell cycle / cytoplasmic ribonucleoprotein granule / neuron differentiation / cytoplasmic stress granule / regulation of translation / postsynapse / DNA-binding transcription factor binding / negative regulation of translation / nuclear body / nuclear speck / translation / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / protein-containing complex / nucleus / cytosol / cytoplasm
Similarity search - Function
RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Eukaryotic translation initiation factor 4E (eIF-4E), conserved site / Eukaryotic initiation factor 4E signature. / Translation Initiation factor eIF- 4e / Eukaryotic initiation factor 4E / Translation Initiation factor eIF- 4e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AKW / : / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsWarminski, M. / Nowak, E. / Wojtczak, B.A. / Fac-Dabrowska, K. / Kubacka, D. / Nowicka, A. / Sikorski, P.J. / Kowalska, J. / Jemielity, J. / Nowotny, M.
Funding support Poland, 2items
OrganizationGrant numberCountry
Ministry of Science and Higher EducationDI2012 024842 Poland
Foundation for Polish ScienceTEAM/2016-2/13 Poland
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: 5'-Phosphorothiolate Dinucleotide Cap Analogues: Reagents for Messenger RNA Modification and Potent Small-Molecular Inhibitors of Decapping Enzymes.
Authors: Wojtczak, B.A. / Sikorski, P.J. / Fac-Dabrowska, K. / Nowicka, A. / Warminski, M. / Kubacka, D. / Nowak, E. / Nowotny, M. / Kowalska, J. / Jemielity, J.
History
DepositionAug 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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 translation initiation factor 4E
B: Eukaryotic translation initiation factor 4E
C: Eukaryotic translation initiation factor 4E
D: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2917
Polymers88,5804
Non-polymers1,7103
Water3,909217
1
A: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9812
Polymers22,1451
Non-polymers8361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0203
Polymers22,1451
Non-polymers8752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Eukaryotic translation initiation factor 4E


Theoretical massNumber of molelcules
Total (without water)22,1451
Polymers22,1451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Eukaryotic translation initiation factor 4E


Theoretical massNumber of molelcules
Total (without water)22,1451
Polymers22,1451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.843, 37.855, 145.987
Angle α, β, γ (deg.)86.56, 84.56, 77.05
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Eukaryotic translation initiation factor 4E / EIF4E / mRNA cap-binding protein / eIF-4F 25 kDa subunit


Mass: 22145.113 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Eif4e / Production host: Escherichia coli (E. coli) / References: UniProt: P63073
#2: Chemical ChemComp-AKW / [(2~{S},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-3~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl-[[[(3~{R},4~{S})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-phosphinic acid


Mass: 835.572 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N10O16P3S2
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1M BIS-TRIS propane pH 9.0, 20% v/v PEG MME 550 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 57473 / % possible obs: 95.2 % / Redundancy: 2.43 % / CC1/2: 0.997 / Rmerge(I) obs: 0.058 / Net I/σ(I): 10.08
Reflection shellResolution: 1.92→2.03 Å / Redundancy: 2.34 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.04 / Num. unique obs: 9143 / CC1/2: 0.822 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L8B

