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- PDB-5m80: Translation initiation factor 4E in complex with (RP)-iPr-m7GppSp... -

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Basic information

Entry
Database: PDB / ID: 5m80
TitleTranslation initiation factor 4E in complex with (RP)-iPr-m7GppSpG mRNA 5' cap analog
ComponentsEukaryotic translation initiation factor 4E
KeywordsRNA BINDING PROTEIN / Protein-ligand complex / translation initiation factor / eIF4E / iPr-m7GppSpG / phosphorothioate / mRNA 5' cap analog / translation
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 / ISG15 antiviral mechanism / Translation initiation complex formation / Ribosomal scanning and start codon recognition / 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 / ISG15 antiviral mechanism / Translation initiation complex formation / Ribosomal scanning and start codon recognition / 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 / eukaryotic translation initiation factor 4F complex / chromatoid body / mRNA cap binding / RNA 7-methylguanosine cap binding / RISC complex / nuclear export / stem cell population maintenance / negative regulation of neuron differentiation / behavioral fear response / mRNA export from nucleus / translation initiation factor activity / positive regulation of mitotic cell cycle / cellular response to dexamethasone stimulus / translational initiation / P-body / G1/S transition of mitotic cell cycle / neuron differentiation / cytoplasmic stress granule / regulation of translation / DNA-binding transcription factor binding / postsynapse / negative regulation of translation / nuclear speck / nuclear body / translation / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / 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-7L2 / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsWarminski, M. / Nowak, E. / Kowalska, J. / Jemielity, J. / Nowotny, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher EducationDI2012 024842 Poland
CitationJournal: To Be Published
Title: Translation initiation factor 4E in complex with (RP)-iPr-m7GppSpG mRNA 5' cap analog
Authors: Warminski, M. / Nowak, E. / Kubacka, D. / Kowalska, J. / Nowotny, M. / Jemielity, J.
History
DepositionOct 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 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
C: Eukaryotic translation initiation factor 4E
B: Eukaryotic translation initiation factor 4E
D: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4848
Polymers88,5804
Non-polymers1,9034
Water5,783321
1
A: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0973
Polymers22,1451
Non-polymers9522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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
3
B: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0973
Polymers22,1451
Non-polymers9522
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)38.237, 38.271, 146.818
Angle α, β, γ (deg.)87.53, 95.37, 102.94
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-7L2 / [[[(3~{a}~{R},4~{R},6~{R},6~{a}~{R})-4-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-2,2-dimethyl-3~{a},4,6,6~{a}-tetrahydrofuro[3,4-d][1,3]dioxol-6-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 859.570 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H34N10O17P3S
#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.: 321 / 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: 2.35 Å3/Da / Density % sol: 47.72 % / Description: Thin plates
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 19% PEG 10000, 0.2M CH3COONa, 0.1M TRIS pH 8.0

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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: Apr 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. obs: 43091 / % possible obs: 93.9 % / Redundancy: 1.979 % / CC1/2: 0.996 / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.47
Reflection shellResolution: 2.12→2.25 Å / Redundancy: 1.829 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 2 / CC1/2: 0.68 / % possible all: 89.5

