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- PDB-5m7z: Translation initiation factor 4E in complex with (SP)-m2(7,2'O)Gp... -

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Basic information

Entry
Database: PDB / ID: 5m7z
TitleTranslation initiation factor 4E in complex with (SP)-m2(7,2'O)GppSepG mRNA 5' cap analog (beta-Se-ARCA D2)
ComponentsEukaryotic translation initiation factor 4E
KeywordsRNA BINDING PROTEIN / Protein-ligand complex / translation initiation factor / eIF4E / m2(7 / 2'O)GppSepG / beta-Se-ARCA / selenophosphate / 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 / ISG15 antiviral mechanism / Translation initiation complex formation / Ribosomal scanning and start codon recognition / 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 / ISG15 antiviral mechanism / Translation initiation complex formation / Ribosomal scanning and start codon recognition / 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 / eukaryotic translation initiation factor 4F complex / chromatoid body / mRNA cap binding / RNA 7-methylguanosine cap binding / RISC complex / nuclear export / stem cell population maintenance / negative regulation of neuron differentiation / behavioral fear response / mRNA export from nucleus / translation initiation factor activity / positive regulation of mitotic cell cycle / cellular response to dexamethasone stimulus / translational initiation / P-body / G1/S transition of mitotic cell cycle / neuron differentiation / cytoplasmic stress granule / regulation of translation / DNA-binding transcription factor binding / postsynapse / negative regulation of translation / nuclear speck / nuclear body / translation / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / 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-7LO / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.689 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)GppSepG mRNA 5' cap analog (beta-Se-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: 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)91,44110
Polymers88,5804
Non-polymers2,8616
Water7,819434
1
A: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1183
Polymers22,1451
Non-polymers9732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1534
Polymers22,1451
Non-polymers1,0083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0262
Polymers22,1451
Non-polymers8801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Eukaryotic translation initiation factor 4E


Theoretical massNumber of molelcules
Total (without water)22,1451
Polymers22,1451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.140, 38.140, 147.180
Angle α, β, γ (deg.)88.28, 84.07, 76.64
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-7LO / [[[(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]methoxy-oxidanyl-phosphoryl]oxy-selanyl-phosphoryl] [(2~{R},3~{S},4~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 880.428 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H32N10O17P3Se
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 47.41 % / Description: Thin plate
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 18% PEG 5000 MME, 0.2M HCOONa, 0.1M BICINE pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97957 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: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 88368 / % possible obs: 98.1 % / Redundancy: 3.756 % / CC1/2: 0.996 / Rmerge(I) obs: 0.075 / Net I/σ(I): 10.84
Reflection shellResolution: 1.69→1.73 Å / Redundancy: 3.704 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 2.01 / CC1/2: 0.675 / % possible all: 94.8

