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- PDB-5m7w: Translation initiation factor 4E in complex with (SP)-m2(7,2'O)Gp... -

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Basic information

Entry
Database: PDB / ID: 5m7w
TitleTranslation initiation factor 4E in complex with (SP)-m2(7,2'O)GppSpG mRNA 5' cap analog (beta-S-ARCA D2)
ComponentsEukaryotic translation initiation factor 4E
KeywordsTRANSLATION / Protein-ligand complex / translation initiation factor / eIF4E / m2(7 / 2'O)GppSpG / beta-S-ARCA / phosphorothioate / 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 / 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 / RISC complex / nuclear export / postsynaptic cytosol / stem cell population maintenance / behavioral fear response / negative regulation of neuron differentiation / mRNA export from nucleus / translation initiation factor activity / positive regulation of mitotic cell cycle / cellular response to dexamethasone stimulus / translational initiation / P-body / neuron differentiation / cytoplasmic stress granule / G1/S transition of mitotic cell cycle / regulation of translation / DNA-binding transcription factor binding / postsynapse / 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-WZO / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 (SP)-m2(7,2'O)GppSpG mRNA 5' cap analog (beta-S-ARCA D2)
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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)91,03810
Polymers88,5804
Non-polymers2,4576
Water5,945330
1
A: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8063
Polymers22,1451
Non-polymers6602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8063
Polymers22,1451
Non-polymers6602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7132
Polymers22,1451
Non-polymers5681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7132
Polymers22,1451
Non-polymers5681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.048, 38.032, 147.340
Angle α, β, γ (deg.)95.98, 88.31, 103.47
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-WZO / [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl [phosphonooxy(sulfanyl)phosphoryl] hydrogen phosphate


Mass: 568.307 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H21N5O13P3S
#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.: 330 / 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: 2.33 Å3/Da / Density % sol: 47.16 % / Description: Thin plate
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5% PEG 8000, 9% ethylene glycol, 0.03M ethylene glycols, 0.1M Trisma/bicine pH 8.5

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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: Feb 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 54201 / % possible obs: 95.7 % / Redundancy: 1.782 % / CC1/2: 0.996 / Rmerge(I) obs: 0.064 / Net I/σ(I): 8.15
Reflection shellResolution: 1.97→2.09 Å / Redundancy: 1.726 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 1.98 / CC1/2: 0.753 / % possible all: 94.1

