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- PDB-5j5o: Translation initiation factor 4E in complex with m7GppppG mRNA 5'... -

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Basic information

Entry
Database: PDB / ID: 5j5o
TitleTranslation initiation factor 4E in complex with m7GppppG mRNA 5' cap analog
ComponentsEukaryotic translation initiation factor 4E
KeywordsTRANSLATION / Protein-ligand complex / translation initiation factor / eIF4E / m7GppppG / 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 / ISG15 antiviral mechanism / Translation initiation complex formation / Ribosomal scanning and start codon recognition / 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 / ISG15 antiviral mechanism / Translation initiation complex formation / Ribosomal scanning and start codon recognition / 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 / eukaryotic translation initiation factor 4F complex / chromatoid body / mRNA cap binding / RNA 7-methylguanosine cap binding / nuclear export / RISC complex / stem cell population maintenance / negative regulation of neuron differentiation / cellular response to dexamethasone stimulus / postsynaptic cytosol / mRNA export from nucleus / behavioral fear response / translation initiation factor activity / positive regulation of mitotic cell cycle / P-body / translational initiation / G1/S transition of mitotic cell cycle / cytoplasmic stress granule / cytoplasmic ribonucleoprotein granule / regulation of translation / DNA-binding transcription factor binding / negative regulation of translation / postsynapse / nuclear speck / nuclear body / perinuclear region of cytoplasm / glutamatergic synapse / 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-6G0 / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.867 Å
AuthorsWarminski, M. / Nowak, E. / Rydzik, A.M. / Kowalska, J. / Jemielity, J. / Nowotny, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher EducationDI2012 024842 Poland
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: mRNA cap analogues substituted in the tetraphosphate chain with CX2: identification of O-to-CCl2 as the first bridging modification that confers resistance to decapping without impairing translation.
Authors: Rydzik, A.M. / Warminski, M. / Sikorski, P.J. / Baranowski, M.R. / Walczak, S. / Kowalska, J. / Zuberek, J. / Lukaszewicz, M. / Nowak, E. / W Claridge, T.D. / Darzynkiewicz, E. / Nowotny, M. / Jemielity, J.
History
DepositionApr 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 10, 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)91,23710
Polymers88,5804
Non-polymers2,6576
Water6,359353
1
A: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8553
Polymers22,1451
Non-polymers7102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8553
Polymers22,1451
Non-polymers7102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7632
Polymers22,1451
Non-polymers6181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7632
Polymers22,1451
Non-polymers6181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.990, 38.030, 146.640
Angle α, β, γ (deg.)88.55, 84.70, 76.67
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 / Fragment: UNP residues 28-217
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-6G0 / 5'-O-[(R)-hydroxy{[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]-7-methylguanosine


Mass: 618.195 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C11H20N5O17P4
#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.: 353 / 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: 2.37 Å3/Da / Density % sol: 48.14 % / Description: Thin plates
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 13% PEG5000MME, 0.1M Tris

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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: 1.867→36.82 Å / Num. obs: 60259 / % possible obs: 91.2 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.5
Reflection shellResolution: 1.867→1.92 Å / Rmerge(I) obs: 0.555