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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: 2.12→37.29 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.97 / Phase error: 26.68
RfactorNum. reflection% reflection
Rfree0.2583 2100 4.87 %
Rwork0.204 --
obs0.2066 43088 93.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.12→37.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5168 0 122 321 5611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085516
X-RAY DIFFRACTIONf_angle_d1.0817569
X-RAY DIFFRACTIONf_dihedral_angle_d17.0393173
X-RAY DIFFRACTIONf_chiral_restr0.067828
X-RAY DIFFRACTIONf_plane_restr0.007944
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1182-2.16750.30631270.27162480X-RAY DIFFRACTION86
2.1675-2.22170.31311360.25432660X-RAY DIFFRACTION91
2.2217-2.28170.27561400.23882730X-RAY DIFFRACTION94
2.2817-2.34890.28441410.2342757X-RAY DIFFRACTION95
2.3489-2.42470.27781410.22212749X-RAY DIFFRACTION94
2.4247-2.51130.28041440.23552823X-RAY DIFFRACTION95
2.5113-2.61180.3061380.22572678X-RAY DIFFRACTION94
2.6118-2.73070.28221440.21972813X-RAY DIFFRACTION94
2.7307-2.87460.28871350.20912647X-RAY DIFFRACTION93
2.8746-3.05460.27251420.20522767X-RAY DIFFRACTION96
3.0546-3.29030.25861440.19082803X-RAY DIFFRACTION96
3.2903-3.62120.25611430.18152789X-RAY DIFFRACTION95
3.6212-4.14460.2211390.17862717X-RAY DIFFRACTION93
4.1446-5.21950.23671430.17382796X-RAY DIFFRACTION96
5.2195-37.29570.22621430.21182779X-RAY DIFFRACTION95
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)
13.9301-1.6984-3.11914.68741.91247.4287-0.0021-0.0983-0.1662-0.56510.3342-0.9197-0.07670.7242-0.30740.2481-0.0280.04640.1559-0.10890.517849.774549.1041-60.181
24.53850.24730.35750.1283-0.11990.4521-0.12660.08910.0353-0.02920.0540.272-0.1448-0.090.06420.19850.0037-0.030.1222-0.04720.416622.072957.7038-53.9716
36.9589-3.7952-0.65862.6291.00110.7981-0.0179-0.1195-0.828-0.044-0.06790.21920.2202-0.13180.11770.2018-0.0381-0.060.1484-0.0270.399526.959153.2099-56.4876
43.2032-1.7659-2.1995.00070.35823.13090.14060.2975-0.1248-0.3789-0.17070.1705-0.0796-0.21770.03390.1637-0.0102-0.05820.1133-0.08320.233634.405961.3491-58.8376
50.7775-0.01480.45825.8057-3.1622.3116-0.074-0.1390.16410.32890.07780.0101-0.2615-0.1429-0.02020.15530.0317-0.00050.1564-0.0610.291330.450562.3402-45.0426
61.5780.8343-1.0591.32760.9783.3903-0.0611-0.1647-0.08020.1137-0.0373-0.22090.12760.24970.08120.12250.0071-0.05840.1065-0.04920.35539.888160.6217-47.714
72.14880.67970.25740.4010.73992.36560.0527-0.1572-0.22020.2504-0.09640.0066-0.1035-0.13670.01840.19510.0021-0.03610.1339-0.050.302531.244161.4009-41.8877
81.9017-0.564-2.66446.5532-1.7456.13910.0861-0.40930.19590.7776-0.1503-0.646-0.0060.89510.03430.29150.0008-0.17950.2312-0.0670.375843.755762.5642-37.7662
94.15644.7364-1.09595.3915-1.24195.03840.3706-0.49920.38980.7179-0.36130.5143-0.22040.07580.01750.36460.0503-0.03010.1778-0.02060.316133.908765.456-35.0421
103.62371.1682-1.08426.8378-1.65867.88340.05550.1126-0.0194-0.19250.034-0.38870.779-0.4809-0.07330.63780.0294-0.01660.1262-0.03390.292330.606264.4341-70.8485
112.6317-1.0329-0.25250.7772-0.8412.86370.29710.05610.4242-0.55010.1673-1.1461-0.91960.6381-0.47940.9296-0.03640.45310.3939-0.09880.79850.322882.9878-77.1963
120.2967-0.5078-0.12830.9776-0.00050.58420.36390.17120.3948-0.67620.0062-1.0516-0.25450.1766-0.26680.68730.07010.25270.2449-0.06030.600143.22679.7835-75.6035
130.4512-0.7382-0.81051.20551.31521.43940.23970.22760.0091-0.6034-0.3416-0.0435-0.2298-0.0358-0.02771.25610.26150.35030.38660.03250.528438.512788.8106-86.8942
143.73610.8723-0.68893.95241.51392.41530.14090.2613-0.0259-0.5411-0.11860.03070.1236-0.12050.08070.94830.19780.12920.2814-0.02760.276934.341679.2321-83.4398
