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Basic information

Entry
Database: PDB / ID: 6gkl
TitleTranslation initiation factor 4E in complex with beta-phosphorothioate trinucleotide mRNA 5' cap diastereomer 2 (m7GppSpApG D2)
ComponentsEukaryotic translation initiation factor 4E
KeywordsTRANSLATION / Protein-ligand complex / translation initiation factor / eIF4E / mRNA 5' cap / m7GppSpApG / phosphorothioate / thiophosphate
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 / mTORC1-mediated signalling / L13a-mediated translational silencing of Ceruloplasmin expression ...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 / mTORC1-mediated signalling / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / 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 / positive regulation of mitotic cell cycle / cellular response to dexamethasone stimulus / P-body / neuron differentiation / cytoplasmic stress granule / G1/S transition of mitotic cell cycle / regulation of translation / postsynapse / DNA-binding transcription factor binding / nuclear body / negative regulation of translation / nuclear speck / translation / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / protein-containing complex / nucleus / cytoplasm / cytosol
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-G0Z / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWarminski, M. / Nowak, E. / Kowalska, J. / Jemielity, J. / Nowotny, M.
Funding support Poland, 2items
OrganizationGrant numberCountry
DI2012 024842 Poland
ETIUDA 2017/24/T/NZ1/00345 Poland
CitationJournal: To Be Published
Title: Translation initiation factor 4E in complex with beta-phosphorothioate trinucleotide mRNA 5' cap diastereomer 2 (m7GppSpApG D2)
Authors: Warminski, M. / Nowak, E. / Kubacka, D. / Kowalska, J. / Nowotny, M. / Jemielity, J.
History
DepositionMay 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 2.0Oct 23, 2019Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Jan 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)93,30810
Polymers88,5804
Non-polymers4,7276
Water3,423190
1
A: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3733
Polymers22,1451
Non-polymers1,2282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3733
Polymers22,1451
Non-polymers1,2282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2812
Polymers22,1451
Non-polymers1,1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2812
Polymers22,1451
Non-polymers1,1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.170, 38.180, 147.020
Angle α, β, γ (deg.)88.80, 84.67, 76.13
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Eukaryotic translation initiation factor 4E / 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-G0Z / [[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-4,5-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 1135.736 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C31H45N15O22P4S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.34 Å3/Da / Density % sol: 47.39 % / Description: thin plate
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 16% PEG 10000, 0.1M TrisHCl pH 8.0, 0.2M CH3COONH4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.2→48.8 Å / Num. obs: 39200 / % possible obs: 96.1 % / Redundancy: 3.478 % / CC1/2: 0.991 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.145 / Net I/σ(I): 6.35