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L8B

1l8b


Resolution: 1.867→36.82 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.98 / Phase error: 27.99
RfactorNum. reflection% reflection
Rfree0.2634 2234 3.71 %
Rwork0.2208 --
obs0.2223 60257 91.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.867→36.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5765 0 160 353 6278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086212
X-RAY DIFFRACTIONf_angle_d1.0318502
X-RAY DIFFRACTIONf_dihedral_angle_d18.2273645
X-RAY DIFFRACTIONf_chiral_restr0.056902
X-RAY DIFFRACTIONf_plane_restr0.0061063
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8673-1.90790.37141140.29132960X-RAY DIFFRACTION74
1.9079-1.95220.32241200.26353120X-RAY DIFFRACTION80
1.9522-2.00110.27711260.24933272X-RAY DIFFRACTION80
2.0011-2.05520.28091250.24063250X-RAY DIFFRACTION83
2.0552-2.11560.28071350.23583492X-RAY DIFFRACTION87
2.1156-2.18390.25591340.23993491X-RAY DIFFRACTION90
2.1839-2.2620.32561410.23653649X-RAY DIFFRACTION91
2.262-2.35250.31861440.22773747X-RAY DIFFRACTION94
2.3525-2.45960.27631440.23973753X-RAY DIFFRACTION96
2.4596-2.58920.29451470.22943824X-RAY DIFFRACTION96
2.5892-2.75140.26261530.23043975X-RAY DIFFRACTION99
2.7514-2.96370.27191520.22173927X-RAY DIFFRACTION99
2.9637-3.26180.27361480.21223850X-RAY DIFFRACTION98
3.2618-3.73340.23921510.1983930X-RAY DIFFRACTION98
3.7334-4.70220.21741510.19513937X-RAY DIFFRACTION98
4.7022-36.82680.23861490.21713846X-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)
12.12662.89870.47816.31771.73443.07880.2426-0.103-0.20960.4188-0.0279-0.78230.08980.3069-0.24390.1534-0.06830.00160.0798-0.04370.4548-44.615678.3776-4.3929
24.3195-1.13880.53260.4146-0.32940.46250.133-0.0595-0.3959-0.02880.01560.1966-0.0438-0.1344-0.11080.18470.02080.00770.0637-0.02090.2454-72.680770.1535-11.1414
34.7290.72490.77782.3157-0.16930.55440.0305-0.0580.49710.1158-0.01920.01790.1146-0.0095-0.0140.1790.0091-0.0020.0805-0.04440.1982-59.359772.1714-5.246
41.1325-0.46570.37582.2787-0.27481.6331-0.06610.0745-0.0187-0.12110.0473-0.09640.0429-0.00750.01510.1293-0.00560.02340.0712-0.0390.175-60.538966.3919-16.8855
51.90871.0434-0.69064.3682-1.4322.1568-0.08840.2048-0.0305-0.36480.09090.02950.1607-0.0764-0.05630.1759-0.03070.02570.0906-0.07830.1831-63.45166.3836-23.4481
62.6308-0.99360.7412.6454-0.76641.50480.1780.3839-0.0119-0.4437-0.1099-0.19730.0750.3471-0.03930.2233-0.00340.17250.1775-0.09680.2273-50.8765.0779-27.3197
71.4169-1.9668-0.73152.9620.51472.48350.35730.5417-0.4032-0.7887-0.26540.12190.0641-0.0455-0.0760.34810.0110.01950.2118-0.09910.2208-61.393662.9217-30.4491
85.12562.3175-2.76932.7205-2.44837.2410.20060.26170.74630.07780.0570.1356-0.65330.17-0.30730.1275-0.05240.0830.26870.08010.3889-29.609363.1025-64.1972
91.71832.9877-0.2255.8613-0.80290.28770.02310.0036-0.2256-0.06110.0674-0.0937-0.0191-0.008-0.02240.09080.03110.07690.1931-0.0440.2639-44.150737.0931-57.3404
101.9523-0.2845-0.55781.3178-0.92213.03190.04220.134-0.1202-0.0599-0.0811-0.01790.16670.11590.01530.08610.01520.05760.0834-0.03580.1777-41.060547.5997-57.6331
113.5531-0.42691.60380.2881-0.36970.8558-0.01390.1661-0.1690.0877-0.02330.36310.07-0.0130.04320.14410.01390.08160.1908-0.11210.3235-56.856151.5426-49.6876
122.7168-1.8638-0.36832.2327-1.10581.9961-0.0049-0.11270.18450.1937-0.0587-0.098-0.19780.13110.04110.09430.01890.07920.0792-0.06650.2002-42.696156.4384-51.0014
138.71221.58382.82391.68251.22893.15140.0792-0.6804-0.11330.1426-0.10150.02660.2128-0.22630.0170.0981-0.00820.11460.14210.01380.213-46.443247.4403-45.4343
140.9908-0.6853-0.05861.4514-0.47052.9652-0.1628-0.29180.13780.35060.15260.0291-0.3651-0.0704-0.06170.21040.02780.08690.1946-0.13630.1896-44.587360.3171-41.8094
151.9996-1.4512-0.85273.06590.20083.709-0.2848-0.3563-0.18470.43220.21920.31840.2777-0.11540.07160.27760.04640.13080.2439-0.06870.1876-49.398850.9589-38.4198
160.3286-1.47620.80426.7566-4.2765.1792-0.0014-0.1384-0.1344-0.37140.47230.1514-0.0013-0.6664-0.38580.4781-0.10880.03740.2092-0.02840.1422-63.684763.25836.8962
170.73931.3507-0.02112.6006-0.70873.44110.03930.0448-0.43570.3716-0.0886-1.08530.53940.5256-0.02420.59210.0059-0.3010.2062-0.00130.7386-43.676646.396311.7815
180.14440.18140.10990.9001-0.16210.25450.2209-0.1875-0.11030.731-0.1575-0.37950.12130.0685-0.06020.7341-0.1299-0.23780.13070.01220.3847-55.639645.318915.294