1l8b


Resolution: 1.92→48.405 Å / SU ML: 0.25 / Cross valid method: NONE / σ(F): 1.98 / Phase error: 28.39
RfactorNum. reflection% reflection
Rfree0.2689 2100 3.65 %
Rwork0.2243 --
obs0.2259 57460 95.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.92→48.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4772 0 67 217 5056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095002
X-RAY DIFFRACTIONf_angle_d0.96842
X-RAY DIFFRACTIONf_dihedral_angle_d15.8222925
X-RAY DIFFRACTIONf_chiral_restr0.056747
X-RAY DIFFRACTIONf_plane_restr0.006870
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9155-1.960.30011330.29093526X-RAY DIFFRACTION91
1.96-2.0090.30421400.27213686X-RAY DIFFRACTION96
2.009-2.06340.31511410.25793723X-RAY DIFFRACTION96
2.0634-2.12410.32571430.25263762X-RAY DIFFRACTION96
2.1241-2.19260.28041400.24983700X-RAY DIFFRACTION96
2.1926-2.2710.30371410.24373701X-RAY DIFFRACTION96
2.271-2.36190.28271440.22663819X-RAY DIFFRACTION97
2.3619-2.46940.291410.2363709X-RAY DIFFRACTION96
2.4694-2.59960.26821420.22713738X-RAY DIFFRACTION97
2.5996-2.76250.29121430.22113765X-RAY DIFFRACTION97
2.7625-2.97570.25521420.21643754X-RAY DIFFRACTION97
2.9757-3.27510.24731390.21543665X-RAY DIFFRACTION95
3.2751-3.74890.25681380.19733629X-RAY DIFFRACTION93
3.7489-4.72260.24211360.19623582X-RAY DIFFRACTION92
4.7226-48.420.26911370.24633601X-RAY DIFFRACTION94
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)
15.17753.26444.1014.37224.06224.85870.28340.1109-0.16640.50.392-0.99490.10010.6801-0.59130.37-0.056-0.0640.2791-0.09090.6654-49.287775.6615-6.4513
24.4247-0.06050.77430.0369-0.01920.1431-0.051-0.09180.0522-0.14690.04220.17790.0592-0.15680.04120.2448-0.01970.01950.1622-0.01840.4131-75.933866.845-12.8946
34.68640.8271.27631.09110.47421.0288-0.1286-0.16840.83110.0584-0.07220.253-0.194-0.16620.19750.23910.0079-0.01530.1596-0.04070.3355-63.081869.1181-7.7638
42.3117-0.6660.33243.04850.02622.5814-0.02470.2288-0.0383-0.4556-0.0453-0.03050.1627-0.09140.07970.2579-0.02340.01230.1327-0.01730.2712-64.259863.0773-19.8809
54.1614-1.53860.16843.87940.59442.58110.09420.8167-0.1334-0.9074-0.0939-0.19210.090.1327-0.02690.4747-0.01420.07460.3048-0.06360.2191-59.54660.653-31.027
69.21250.3218-3.24774.0275-3.04169.55290.5450.53520.27730.1718-0.17440.1742-0.8727-0.1378-0.34230.23840.01280.0980.3214-0.03090.4422-34.395858.2541-65.2165
73.48724.5485-0.32917.019-0.69920.1163-0.0546-0.0402-0.6117-0.115-0.0934-0.48360.08670.01520.15370.18580.02250.0620.2490.00070.5196-45.935636.0344-60.5469
81.2296-0.59920.24321.7281-0.84923.10160.0286-0.1007-0.0076-0.0719-0.0953-0.07650.1870.03670.08080.1460.01160.06430.24860.01230.3255-45.516544.8561-59.5846
93.0133-0.38010.081.3737-0.36842.0718-0.1539-0.4330.1440.25270.03160.1524-0.0575-0.22160.13140.17270.03990.07150.2711-0.04580.3823-50.88749.5294-51.3692
102.8652-1.5826-0.45153.9856-0.55733.8486-0.3554-0.98320.2160.55970.43970.1704-0.0293-0.2584-0.0850.32190.10660.08290.5188-0.08110.2464-50.87752.2271-42.0098
114.8466-1.19912.43316.3033-5.35965.30460.2930.89960.2824-0.6063-0.4819-0.15370.4980.16780.16810.26970.15720.06790.6591-0.07340.3639-52.733145.3478-77.5078
123.11032.6031-0.00693.5045-1.13261.3521-0.26730.51690.909-0.04350.24540.5647-0.1753-0.13-0.44820.2702-0.0280.10250.56890.43230.7985-65.819266.9606-82.8442
136.47990.2015-0.55992.36060.29816.2160.24280.78521.0574-0.06810.10620.141-0.10660.2104-0.2810.2336-0.00370.05910.51190.12950.3321-61.713953.6049-76.2946
141.9116-0.13680.02720.541-0.04840.82070.14891.07230.852-0.13790.05640.1478-0.2961-0.3207-0.3420.2320.12650.19220.80440.36680.7212-67.028161.635-85.4747
150.51471.01630.18592.00870.36530.06820.09070.87170.4381-0.30210.1990.7181-0.1979-0.4304-0.25920.33830.00590.00981.0870.27370.5007-74.868952.6489-87.8276
160.3510.8087-0.35661.9892-0.20093.106-0.09361.23120.1008-0.36620.31460.2172-0.0040.1831-0.20180.42740.0057-0.05631.32210.13190.4084-66.678452.6994-94.4328
173.8356-0.56950.47953.753-0.65342.9240.2641-0.3724-0.13140.6626-0.0779-0.998-0.26360.2771-0.22280.6613-0.0677-0.17590.2297-0.03690.4441-57.566652.94426.9936
183.1011-2.8501-0.80497.0763-0.47312.23370.12880.1051-0.47760.09160.1936-0.13540.6208-0.041-0.29080.4359-0.0507-0.1210.1973-0.0310.2976-61.853543.5032.7572
190.6480.52750.18140.67170.80591.85410.3011-0.4079-0.34470.65640.1056-0.52580.26450.3928-0.29321.0913-0.1233-0.66470.54310.00250.8498-51.020645.743916.5748
201.59550.10630.19440.20720.18970.74250.1881-0.0737-0.44030.6817-0.057-0.23120.3310.0338-0.03271.2304-0.1878-0.3370.21210.02510.4447-61.842440.542416.9539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 55 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 78 )
4X-RAY DIFFRACTION4chain 'A' and (resid 79 through 172 )
5X-RAY DIFFRACTION5chain 'A' and (resid 173 through 217 )
6X-RAY DIFFRACTION6chain 'B' and (resid 32 through 42 )
7X-RAY DIFFRACTION7chain 'B' and (resid 43 through 66 )
8X-RAY DIFFRACTION8chain 'B' and (resid 67 through 110 )
9X-RAY DIFFRACTION9chain 'B' and (resid 111 through 172 )
10X-RAY DIFFRACTION10chain 'B' and (resid 173 through 217 )
11X-RAY DIFFRACTION11chain 'C' and (resid 32 through 42 )
12X-RAY DIFFRACTION12chain 'C' and (resid 43 through 60 )
13X-RAY DIFFRACTION13chain 'C' and (resid 61 through 78 )
14X-RAY DIFFRACTION14chain 'C' and (resid 79 through 112 )
15X-RAY DIFFRACTION15chain 'C' and (resid 113 through 138 )
16X-RAY DIFFRACTION16chain 'C' and (resid 139 through 200 )
17X-RAY DIFFRACTION17chain 'D' and (resid 34 through 68 )
18X-RAY DIFFRACTION18chain 'D' and (resid 69 through 84 )
19X-RAY DIFFRACTION19chain 'D' and (resid 85 through 112 )
20X-RAY DIFFRACTION20chain 'D' and (resid 113 through 167 )

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