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- PDB-5m81: Translation initiation factor 4E in complex with (SP)-iPr-m7GppSp... -

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Basic information

Entry
Database: PDB / ID: 5m81
TitleTranslation initiation factor 4E in complex with (SP)-iPr-m7GppSpG mRNA 5' cap analog
ComponentsEukaryotic translation initiation factor 4EEIF4E
KeywordsTRANSLATION / Protein-ligand complex / translation initiation factor / eIF4E / iPr-m7GppSpG / 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 / 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 / positive regulation of mitotic cell cycle / cellular response to dexamethasone stimulus / P-body / neuron differentiation / G1/S transition of mitotic cell cycle / cytoplasmic stress granule / cytoplasmic ribonucleoprotein 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
Chem-7L2 / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)-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: 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)92,29511
Polymers88,5804
Non-polymers3,7157
Water9,008500
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
B: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1894
Polymers22,1451
Non-polymers1,0443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0052
Polymers22,1451
Non-polymers8601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0052
Polymers22,1451
Non-polymers8601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.100, 38.120, 147.240
Angle α, β, γ (deg.)88.77, 95.82, 103.44
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-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.: 4 / Source method: obtained synthetically / Formula: C24H34N10O17P3S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.34 Å3/Da / Density % sol: 47.34 % / Description: Thin plate
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 12% 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: 1.9→50 Å / Num. obs: 62076 / % possible obs: 98.2 % / Redundancy: 2.919 % / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Net I/σ(I): 11.88
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 2.971 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 1.99 / CC1/2: 0.72 / % possible all: 97.6

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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: 1.9→48.827 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.97 / Phase error: 23.25
RfactorNum. reflection% reflection
Rfree0.2187 1462 2.36 %
Rwork0.1775 --
obs0.1785 62068 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→48.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5721 0 238 500 6459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076212
X-RAY DIFFRACTIONf_angle_d0.9758527
X-RAY DIFFRACTIONf_dihedral_angle_d15.1863612
X-RAY DIFFRACTIONf_chiral_restr0.059913
X-RAY DIFFRACTIONf_plane_restr0.0051059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8989-1.96680.31021450.2515984X-RAY DIFFRACTION98
1.9668-2.04550.2671440.22765998X-RAY DIFFRACTION97
2.0455-2.13860.26941470.20466070X-RAY DIFFRACTION97
2.1386-2.25140.24311460.19026067X-RAY DIFFRACTION98
2.2514-2.39240.24861460.19056087X-RAY DIFFRACTION98
2.3924-2.57710.24451460.18666030X-RAY DIFFRACTION99
2.5771-2.83640.2261450.18316030X-RAY DIFFRACTION98
2.8364-3.24680.21171480.1756116X-RAY DIFFRACTION99
3.2468-4.09030.19051470.14946123X-RAY DIFFRACTION99
4.0903-48.84280.17841480.15856101X-RAY DIFFRACTION99
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)
15.2897-3.5128-3.72736.75252.3329.01940.11620.0123-0.0146-0.46440.1391-0.85260.06510.8387-0.26570.21560.00750.01810.1912-0.09110.3666-43.9776-79.19423.2005
28.04-2.4924-2.05191.49611.23411.01480.14510.4192-0.1949-0.0663-0.21450.2457-0.0673-0.20880.07950.1306-0.0004-0.04730.1212-0.00970.2463-71.3248-72.14219.6703
