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- PDB-6gkj: Translation initiation factor 4E in complex with trinucleotide mR... -

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Basic information

Entry
Database: PDB / ID: 6gkj
TitleTranslation initiation factor 4E in complex with trinucleotide mRNA 5' cap (m7GpppApG)
ComponentsEukaryotic translation initiation factor 4EEIF4E
KeywordsTRANSLATION / Protein-ligand complex / translation initiation factor / eIF4E / mRNA 5' cap / m7GpppApG
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 / 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 / Translation initiation complex formation / Ribosomal scanning and start codon recognition / ISG15 antiviral mechanism / 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 / 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 / cellular response to dexamethasone stimulus / positive regulation of mitotic cell cycle / P-body / G1/S transition of mitotic cell cycle / cytoplasmic ribonucleoprotein granule / neuron differentiation / cytoplasmic stress granule / regulation of translation / postsynapse / DNA-binding transcription factor binding / 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
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.068 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 trinucleotide mRNA 5' cap (m7GpppApG)
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 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
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)90,91810
Polymers88,5804
Non-polymers2,3376
Water5,909328
1
A: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7753
Polymers22,1451
Non-polymers6302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7753
Polymers22,1451
Non-polymers6302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6832
Polymers22,1451
Non-polymers5381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6832
Polymers22,1451
Non-polymers5381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.190, 38.190, 147.020
Angle α, β, γ (deg.)84.18, 88.55, 76.96
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Eukaryotic translation initiation factor 4E / EIF4E / 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-MGP / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE


Mass: 538.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H19N5O14P3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 328 / 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: 47.57 % / Description: thin plates
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 15% 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: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Feb 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.068→48.76 Å / Num. obs: 46288 / % possible obs: 94.1 % / Redundancy: 4.343 % / CC1/2: 0.987 / Rmerge(I) obs: 0.194 / Rrim(I) all: 0.214 / Net I/σ(I): 7.08
Reflection shellResolution: 2.068→2.12 Å / Redundancy: 2.966 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 1.65 / Num. unique obs: 3273 / CC1/2: 0.637 / Rrim(I) all: 0.715 / % possible all: 88.7