153.18220.4227-0.02293.27110.15040.02410.30850.37830.0832-0.6602-0.1374-0.1014-0.08390.0485-0.16551.18640.14250.3980.34640.04990.453241.294983.3788-90.2529
163.82480.98213.54330.72530.67973.39350.04110.1544-0.0071-0.21740.00850.002-0.0592-0.2745-0.05251.43630.3084-0.07070.50470.00370.358929.898979.6446-92.1846
173.7202-0.919-3.64550.37850.98873.62230.4852-0.50950.7515-0.3527-0.1245-0.2102-0.31670.1449-0.36591.19660.44430.23020.8245-0.02340.498740.14484.5926-95.2657
187.38-2.81473.29992.8437-1.65134.54970.4173-0.5238-0.83770.05710.0496-0.07570.5630.0032-0.51090.186-0.0028-0.15770.30020.00390.530464.127365.1678-1.6206
191.8247-2.66810.14975.0315-0.56950.1992-0.0272-0.10130.41150.3237-0.0741-0.3178-0.11660.0620.10380.1578-0.0315-0.06430.2193-0.07010.387951.791988.608-6.5096
201.51760.6352-0.4821.3633-0.74832.7599-0.04320.0493-0.0553-0.0351-0.03580.0292-0.0172-0.08650.06550.11430.0165-0.07330.1652-0.06140.320948.569276.9387-10.9792
214.8621.9856-0.02653.1206-0.30353.083-0.43220.65610.1156-0.65070.29650.02810.0046-0.13110.1170.2643-0.0299-0.06550.2685-0.04760.191848.233874.9119-24.5429
224.9178-0.1931-2.99563.0275-3.48417.71850.2551-0.56720.06490.4345-0.0568-0.1962-0.7835-0.0668-0.17370.2497-0.0928-0.0650.607-0.13580.297445.227880.17789.1164
235.2056-0.30470.33360.0237-0.14592.68980.2393-0.6686-1.5037-0.0085-0.00860.17290.6036-0.6938-0.28960.3521-0.119-0.13440.9430.42410.894331.701256.137315.7571
242.1924-1.91190.58541.708-0.92024.5740.0942-0.9312-1.05890.07550.15780.25720.07710.0162-0.21770.20010.0304-0.08890.53540.08130.479635.567167.74210.2119
255.74680.498-1.14690.1647-0.46661.33730.1818-0.7609-1.21970.17080.21160.25270.4343-0.6792-0.42540.298-0.0856-0.13780.79420.37120.722721.693662.858311.3721
262.6462-0.60081.29920.5145-0.460.9776-0.0082-1.1617-0.34450.26340.0418-0.00880.0365-0.3498-0.05310.23870.03-0.10391.27530.25610.42730.48167.752322.787
270.92530.2922-0.96251.7925-1.261.5377-0.0207-0.3181-0.02960.09250.15760.144-0.0218-0.1154-0.16740.4729-0.1051-0.00461.58360.33430.477828.990764.836528.3072
280.7567-0.0283-2.33173.51-0.87637.4489-0.2156-0.2516-0.00480.3036-0.0032-0.0507-0.27750.18690.17780.56290.29-0.03081.767-0.2260.488330.063376.547831.3797
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 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 66 )
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 95 )
5X-RAY DIFFRACTION5chain 'A' and (resid 96 through 125 )
6X-RAY DIFFRACTION6chain 'A' and (resid 126 through 156 )
7X-RAY DIFFRACTION7chain 'A' and (resid 157 through 172 )
8X-RAY DIFFRACTION8chain 'A' and (resid 173 through 186 )
9X-RAY DIFFRACTION9chain 'A' and (resid 187 through 217 )
10X-RAY DIFFRACTION10chain 'C' and (resid 31 through 42 )
11X-RAY DIFFRACTION11chain 'C' and (resid 43 through 55 )
12X-RAY DIFFRACTION12chain 'C' and (resid 56 through 104 )
13X-RAY DIFFRACTION13chain 'C' and (resid 105 through 125 )
14X-RAY DIFFRACTION14chain 'C' and (resid 126 through 155 )
15X-RAY DIFFRACTION15chain 'C' and (resid 156 through 174 )
16X-RAY DIFFRACTION16chain 'C' and (resid 175 through 187 )
17X-RAY DIFFRACTION17chain 'C' and (resid 188 through 201 )
18X-RAY DIFFRACTION18chain 'B' and (resid 31 through 42 )
19X-RAY DIFFRACTION19chain 'B' and (resid 43 through 66 )
20X-RAY DIFFRACTION20chain 'B' and (resid 67 through 161 )
21X-RAY DIFFRACTION21chain 'B' and (resid 162 through 217 )
22X-RAY DIFFRACTION22chain 'D' and (resid 31 through 42 )
23X-RAY DIFFRACTION23chain 'D' and (resid 43 through 56 )
24X-RAY DIFFRACTION24chain 'D' and (resid 57 through 78 )
25X-RAY DIFFRACTION25chain 'D' and (resid 79 through 88 )
26X-RAY DIFFRACTION26chain 'D' and (resid 89 through 156 )
27X-RAY DIFFRACTION27chain 'D' and (resid 157 through 172 )
28X-RAY DIFFRACTION28chain 'D' and (resid 173 through 188 )

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