32.6974-1.0146-1.48443.734-0.01512.30020.14740.22750.0606-0.279-0.04730.0609-0.1518-0.1245-0.10120.1132-0.0088-0.05330.111-0.03110.127-60.4639-66.6255.6674
46.16430.7067-4.75383.53131.66727.1256-0.09590.0277-0.44260.1867-0.08350.33930.556-0.17470.16050.165-0.0395-0.03830.12660.01320.24-66.5734-78.414421.4576
50.44340.5661-0.5412.3699-0.01712.35-0.0026-0.05620.15650.04920.0044-0.1029-0.27650.01390.00010.1328-0.0163-0.05080.1177-0.02430.2031-57.9987-60.286416.3212
63.5829-0.15131.46953.0848-1.12785.15750.0955-0.2411-0.06760.3512-0.0915-0.13790.090.0591-0.06070.1075-0.0271-0.03090.1093-0.01850.1549-60.4552-69.025422.1575
73.09662.8932-1.32525.2976-0.73694.70480.288-0.26850.16760.5179-0.18540.1583-0.2064-0.0579-0.05520.2298-0.0317-0.07770.1863-0.03590.178-58.885-63.915828.7102
85.1865-1.28591.12751.3967-1.18253.80040.0948-0.2593-0.43390.206-0.1328-0.4470.65980.52550.13020.31930.0826-0.1360.23790.00470.3734-30.1441-64.224764.3281
90.1770.8765-0.12674.84490.03660.9679-0.11990.03350.19960.25070.11140.3693-0.1676-0.04280.00670.1330.0043-0.04340.1333-0.00960.2288-45.814-37.898157.7794
105.3771-6.15983.58797.7809-3.77862.6121-0.2645-0.07290.28180.31880.0393-0.5911-0.1790.04230.19570.1214-0.0078-0.05560.1222-0.05620.2655-40.8896-40.796658.5123
113.2561-0.4768-1.32642.1525-0.47811.9294-0.0246-0.19190.05240.19780.07310.0531-0.0105-0.0415-0.0380.1041-0.0089-0.05830.1047-0.03380.1186-46.4495-50.806861.9735
127.368-0.97771.04177.4595-0.82886.5048-0.03540.22810.4279-0.23030.0966-0.5238-0.47290.45780.00010.1446-0.0547-0.01030.14020.00410.1868-36.6043-42.148246.3032
133.02810.6498-0.37880.3657-0.45212.6409-0.05340.02640.0131-0.06340.04710.22060.0061-0.38920.0010.1614-0.0152-0.05860.1417-0.03740.2313-53.988-54.02551.7568
145.35141.71620.48221.4724-2.02895.3157-0.10370.2272-0.3647-0.35340.0687-0.54430.46540.41040.02490.1619-0.0283-0.01240.1117-0.01190.1818-39.7517-55.877746.9393
157.0719-2.6353-3.8193.63051.97292.69570.01790.5746-0.0461-0.4175-0.0140.2582-0.1919-0.3604-0.04760.172-0.0116-0.10030.16030.02270.1618-47.4804-47.382445.1902
161.74291.59650.15733.1733-1.12462.2987-0.23060.3117-0.0513-0.36320.37470.05660.1149-0.1916-0.09860.2625-0.087-0.03320.2097-0.05640.1787-48.7138-55.580540.4888
172.33832.73671.45853.23771.72281.1719-0.34840.24250.3910.08970.38450.0736-0.2459-0.1659-0.00130.4483-0.1051-0.10330.35220.00480.3194-50.8515-46.186535.4696
187.15972.8944-5.75375.7286-4.19227.87540.04690.5359-0.1296-0.54860.0234-0.1804-0.0573-0.6385-0.11010.46970.023-0.04150.1967-0.01570.1717-63.3245-63.129-6.7324
194.4831-0.621-1.51150.468-0.41721.53780.3184-0.11730.9858-0.48860.2453-1.0197-0.41870.614-0.50240.6270.01760.40650.4172-0.12970.871-42.964-44.56-12.9087
200.8847-0.4904-0.76521.2890.39052.64020.208-0.03010.2548-0.61810.0563-0.6317-0.23520.179-0.23720.39610.06470.14240.1836-0.02110.3114-54.2253-47.5358-8.7234
212.08990.5642-0.06162.13451.56327.14420.41520.27830.5743-0.21860.3201-0.6103-0.54540.8587-0.77970.86290.15790.38990.4403-0.01180.585-44.7676-53.423-23.4527
220.17390.10790.0450.06790.02440.0120.23530.28040.3537-0.9018-0.1641-0.1286-0.3026-0.0633-0.10270.87470.16310.1730.23630.05820.3794-60.1766-39.73-18.7615
233.0806-0.7243-1.62992.3401-1.0053.01120.23710.6444-0.3036-0.3641-0.0145-0.0850.7876-0.11560.29550.89050.16580.16580.3444-0.05030.2375-58.9677-53.9236-23.3788
241.86030.2353-0.67460.2489-0.25871.660.17730.30770.249-0.2712-0.0004-0.039-0.23830.0876-0.20520.97420.09310.33060.3170.07060.2967-52.4716-44.4722-25.314
255.0644-0.2166-1.50933.36772.56518.9854-0.03680.616-0.12930.1604-0.00730.0950.4118-0.91440.05240.97840.2492-0.00120.5058-0.00220.2405-64.3037-49.3788-28.4234
260.13260.4852-0.82712.4466-2.47955.5940.04760.2180.29310.66570.170.4134-1.2791-0.7517-0.28911.22870.38190.24950.67830.19830.491-62.2532-40.4472-30.3531