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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: 2.068→24.074 Å / SU ML: 0.31 / Cross valid method: NONE / σ(F): 1.98 / Phase error: 26.96
RfactorNum. reflection% reflection
Rfree0.2486 1706 3.69 %
Rwork0.1996 --
obs0.2014 46227 94.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.068→24.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5565 0 144 328 6037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075865
X-RAY DIFFRACTIONf_angle_d0.9238028
X-RAY DIFFRACTIONf_dihedral_angle_d16.653382
X-RAY DIFFRACTIONf_chiral_restr0.056881
X-RAY DIFFRACTIONf_plane_restr0.0071010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0681-2.12890.35021350.27953524X-RAY DIFFRACTION89
2.1289-2.19760.34031380.25573591X-RAY DIFFRACTION92
2.1976-2.27610.33251380.26463621X-RAY DIFFRACTION91
2.2761-2.36720.2761360.2323552X-RAY DIFFRACTION90
2.3672-2.47480.27421270.21473318X-RAY DIFFRACTION85
2.4748-2.60510.2741400.21033650X-RAY DIFFRACTION92
2.6051-2.76810.27941490.21223895X-RAY DIFFRACTION98
2.7681-2.98150.26671500.21063914X-RAY DIFFRACTION99
2.9815-3.28090.24181470.19793834X-RAY DIFFRACTION99
3.2809-3.75410.23741470.17813842X-RAY DIFFRACTION96
3.7541-4.72390.19611500.16483929X-RAY DIFFRACTION99
4.7239-24.07530.2181490.18823851X-RAY DIFFRACTION98
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)
17.32286.00326.61597.12656.50118.57740.3180.2953-0.8610.28530.1690.32340.79780.3018-0.53510.27930.0242-0.10240.32170.00260.6183-67.620461.05982.0323
22.96564.46240.54237.73560.94930.3871-0.1319-0.02510.4842-0.16830.0290.3382-0.12450.14510.13510.17030.0441-0.01960.25540.04670.3216-53.955685.88388.7809
30.8210.09610.65012.02170.97723.0994-0.0049-0.1143-0.04630.02320.02370.04050.0049-0.03880.00470.15340.0454-0.02320.22260.03440.2494-54.399877.14489.7912
42.1649-0.82160.1742.80820.5473.0087-0.1131-0.5125-0.17520.36140.10910.03960.17990.06970.01210.18270.0208-0.02240.2930.08880.2423-49.189971.867521.5239
55.90411.8724-4.64457.5097-1.26899.1874-0.33350.39050.00580.39740.36130.72490.0455-1.0047-0.03030.2954-0.01890.06130.26360.10990.4807-54.720444.679463.0771
66.26010.4646-0.67380.19720.10070.20860.2240.02030.13120.1271-0.0769-0.34550.04670.0915-0.11940.23850.0128-0.00910.1830.05360.3469-26.802853.607656.9394
76.8471.0759-2.81791.2015-0.99511.5193-0.169-0.4223-0.59250.1509-0.03260.10920.03650.08770.21630.22550.0159-0.02160.17310.06390.2463-38.652751.527261.357
81.9961-0.1885-0.14223.16720.35112.85750.07280.22670.084-0.4256-0.1263-0.0552-0.08970.02510.05470.21270.0461-0.00540.18270.07190.2114-39.040758.068446.513
94.45990.8795-2.69661.77741.98676.044-0.126-0.3166-0.30511.09610.05-0.06810.35480.6478-0.03410.73680.0266-0.06530.22340.05870.323-35.395860.134973.3006
100.99590.0742-0.27570.9669-0.48141.51980.11780.09310.26830.8707-0.08721.03320.0463-0.2456-0.00390.5897-0.03460.21930.22380.02590.6482-48.74474.701575.9494
111.29821.1655-0.73685.4064-2.31021.37050.2581-0.19910.34791.23-0.05830.8623-0.3932-0.2615-0.31760.7339-0.07420.2950.17930.00830.5221-47.32282.105578.2239
120.90140.9745-0.2221.1319-0.03410.97190.3804-0.30550.35651.3844-0.40090.8053-0.253-0.0626-0.20371.1532-0.20250.28110.3185-0.00110.4239-43.563279.691286.1213
130.9711.096-0.23322.0673-0.26110.05440.1941-0.3552-0.25271.0608-0.1242-0.13010.68820.03040.36611.4698-0.11190.1510.3440.00410.4027-40.265470.08789.7875
141.72570.4973-0.93950.416-0.510.78130.3112-0.474-0.07040.6521-0.2835-0.03390.13790.3340.37811.4617-0.20580.1990.44330.03610.3174-41.146277.41793.5002
155.5771-2.45080.44562.21051.10297.17570.6502-1.22010.9281.0104-0.49520.0318-1.07991.0038-0.13381.5347-0.43870.18440.6025-0.0550.5189-38.296582.87798.6622
166.0837-0.7051-3.2377.81315.82748.89350.30920.0194-0.1431-0.4639-0.18020.3897-0.6429-0.2258-0.15220.19790.1233-0.080.60590.0190.2873-47.472776.7297-7.6191
171.63121.42730.04864.08411.51013.73860.41820.5321-1.45260.0454-0.2293-0.07470.70760.0348-0.21290.31810.0282-0.12120.5708-0.19650.7332-35.400854.2763-12.8598
181.867-1.2578-0.92151.12070.1881.18530.08150.404-0.61970.00470.1672-0.1320.05040.251-0.19490.16480.0273-0.07550.4737-0.14280.4581-32.676265.1936-9.4578
191.12930.33560.25161.16520.43980.21450.06971.2665-0.5131-0.42380.1066-0.1713-0.03180.1196-0.07020.2480.0064-0.00991.0529-0.27370.4419-32.450765.0503-22.6132
200.2479-0.55491.23088.4342-2.03126.1591-0.15310.4640.1179-0.8143-0.2880.1907-0.49220.12730.44040.4241-0.024-0.02731.22860.00760.3206-34.301973.6537-30.5279
210.0879-0.40390.34376.73642.65434.947-0.26680.9114-0.5304-1.16490.1287-1.1623-0.4960.61240.03930.4605-0.19150.13381.4554-0.21560.5527-28.152265.155-32.3413
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 66 )
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 110 )
4X-RAY DIFFRACTION4chain 'A' and (resid 111 through 217 )
5X-RAY DIFFRACTION5chain 'B' and (resid 30 through 42 )
6X-RAY DIFFRACTION6chain 'B' and (resid 43 through 55 )
7X-RAY DIFFRACTION7chain 'B' and (resid 56 through 78 )
8X-RAY DIFFRACTION8chain 'B' and (resid 79 through 217 )
9X-RAY DIFFRACTION9chain 'C' and (resid 31 through 42 )
10X-RAY DIFFRACTION10chain 'C' and (resid 43 through 78 )
11X-RAY DIFFRACTION11chain 'C' and (resid 79 through 95 )
12X-RAY DIFFRACTION12chain 'C' and (resid 96 through 138 )
13X-RAY DIFFRACTION13chain 'C' and (resid 139 through 155 )
14X-RAY DIFFRACTION14chain 'C' and (resid 156 through 187 )
15X-RAY DIFFRACTION15chain 'C' and (resid 188 through 217 )
16X-RAY DIFFRACTION16chain 'D' and (resid 31 through 42 )
17X-RAY DIFFRACTION17chain 'D' and (resid 43 through 66 )
18X-RAY DIFFRACTION18chain 'D' and (resid 67 through 95 )
19X-RAY DIFFRACTION19chain 'D' and (resid 96 through 172 )
20X-RAY DIFFRACTION20chain 'D' and (resid 173 through 186 )
21X-RAY DIFFRACTION21chain 'D' and (resid 187 through 217 )

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