192.30271.43041.85621.21010.83153.1281-0.0071-0.3860.32130.121-0.26240.0873-0.4325-0.33810.46570.72-0.1339-0.35570.2950.00640.3816-57.061652.240722.8611
201.6760.99970.86990.68610.51580.45350.0564-0.35360.28620.7855-0.24230.0188-0.1086-0.09570.16061.0117-0.2545-0.16940.30020.05080.2954-58.474247.020526.4732
210.6629-0.60021.1081.9632-0.95637.07990.5709-0.3738-0.609-0.2455-0.21930.29091.8439-0.8041-0.37261.2885-0.2337-0.26240.81960.13310.4361-61.766740.601730.0835
221.4245-0.72380.06210.3671-0.03180.0026-0.1678-0.9412-0.35330.19330.37470.1315-0.0195-0.5136-0.17341.1734-0.2273-0.39290.8630.25970.6038-52.302243.776933.8797
235.61170.8122-0.32014.6211-4.70248.6862-0.06080.0395-0.1495-0.4755-0.3142-0.350.88510.33020.37730.15930.07050.06450.4134-0.0820.1874-49.085347.8015-75.0018
242.4424-0.02150.62260.1641-0.50371.6730.07250.65371.3895-0.0932-0.021-0.0518-0.4732-0.2862-0.02230.25970.05820.02340.6290.3530.8555-63.06372.6324-81.2567
253.5758-0.76790.30440.56730.33841.45310.01640.51970.8219-0.0397-0.03940.0169-0.18590.0023-0.01650.11670.02880.05570.40740.05820.3193-58.368860.5155-75.4365
265.5164-0.00091.30810.7302-1.08052.17210.07060.42830.665-0.06340.15990.231-0.2513-0.4021-0.25910.12080.05030.07660.50470.18320.3874-72.526964.634-76.4002
272.63020.2685-1.16270.0282-0.09940.93680.01910.39880.3417-0.08890.0244-0.0637-0.1016-0.0445-0.10240.14260.00690.08320.71930.29840.419-57.252966.6455-85.9557
282.87120.57050.27210.8337-0.2690.3076-0.04540.92930.2995-0.2044-0.01130.0526-0.061-0.04140.01250.17680.0113-0.00820.90750.05950.2807-67.2957.4094-87.8413
294.59770.0765-1.8532.1121-0.78952.6878-0.19440.7124-0.0873-0.318-0.0407-0.28110.32170.32650.42780.27180.02770.06980.96520.26990.3624-58.387957.3105-91.3968
302.3409-1.2842-0.53954.10920.67121.92820.19880.53250.2018-0.3980.0325-0.2223-0.1476-0.0652-0.24980.27650.03650.03891.04390.2560.3167-64.249262.6358-93.9521
310.3997-0.2029-0.80231.52510.13181.6627-0.190.3613-0.1733-0.6038-0.0174-0.30440.2044-0.32330.18840.4052-0.05190.10541.2049-0.02030.3394-62.633650.6217-96.9335
321.6379-0.63350.97011.1143-1.97697.392-0.2397-0.12390.1647-0.64860.430.60760.6218-1.3736-0.23110.64040.1542-0.05391.52080.2790.4871-71.932254.102-98.0836
330.0354-0.04310.02070.0527-0.02440.0111-0.32780.44880.3958-1.25410.36651.3314-0.0468-0.5186-0.01850.6509-0.0828-0.23391.45730.31260.7028-66.002964.1422-103.0068
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 78 )
4X-RAY DIFFRACTION4chain 'A' and (resid 79 through 155 )
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 172 )
6X-RAY DIFFRACTION6chain 'A' and (resid 173 through 187 )
7X-RAY DIFFRACTION7chain 'A' and (resid 188 through 217 )
8X-RAY DIFFRACTION8chain 'B' and (resid 31 through 42 )
9X-RAY DIFFRACTION9chain 'B' and (resid 43 through 59 )
10X-RAY DIFFRACTION10chain 'B' and (resid 60 through 110 )
11X-RAY DIFFRACTION11chain 'B' and (resid 111 through 125 )
12X-RAY DIFFRACTION12chain 'B' and (resid 126 through 155 )
13X-RAY DIFFRACTION13chain 'B' and (resid 156 through 172 )
14X-RAY DIFFRACTION14chain 'B' and (resid 173 through 187 )
15X-RAY DIFFRACTION15chain 'B' and (resid 188 through 217 )
16X-RAY DIFFRACTION16chain 'C' and (resid 31 through 42 )
17X-RAY DIFFRACTION17chain 'C' and (resid 43 through 66 )
18X-RAY DIFFRACTION18chain 'C' and (resid 67 through 142 )
19X-RAY DIFFRACTION19chain 'C' and (resid 143 through 156 )
20X-RAY DIFFRACTION20chain 'C' and (resid 157 through 187 )
21X-RAY DIFFRACTION21chain 'C' and (resid 188 through 199 )
22X-RAY DIFFRACTION22chain 'C' and (resid 200 through 217 )
23X-RAY DIFFRACTION23chain 'D' and (resid 31 through 42 )
24X-RAY DIFFRACTION24chain 'D' and (resid 43 through 56 )
25X-RAY DIFFRACTION25chain 'D' and (resid 57 through 78 )
26X-RAY DIFFRACTION26chain 'D' and (resid 79 through 88 )
27X-RAY DIFFRACTION27chain 'D' and (resid 89 through 104 )
28X-RAY DIFFRACTION28chain 'D' and (resid 105 through 142 )
29X-RAY DIFFRACTION29chain 'D' and (resid 143 through 156 )
30X-RAY DIFFRACTION30chain 'D' and (resid 157 through 172 )
31X-RAY DIFFRACTION31chain 'D' and (resid 173 through 187 )
32X-RAY DIFFRACTION32chain 'D' and (resid 188 through 199 )
33X-RAY DIFFRACTION33chain 'D' and (resid 200 through 217 )

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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