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- PDB-5m83: Translation initiation factor 4E in complex with (RP)-m2(7,2'O)Gp... -

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Basic information

Entry
Database: PDB / ID: 5m83
TitleTranslation initiation factor 4E in complex with (RP)-m2(7,2'O)GppSpA mRNA 5' cap analog
ComponentsEukaryotic translation initiation factor 4E
KeywordsRNA BINDING PROTEIN / Protein-ligand complex / translation initiation factor / eIF4E / m2(7 / 2'O)GppSpA / 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 / 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-YDZ / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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)-m2(7,2'O)GppSpA 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 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0175
Polymers44,2902
Non-polymers1,7273
Water2,720151
1
A: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0553
Polymers22,1451
Non-polymers9102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9632
Polymers22,1451
Non-polymers8181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.060, 59.740, 149.180
Angle α, β, γ (deg.)90.00, 96.32, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-462-

HOH

21A-488-

HOH

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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.: 2
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-YDZ / [[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanyl-purin-7-ium-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate


Mass: 817.533 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H32N10O16P3S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 47.73 % / Description: Thin plate
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 16% 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: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 34747 / % possible obs: 99.7 % / Redundancy: 6.436 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.57
Reflection shellResolution: 1.86→1.91 Å / Redundancy: 6.45 % / Rmerge(I) obs: 0.909 / Mean I/σ(I) obs: 2.02 / CC1/2: 0.787 / % possible all: 98.1

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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: 1.86→37.068 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 29.01
RfactorNum. reflection% reflection
Rfree0.2514 817 2.35 %
Rwork0.2059 --
obs0.207 34740 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.86→37.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2725 0 74 151 2950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072894
X-RAY DIFFRACTIONf_angle_d0.9693960
X-RAY DIFFRACTIONf_dihedral_angle_d15.3161662
X-RAY DIFFRACTIONf_chiral_restr0.057421
X-RAY DIFFRACTIONf_plane_restr0.005497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8581-1.97450.34631330.29785583X-RAY DIFFRACTION99
1.9745-2.12690.29251360.25015642X-RAY DIFFRACTION100
2.1269-2.34090.29971350.22685597X-RAY DIFFRACTION100
2.3409-2.67960.30931360.2235651X-RAY DIFFRACTION100
2.6796-3.37560.24841370.20535682X-RAY DIFFRACTION100
3.3756-37.07580.20891400.17855768X-RAY DIFFRACTION100
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)
15.33954.20192.26733.3922.34814.7686-0.27330.4547-0.729-0.01650.4328-0.55130.95730.3106-0.19370.4036-0.0126-0.00960.2227-0.07920.5823-89.6393-13.931345.138
25.9246-7.0015-1.37828.84931.39060.49620.21470.35810.0405-0.3082-0.35520.471-0.074-0.11630.15520.2173-0.0403-0.05940.2434-0.04060.3562-100.134710.232749.631
32.7541-0.2565-1.99673.1376-0.74742.3412-0.01440.1338-0.0674-0.1978-0.0799-0.066-0.1543-0.00240.0870.1811-0.0444-0.08650.2058-0.05120.2401-89.61265.264245.9938
48.1285-2.8231-2.42126.15544.18377.5919-0.146-0.554-0.08210.5652-0.3350.84880.4616-1.04570.4440.2717-0.05560.03080.4028-0.02820.2621-102.43572.93361.7696
50.751-0.7928-0.78271.6585-0.7894.03120.1299-0.61220.45960.404-0.4499-0.5425-0.67910.41460.25830.4084-0.1534-0.16470.4897-0.05720.435-82.054913.902958.826
64.2773-0.4334-1.3062.44461.48183.99040.0127-0.493-0.52570.2882-0.1661-0.37350.24440.21950.17430.1716-0.0474-0.09920.26180.05370.3261-86.5398-0.038457.3615
72.0789-0.77991.08551.3161-1.12012.35530.1225-1.0071-0.01460.5291-0.0812-0.2206-0.24460.0006-0.02320.36-0.1135-0.14360.5890.02610.2799-87.37645.873866.7584
88.32771.4787-6.14317.5393-0.88468.92480.39730.5059-0.0413-0.38730.13710.1867-0.4991-0.7102-0.51150.3914-0.2486-0.10130.4753-0.01420.2857-89.56879.9633.7884
92.59981.0505-0.65734.4484-1.22723.1976-0.27040.2754-0.797-0.56760.2173-1.61570.41790.5605-0.09040.7023-0.21350.30180.5574-0.3761.0323-64.16084.795128.3041
102.01791.2876-0.70031.8216-0.09111.8547-0.18320.3184-0.3329-0.41070.4749-0.8157-0.07290.368-0.28360.4905-0.19910.10710.4096-0.20250.5138-71.343815.483833.9027
110.55010.69420.33591.71871.30061.5266-0.17360.3939-0.5512-0.46290.3731-0.69940.17080.2731-0.20820.818-0.39440.38490.5334-0.41650.8464-68.70984.716922.0614
120.14260.01870.26490.00210.03470.5064-0.42810.4314-0.1741-0.61340.4097-0.2809-0.0790.1993-0.21061.1124-0.57740.35960.8379-0.34250.619-65.479418.687317.4559
135.88230.4386-1.22193.764-0.17697.2235-0.18350.40290.2619-0.94450.4610.078-0.2395-0.5934-0.22870.763-0.31430.10570.5198-0.08350.3094-75.613618.819323.3114
143.13451.27930.56882.2071.08281.069-0.33210.4486-0.0821-0.69430.325-0.10180.1422-0.12630.20891.0273-0.56270.37920.8075-0.34190.6403-70.691212.15416.318
154.2522-3.4498-0.04324.97481.24342.9794-0.08180.9418-0.2086-0.9734-0.1293-0.1793-0.0772-0.08820.13841.4114-0.43620.14670.8068-0.09890.392-72.821517.931410.4643
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 217 )
8X-RAY DIFFRACTION8chain 'B' and (resid 31 through 42 )
9X-RAY DIFFRACTION9chain 'B' and (resid 43 through 66 )
10X-RAY DIFFRACTION10chain 'B' and (resid 67 through 88 )
11X-RAY DIFFRACTION11chain 'B' and (resid 89 through 104 )
12X-RAY DIFFRACTION12chain 'B' and (resid 105 through 125 )
13X-RAY DIFFRACTION13chain 'B' and (resid 126 through 142 )
14X-RAY DIFFRACTION14chain 'B' and (resid 143 through 172 )
15X-RAY DIFFRACTION15chain 'B' and (resid 173 through 203 )

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