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 1.918 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 1.85 / Num. unique obs: 2365 / CC1/2: 0.654 / Rrim(I) all: 0.555 / % possible all: 75.5

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M7X

5m7x


Resolution: 2.2→48.795 Å / SU ML: 0.28 / Cross valid method: NONE / σ(F): 1.99 / Phase error: 26.26
RfactorNum. reflection% reflection
Rfree0.2573 1445 3.69 %
Rwork0.2181 --
obs0.2195 39196 96.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→48.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5525 0 175 190 5890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065868
X-RAY DIFFRACTIONf_angle_d0.9518050
X-RAY DIFFRACTIONf_dihedral_angle_d14.1413377
X-RAY DIFFRACTIONf_chiral_restr0.057890
X-RAY DIFFRACTIONf_plane_restr0.0061012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27860.30411160.27573032X-RAY DIFFRACTION76
2.2786-2.36990.31631470.25393858X-RAY DIFFRACTION97
2.3699-2.47770.28891490.2583874X-RAY DIFFRACTION99
2.4777-2.60830.29841480.24393880X-RAY DIFFRACTION99
2.6083-2.77170.27371470.23863837X-RAY DIFFRACTION98
2.7717-2.98570.26781490.23143901X-RAY DIFFRACTION99
2.9857-3.28610.28481480.22113861X-RAY DIFFRACTION99
3.2861-3.76150.22341470.20163846X-RAY DIFFRACTION98
3.7615-4.73850.24811500.19053909X-RAY DIFFRACTION99
4.7385-48.80690.23151440.21033753X-RAY DIFFRACTION97
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)
13.77141.26873.98565.66811.61134.3773-0.29120.56250.41580.17630.3815-1.0303-0.32670.962-0.18450.2362-0.02610.04230.4061-0.08580.5997-45.702277.6725-0.6678
29.3928-1.29711.58591.2978-0.32630.99020.319-0.5472-0.07970.0241-0.15070.27920.0807-0.1515-0.15990.2126-0.0020.0620.1933-0.0230.3586-71.542770.936-6.2989
32.33530.02572.30633.13570.1274.7420.0699-0.4087-0.14380.16930.0380.04540.201-0.1395-0.09460.1706-0.00390.06140.2244-0.00540.3587-61.112465.7658-2.5806
43.2441.3145.16476.6052.67958.2969-0.46280.10880.6924-0.80560.4020.3353-0.2602-0.00180.11720.3713-0.06370.07530.36320.05340.3052-67.121177.1992-17.8046
52.9685-1.79742.63032.0308-1.46912.38490.31520.1264-0.7498-0.295-0.1388-0.06070.25070.463-0.16970.3194-0.0910.11250.2743-0.06560.4183-63.428654.0673-15.0547
62.3246-1.29652.17092.1715-0.52793.3343-0.2724-0.02270.0522-0.36740.2163-0.4827-0.05470.25610.07810.2275-0.03730.11950.2657-0.08370.402-55.124366.5191-13.7949
74.8819-0.5222-0.00165.2835-1.98188.3837-0.30370.2343-0.2956-0.89590.1003-0.24390.0117-0.27860.19150.2919-0.04640.09850.267-0.10720.3782-64.520165.5267-19.496
84.2228-2.84550.37043.8935-0.70962.6178-0.14140.1367-0.0909-0.90970.2252-0.40610.49960.0768-0.04650.4056-0.05080.20060.2326-0.07710.329-56.98162.7332-24.1103
95.0185-4.2472-4.22858.178-0.63587.4430.78221.2804-0.1288-1.4773-0.3141-0.1743-0.2162-0.8778-0.34930.63290.07450.05150.5642-0.19830.4978-64.650963.9178-30.0938
108.928-2.2177-4.10511.063-0.49128.85720.43740.19850.4418-0.0395-0.397-0.579-1.27290.36330.00440.3738-0.07470.03650.3877-0.02290.4488-29.050362.8148-61.3131
110.1335-0.0198-0.30165.1547-2.46421.8534-0.0576-0.00220.1246-0.49490.11450.24920.3317-0.0985-0.0630.2619-0.04290.06770.2132-0.0350.3556-44.897536.9528-53.7054