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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: 1.97→48.845 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.98 / Phase error: 27.25
RfactorNum. reflection% reflection
Rfree0.2621 2100 3.87 %
Rwork0.2131 --
obs0.215 54195 95.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.97→48.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5379 0 148 330 5857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075715
X-RAY DIFFRACTIONf_angle_d1.037830
X-RAY DIFFRACTIONf_dihedral_angle_d15.4883294
X-RAY DIFFRACTIONf_chiral_restr0.06847
X-RAY DIFFRACTIONf_plane_restr0.007982
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9682-2.0140.27841350.27193343X-RAY DIFFRACTION92
2.014-2.06430.31811380.26223440X-RAY DIFFRACTION95
2.0643-2.12010.28491410.25513502X-RAY DIFFRACTION96
2.1201-2.18250.30311380.24813403X-RAY DIFFRACTION95
2.1825-2.2530.26511420.23433547X-RAY DIFFRACTION96
2.253-2.33350.27741390.2263447X-RAY DIFFRACTION96
2.3335-2.42690.33451390.24123448X-RAY DIFFRACTION96
2.4269-2.53740.29971430.23763539X-RAY DIFFRACTION96
2.5374-2.67110.26511390.21773438X-RAY DIFFRACTION97
2.6711-2.83850.24371410.21133511X-RAY DIFFRACTION96
2.8385-3.05760.25481400.21073480X-RAY DIFFRACTION96
3.0576-3.36520.23831430.19493529X-RAY DIFFRACTION96
3.3652-3.8520.25071400.18273496X-RAY DIFFRACTION96
3.852-4.85250.22981410.18023488X-RAY DIFFRACTION96
4.8525-48.86020.26111410.22563484X-RAY DIFFRACTION96
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)
17.3332-2.65112.46882.5114-2.90583.73650.2074-0.5265-0.86440.11490.0544-0.06210.48880.1156-0.23550.2370.0008-0.07290.24020.01980.370165.458163.1228-0.7837
21.4753-2.67990.37955.1036-0.80220.3-0.03020.0106-0.09210.1509-0.00450.2544-0.1398-0.03210.04320.1415-0.0051-0.04520.20250.00130.306750.737988.2268-7.7361
32.6036-3.28551.44047.3526-2.0430.8191-0.0953-0.30830.17370.37620.0086-0.5308-0.1172-0.03130.07260.1538-0.0219-0.03810.211-0.010.208155.751775.0574-1.6061
42.48620.8285-0.04682.50970.02272.6909-0.18870.32580.0598-0.20050.17390.0479-0.0046-0.17750.03250.1305-0.0301-0.03210.18280.00350.212849.601175.9364-14.5297
50.8306-0.7134-1.33942.5912-0.03432.8742-0.08470.5079-0.2932-0.48850.2596-0.07240.2468-0.2466-0.04670.4043-0.24730.03480.4073-0.20160.234647.358465.7011-23.6013
63.04013.34721.59594.37762.72382.1917-0.38610.51450.0883-0.7050.30570.3187-0.2346-0.32920.09340.3378-0.152-0.04210.4459-0.02150.187148.835579.0832-28.0759
75.6211-1.2404-3.67645.63792.34899.16740.0195-0.04850.0809-0.29220.3229-0.61390.01310.8744-0.3520.20350.04280.02680.1951-0.07470.469351.773146.1041-60.7447
87.9797-1.6338-1.25240.39850.13050.5909-0.06040.3905-0.3403-0.0676-0.02780.2239-0.0348-0.15340.08270.1791-0.0054-0.01130.1772-0.04710.287626.726553.0859-55.3834
94.1915-1.0464-1.06693.3803-0.22633.32950.01950.1154-0.0909-0.2605-0.0440.1371-0.1614-0.10110.02850.1419-0.0241-0.01650.1189-0.04690.172737.275758.0248-59.1139
107.5578-0.7589-2.14946.72140.39176.13080.1543-0.0457-0.62620.4546-0.09420.51380.6813-0.5302-0.02220.2218-0.0863-0.00550.1638-0.00950.26231.162546.7942-43.5109
110.86930.45920.45482.8832-1.33132.4587-0.0134-0.09670.25190.5254-0.0764-0.0149-0.4491-0.04740.07820.2385-0.04620.00110.1765-0.05210.223338.653866.2327-49.0804
122.47491.9714-2.22624.5421.24465.0720.1024-0.3972-0.31540.3941-0.044-0.53940.2750.5749-0.04980.1802-0.0262-0.0330.17540.06410.266643.806152.6233-44.0897
132.08561.26450.552.39270.42692.78780.3007-0.385-0.03370.7769-0.2349-0.0767-0.15450.0697-0.03890.3323-0.1005-0.03650.2057-0.04520.212639.36658.8421-40.3891
141.0071-0.5102-0.96890.36350.0832.53080.482-0.65090.51020.5483-0.42030.2423-0.48940.2217-0.02180.4232-0.1218-0.01020.3324-0.08040.231337.26463.2473-37.3284