270.86960.03080.77530.00120.02750.69140.23850.95760.4873-0.31470.04260.041-0.487-0.2015-0.2241.19690.33120.27130.84150.17690.4748-52.4885-43.7526-34.2357
282.25941.7919-1.5184.6669-4.68767.521-0.016-0.5463-0.0310.3336-0.0293-0.1839-0.64090.08950.04750.1901-0.0503-0.00990.47-0.06720.1769-50.6998-48.799875.0702
292.3766-2.2955-0.1073.9373-2.23893.19520.313-0.4228-1.363-0.12250.27590.53940.7203-0.1906-0.5780.3466-0.0076-0.18480.55140.24930.6587-63.8465-71.560780.0508
300.0135-0.0243-0.05920.0631-0.05131.60240.1887-0.776-1.2560.0792-0.12810.25520.51540.1073-0.02040.34740.0513-0.10510.47170.23750.7893-59.4176-69.609678.2243
310.7003-0.82710.69140.9794-0.83333.02550.2271-0.7805-0.5813-0.04430.00140.20390.1526-0.2524-0.1840.1845-0.0026-0.06970.41930.13340.2706-65.4282-60.47376.1694
321.4360.17861.83311.6219-1.14454.4950.177-0.5148-0.35670.22170.1630.13830.4031-0.4522-0.23570.4603-0.0001-0.08321.16060.46030.6084-54.9966-68.114991.1964
332.5726-0.73281.80110.363-0.53851.26610.1467-0.5419-0.2482-0.0043-0.04340.23320.1133-0.1456-0.12570.2988-0.0465-0.04711.29330.19650.4173-77.1191-59.368588.6497
342.74970.79282.92394.8417-1.3424.1458-0.0468-0.71460.22190.31380.22630.1011-0.478-0.0466-0.09580.21450.0094-0.01350.7443-0.08370.1937-65.9545-53.346684.4957
352.61731.08761.73441.82431.24422.7043-0.0012-0.7314-0.00380.27450.0629-0.1637-0.17670.37140.3250.3494-0.0693-0.11441.0790.18310.3151-60.1527-57.773490.8736
360.1859-0.2341-0.03160.992-0.2621.20790.0068-0.5554-0.01560.30950.111-0.0013-0.23050.1024-0.05370.4213-0.06450.00211.29530.17780.2387-65.8049-58.05794.316
370.252-0.2385-0.63560.41120.90822.1137-0.2552-0.0611-0.11620.5365-0.06440.24060.2834-0.75520.1490.67140.13070.12291.46810.20430.3873-70.7248-57.2023100.1342
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 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 142 )
6X-RAY DIFFRACTION6chain 'A' and (resid 143 through 172 )
7X-RAY DIFFRACTION7chain 'A' and (resid 173 through 217 )
8X-RAY DIFFRACTION8chain 'B' and (resid 28 through 42 )
9X-RAY DIFFRACTION9chain 'B' and (resid 43 through 55 )
10X-RAY DIFFRACTION10chain 'B' and (resid 56 through 66 )
11X-RAY DIFFRACTION11chain 'B' and (resid 67 through 95 )
12X-RAY DIFFRACTION12chain 'B' and (resid 96 through 110 )
13X-RAY DIFFRACTION13chain 'B' and (resid 111 through 138 )
14X-RAY DIFFRACTION14chain 'B' and (resid 139 through 155 )
15X-RAY DIFFRACTION15chain 'B' and (resid 156 through 172 )
16X-RAY DIFFRACTION16chain 'B' and (resid 173 through 204 )
17X-RAY DIFFRACTION17chain 'B' and (resid 205 through 217 )
18X-RAY DIFFRACTION18chain 'C' and (resid 32 through 42 )
19X-RAY DIFFRACTION19chain 'C' and (resid 43 through 59 )
20X-RAY DIFFRACTION20chain 'C' and (resid 60 through 95 )
21X-RAY DIFFRACTION21chain 'C' and (resid 96 through 110 )
22X-RAY DIFFRACTION22chain 'C' and (resid 111 through 138 )
23X-RAY DIFFRACTION23chain 'C' and (resid 139 through 155 )
24X-RAY DIFFRACTION24chain 'C' and (resid 156 through 172 )
25X-RAY DIFFRACTION25chain 'C' and (resid 173 through 187 )
26X-RAY DIFFRACTION26chain 'C' and (resid 188 through 199 )
27X-RAY DIFFRACTION27chain 'C' and (resid 200 through 217 )
28X-RAY DIFFRACTION28chain 'D' and (resid 32 through 42 )
29X-RAY DIFFRACTION29chain 'D' and (resid 43 through 55 )
30X-RAY DIFFRACTION30chain 'D' and (resid 56 through 66 )
31X-RAY DIFFRACTION31chain 'D' and (resid 67 through 95 )
32X-RAY DIFFRACTION32chain 'D' and (resid 96 through 110 )
33X-RAY DIFFRACTION33chain 'D' and (resid 111 through 125 )
34X-RAY DIFFRACTION34chain 'D' and (resid 126 through 142 )
35X-RAY DIFFRACTION35chain 'D' and (resid 143 through 156 )
36X-RAY DIFFRACTION36chain 'D' and (resid 157 through 187 )
37X-RAY DIFFRACTION37chain 'D' and (resid 188 through 217 )

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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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