126.99796.3917-5.55995.9175-5.39495.5674-0.15030.3804-0.4667-0.07740.0079-0.1435-0.1601-0.05010.11150.25380.06850.00540.2798-0.20480.4395-39.472240.3779-56.5435
133.6297-1.46341.30653.2313-1.18565.6055-0.09620.0028-0.16460.06350.05680.14230.11490.12130.04420.210.01030.09790.167-0.04180.2648-42.229346.9461-53.4317
141.93480.77542.31240.9783-0.11964.4505-0.1401-0.15330.0445-0.27930.10120.4079-0.3415-0.27790.03560.4122-0.00080.12360.3168-0.07220.5824-56.959750.6892-45.9525
156.2267-0.38712.53322.7353-0.39515.8410.0527-0.16350.08930.117-0.08830.0727-0.17350.07940.08670.2238-0.01680.10630.1386-0.03710.3469-43.664255.1726-47.497
164.7774-1.677-0.02462.62010.55654.4979-0.1084-0.52230.00660.73320.09780.44680.2456-0.2095-0.02190.40970.00360.16270.281-0.02550.3381-47.540751.6744-37.5866
174.01-3.58415.21193.6008-4.72637.00730.451.09030.0725-0.8869-0.668-0.02390.86190.50850.14520.36520.11520.0350.6375-0.06820.2851-49.383147.1964-70.7854
184.9919-0.11051.41476.3558-2.99486.2972-0.06490.34761.92650.49310.24160.2043-1.0295-0.2733-0.23860.3880.04860.15140.71370.33190.9883-62.861271.6753-77.5925
195.0762-0.18870.11678.0655-2.15785.84790.13260.36380.74530.69020.09780.1378-0.38960.3987-0.18710.22080.00110.0630.3849-0.04260.3288-58.803959.3141-71.5801
200.84391.18721.08594.2846-0.54923.01930.41450.94111.5514-0.03070.13390.5043-0.2916-0.5219-0.46960.27530.10320.08710.71910.23380.5426-67.934363.7487-75.538
211.46030.19292.04112.09761.12343.20240.28351.74710.7485-0.67480.5453-0.0507-1.18220.5160.14960.6164-0.02740.11151.52480.56690.7082-54.852167.8329-87.7599
220.0443-0.39380.01673.8828-0.17290.0043-0.16980.01130.10150.0817-0.06370.9376-0.05860.0531-0.2879-0.16240.0874-0.00011.75210.13580.4706-77.127458.6605-84.6103
233.41061.829-0.95845.0199-1.1345.99710.21471.8975-0.71520.0020.1150.19611.233-0.4937-0.050.33710.0236-0.00520.7512-0.10260.2708-65.018552.4091-81.1488
241.3059-0.58050.79813.327-0.34752.98210.26511.15510.2514-0.8026-0.19720.1113-0.25440.4808-0.27650.27930.333-0.19941.61450.4379-0.1328-63.14560.7341-88.1388
250.7420.24691.661.60830.45693.7020.04130.4296-0.1757-0.29530.0170.07920.6177-0.1933-0.09880.53410.2088-0.20031.9336-0.30830.0982-63.421350.5895-93.6071
263.0306-0.3508-1.26440.04220.0993.7799-0.17691.80680.3053-0.0840.13340.24450.29010.17390.01430.5212-0.05320.12972.1061-0.17430.426-70.283158.1497-95.1456
270.5720.1048-0.99684.3818-2.89023.42760.22831.01180.343-0.5296-0.15060.28511.3269-0.256-0.0320.828-0.1846-0.22051.80840.29150.4839-67.806761.1503-99.8624
286.2846-1.14853.51413.3187-4.66727.31810.2909-0.5936-0.15710.80740.1628-0.8522-0.4618-0.5234-0.2910.65260.0613-0.06830.294-0.03770.354-63.875962.336910.4046
292.1285-2.85330.40174.3755-1.98793.80850.0852-0.2238-1.06560.8366-0.0112-1.08510.43571.07520.09360.71190.1377-0.39180.5318-0.02381.0327-44.444943.564216.5527
304.1915-2.22290.20091.9543-1.53632.69240.33460.3462-0.15110.2091-0.1896-0.88990.3211-0.0496-0.13520.4114-0.0198-0.15840.223-0.01520.5579-54.984946.396210.6916
312.41642.3342.342.26512.31313.7010.1104-0.1149-0.25850.4502-0.1269-1.9734-0.51640.8702-0.20870.8422-0.1116-0.46890.50780.04720.7863-48.568550.016820.9065
321.6595-0.20910.16020.02470.01530.4919-0.1361-0.1182-0.28880.6155-0.0175-0.23450.13640.0857-0.23431.2775-0.2317-0.37850.4330.13940.5072-56.90337.97525.7228