155.26342.582.20722.56321.82031.5909-0.1376-0.17340.11950.1343-0.10430.10930.0273-0.30990.18440.5649-0.14210.01220.2722-0.10240.174333.495360.0108-32.2524
164.26231.0383-0.42922.01720.14992.18690.39820.08330.429-0.3647-0.0509-0.46210.1540.2959-0.29060.52930.14250.15870.2229-0.02750.426844.308771.0898-74.802
171.2450.598-0.47191.9336-0.16910.77010.3745-0.01860.3523-0.5654-0.2319-0.8508-0.17180.1673-0.11050.5170.0970.20590.2441-0.00090.465344.078677.5271-73.99
180.889-0.2561-0.64570.93710.33211.50730.12950.05260.2468-0.27450.028-0.2963-0.16710.202-0.11150.8630.29270.55820.49370.12120.651952.754371.8251-87.1102
191.01790.2172-0.51831.01090.60.83750.39920.42850.3669-1.3402-0.3474-0.0328-0.1841-0.16650.0461.22770.34460.1820.39680.03670.391638.013980.4048-88.2091
206.89580.885-4.30595.4699-3.32724.60880.1407-0.3011-0.14090.18130.2442-0.0695-0.40430.0889-0.36340.1777-0.0855-0.03910.51080.00680.265346.242576.82710.0236
211.6178-3.34710.75826.9285-1.46661.59560.4724-0.0965-0.8828-0.0760.02870.74570.5232-0.1498-0.51970.3608-0.021-0.17260.70210.33540.715633.271254.824615.4546
224.74611.3719-0.0945.39420.40631.9422-0.0246-0.1842-0.83420.0176-0.052-0.09160.18340.11650.0920.19790.0482-0.02470.47370.10630.319536.554664.548310.816
231.9521-0.95851.97580.7264-0.82042.1126-0.0494-0.7034-0.60690.19340.19770.18980.2287-0.1999-0.4350.22180.05-0.12110.75740.42090.638533.598159.256419.5415
241.3165-0.20720.52770.4087-0.0150.2268-0.0818-0.5139-0.20440.1433-0.04470.20180.1080.07630.03830.30290.13760.07481.32780.33140.566919.744666.19724.0637
257.23452.63952.21633.59850.66944.9548-0.1553-0.99440.1640.28380.39920.2568-0.2471-0.1799-0.09330.29650.1698-0.02280.77430.10090.252430.838772.706719.7904
261.5808-1.10951.09081.8212-1.16341.3949-0.1223-0.6899-0.17610.31350.16780.0548-0.0148-0.1275-0.05810.28710.0097-0.05261.09910.34160.47232.992164.898926.793
275.5182-1.1368-1.5316.7919-1.02682.4252-0.0298-0.30480.36420.38770.0134-0.2688-0.07830.39250.03580.3750.2680.03681.1395-0.02310.378632.632274.703931.4092
284.2503-1.86134.94124.3486-5.4658.8284-0.6628-0.7940.15560.92360.80890.4568-0.8091-1.0882-0.1630.56190.34550.0761.22110.33360.512223.539371.678433.1363
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 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 78 )
4X-RAY DIFFRACTION4chain 'A' and (resid 79 through 172 )
5X-RAY DIFFRACTION5chain 'A' and (resid 173 through 194 )
6X-RAY DIFFRACTION6chain 'A' and (resid 195 through 217 )
7X-RAY DIFFRACTION7chain 'B' and (resid 32 through 42 )
8X-RAY DIFFRACTION8chain 'B' and (resid 43 through 66 )
9X-RAY DIFFRACTION9chain 'B' and (resid 67 through 95 )
10X-RAY DIFFRACTION10chain 'B' and (resid 96 through 110 )
11X-RAY DIFFRACTION11chain 'B' and (resid 111 through 138 )
12X-RAY DIFFRACTION12chain 'B' and (resid 139 through 155 )
13X-RAY DIFFRACTION13chain 'B' and (resid 156 through 186 )
14X-RAY DIFFRACTION14chain 'B' and (resid 187 through 203 )
15X-RAY DIFFRACTION15chain 'B' and (resid 204 through 217 )
16X-RAY DIFFRACTION16chain 'C' and (resid 32 through 56 )
17X-RAY DIFFRACTION17chain 'C' and (resid 57 through 95 )
18X-RAY DIFFRACTION18chain 'C' and (resid 96 through 107 )
19X-RAY DIFFRACTION19chain 'C' and (resid 111 through 200 )
20X-RAY DIFFRACTION20chain 'D' and (resid 32 through 42 )
21X-RAY DIFFRACTION21chain 'D' and (resid 43 through 55 )
22X-RAY DIFFRACTION22chain 'D' and (resid 56 through 78 )
23X-RAY DIFFRACTION23chain 'D' and (resid 79 through 110 )
24X-RAY DIFFRACTION24chain 'D' and (resid 111 through 125 )
25X-RAY DIFFRACTION25chain 'D' and (resid 126 through 142 )
26X-RAY DIFFRACTION26chain 'D' and (resid 143 through 172 )
27X-RAY DIFFRACTION27chain 'D' and (resid 173 through 187 )
28X-RAY DIFFRACTION28chain 'D' and (resid 188 through 199 )

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