339.20130.29451.45753.86831.34436.32640.5974-0.1385-0.50711.4382-0.29290.4975-0.6254-0.2914-0.27520.7726-0.0473-0.04090.30110.03240.2821-63.386446.387120.2605
341.95280.96160.32810.5982-0.80548.12640.6399-0.2634-0.26180.278-0.1947-0.285-0.7002-0.33580.52141.0551-0.238-0.42850.40210.08210.4034-57.186450.782626.3615
355.2012-1.29240.55281.26-1.82243.06480.1538-0.3353-0.57440.4195-0.28770.1246-0.44680.3094-0.33021.2349-0.0305-0.35650.44830.13450.392-53.634843.307828.3047
362.7188-3.8859-3.08217.1737.48629.38780.10950.11790.04550.79820.27130.2803-0.66210.2243-0.10421.2722-0.29730.10070.4227-0.00820.3686-64.981948.734232.009
370.4332-0.76930.11371.80120.60461.52730.477-0.8905-0.41450.9204-0.2947-0.7288-0.46770.1695-0.1791.4225-0.3842-0.32630.58890.09020.5888-59.626640.047234.1066
383.3704-0.10633.06110.65350.02582.88490.0542-0.7103-0.09530.45720.0654-0.272-0.2457-0.8109-0.11621.2426-0.3307-0.32470.74120.03070.3466-55.076841.27838.6083
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 66 )
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 95 )
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 110 )
5X-RAY DIFFRACTION5chain 'A' and (resid 111 through 125 )
6X-RAY DIFFRACTION6chain 'A' and (resid 126 through 155 )
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 172 )
8X-RAY DIFFRACTION8chain 'A' and (resid 173 through 204 )
9X-RAY DIFFRACTION9chain 'A' and (resid 205 through 217 )
10X-RAY DIFFRACTION10chain 'B' and (resid 28 through 42 )
11X-RAY DIFFRACTION11chain 'B' and (resid 43 through 56 )
12X-RAY DIFFRACTION12chain 'B' and (resid 57 through 66 )
13X-RAY DIFFRACTION13chain 'B' and (resid 67 through 110 )
14X-RAY DIFFRACTION14chain 'B' and (resid 111 through 125 )
15X-RAY DIFFRACTION15chain 'B' and (resid 126 through 156 )
16X-RAY DIFFRACTION16chain 'B' and (resid 157 through 217 )
17X-RAY DIFFRACTION17chain 'C' and (resid 31 through 42 )
18X-RAY DIFFRACTION18chain 'C' and (resid 43 through 56 )
19X-RAY DIFFRACTION19chain 'C' and (resid 57 through 78 )
20X-RAY DIFFRACTION20chain 'C' and (resid 79 through 95 )
21X-RAY DIFFRACTION21chain 'C' and (resid 96 through 110 )
22X-RAY DIFFRACTION22chain 'C' and (resid 111 through 125 )
23X-RAY DIFFRACTION23chain 'C' and (resid 126 through 142 )
24X-RAY DIFFRACTION24chain 'C' and (resid 143 through 172 )
25X-RAY DIFFRACTION25chain 'C' and (resid 173 through 187 )
26X-RAY DIFFRACTION26chain 'C' and (resid 188 through 203 )
27X-RAY DIFFRACTION27chain 'C' and (resid 204 through 217 )
28X-RAY DIFFRACTION28chain 'D' and (resid 32 through 42 )
29X-RAY DIFFRACTION29chain 'D' and (resid 43 through 56 )
30X-RAY DIFFRACTION30chain 'D' and (resid 57 through 88 )
31X-RAY DIFFRACTION31chain 'D' and (resid 89 through 104 )
32X-RAY DIFFRACTION32chain 'D' and (resid 105 through 125 )
33X-RAY DIFFRACTION33chain 'D' and (resid 126 through 142 )
34X-RAY DIFFRACTION34chain 'D' and (resid 143 through 156 )
35X-RAY DIFFRACTION35chain 'D' and (resid 157 through 172 )
36X-RAY DIFFRACTION36chain 'D' and (resid 173 through 187 )
37X-RAY DIFFRACTION37chain 'D' and (resid 188 through 203 )
38X-RAY DIFFRACTION38chain 'D' and (resid 204 through 217 )

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