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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: 1.689→37.107 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.98 / Phase error: 26.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2555 2080 2.35 %
Rwork0.2186 --
obs0.2195 88362 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.689→37.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5114 0 115 434 5663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065431
X-RAY DIFFRACTIONf_angle_d0.9157428
X-RAY DIFFRACTIONf_dihedral_angle_d14.7983151
X-RAY DIFFRACTIONf_chiral_restr0.054810
X-RAY DIFFRACTIONf_plane_restr0.005935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6892-1.72850.28631350.27825586X-RAY DIFFRACTION95
1.7285-1.77180.29411350.26375617X-RAY DIFFRACTION97
1.7718-1.81970.30721430.25515898X-RAY DIFFRACTION98
1.8197-1.87320.3171350.25015625X-RAY DIFFRACTION98
1.8732-1.93370.26431390.255742X-RAY DIFFRACTION97
1.9337-2.00280.24251390.2245762X-RAY DIFFRACTION98
2.0028-2.08290.25961370.22285690X-RAY DIFFRACTION98
2.0829-2.17770.26371380.21975749X-RAY DIFFRACTION99
2.1777-2.29250.28361410.2225819X-RAY DIFFRACTION99
2.2925-2.43610.27241390.22335794X-RAY DIFFRACTION99
2.4361-2.62420.24741400.22345815X-RAY DIFFRACTION99
2.6242-2.88820.27531410.22145814X-RAY DIFFRACTION99
2.8882-3.30590.2371400.21195821X-RAY DIFFRACTION99
3.3059-4.16420.22291400.19085796X-RAY DIFFRACTION99
4.1642-37.11620.25191380.21485754X-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)
17.25733.13055.25067.7923.53219.60190.06280.2568-0.41330.55820.3172-1.1126-0.020.8424-0.35780.27-0.0479-0.03310.1564-0.06340.4122-46.868778.5399-1.6923
26.2169-1.1660.03520.2804-0.13570.27120.0094-0.2058-0.04430.0722-0.0770.1767-0.035-0.09490.04990.18860.00260.01570.1111-0.05230.2294-72.751371.4774-6.7367
33.19731.74991.55014.7975-0.05122.41060.1222-0.20180.01380.34-0.1156-0.05280.1285-0.07340.0010.18870.02260.02550.0775-0.06270.1687-61.961966.2877-2.9192
47.83881.51961.97146.98940.44924.2842-0.0430.0940.6365-0.385-0.06180.2601-0.7123-0.30460.12640.22480.05950.02850.0936-0.01490.2163-68.178677.8226-18.8335
50.5062-0.68780.41531.7778-0.66571.28970.02680.0412-0.1818-0.2232-0.0589-0.07280.4324-0.02750.01510.29020.03350.0260.1298-0.05260.213-60.632558.4647-13.2043
62.3327-1.63091.13532.92241.4763.44510.12440.38480.4842-0.3926-0.1471-0.415-0.26230.3939-0.0170.21270.05550.06340.12220.03130.2562-55.349371.643-17.9189
72.7772-0.3377-0.82011.66050.53992.65270.23220.5054-0.0702-0.5603-0.1259-0.17420.10250.1151-0.10460.3320.10010.06860.1873-0.03490.204-59.188865.6219-22.3075
82.08551.16541.56941.041-0.35265.0598-0.09650.6675-0.9815-0.76420.0588-0.11770.1720.19640.05140.45930.1410.08450.2636-0.12730.3112-55.063453.4286-22.7566
93.7681-3.0258-2.36063.93422.16353.02880.18420.678-0.3636-0.3732-0.49640.25890.1387-0.27380.29650.45090.09390.05050.2455-0.06770.18-66.23866.1368-28.0538
105.43562.4463-2.95143.4218-3.8194.35150.39710.33230.8760.1406-0.13230.1542-0.57510.148-0.24210.1907-0.0130.07380.2430.04180.3803-33.412461.0086-60.4468
110.58642.0202-0.05058.4479-0.79040.3302-0.0480.0367-0.0986-0.20330.02640.28870.15330.04310.04250.1390.02840.06420.1444-0.03090.2487-47.849236.7455-54.3591
122.29062.6954-1.3274.9007-2.37831.2506-0.11490.3197-0.1888-0.3139-0.0123-0.4510.207-0.0240.09130.1470.01820.06120.2026-0.02110.1887-42.918649.7113-60.4252
133.0309-0.6332-0.27441.8569-0.16841.9988-0.1947-0.2231-0.03350.24570.13520.1028-0.027-0.14940.06730.12430.05550.0520.1491-0.02220.1538-49.026349.0062-47.6324
140.5168-0.3383-0.30621.37170.26861.1474-0.1884-0.32210.00320.36260.16140.06910.0333-0.0009-0.04040.37290.23970.06390.388-0.11750.1909-50.544953.1707-36.534
152.1621-2.10781.26875.5165-4.67144.8563-0.1140.07310.0675-0.31750.0674-0.1730.4357-0.16020.07360.15290.01030.04560.6229-0.06630.1795-52.511247.9319-72.0593
161.93990.6699-0.49890.2707-0.34150.85790.12220.590.9501-0.09150.18130.2842-0.2734-0.324-0.25410.2491-0.0210.05860.66840.35510.662-63.525269.1781-76.5936
170.691-0.10680.41260.3559-0.40060.59560.03270.78720.4925-0.12880.12420.1499-0.1208-0.1397-0.0920.16070.00220.06210.70730.20410.3624-66.961860.3286-76.5343
186.51750.7022-1.15050.65580.30790.52540.05480.54820.2424-0.0940.18740.204-0.0998-0.2027-0.17360.2058-0.06120.00390.91870.08680.2733-74.39654.6157-80.652
193.25760.0066-1.38391.1382-0.08810.5929-0.02390.4139-0.0281-0.25650.0844-0.2504-0.05690.35860.21780.3206-0.08070.08021.0230.14480.3146-61.915155.0136-87.2107
200.61340.0612-0.34610.91620.01940.4324-0.08430.68930.0377-0.0930.14680.06030.0533-0.1178-0.01380.3114-0.089-0.02421.34620.16370.342-70.267255.446-90.7274
213.6886-3.57392.10265.4833-2.7333.1340.0739-0.1480.04410.0420.03290.0306-0.1599-0.1286-0.05970.5868-0.0458-0.02120.1297-0.03590.2249-64.133262.562810.3062
221.30240.75221.02011.23390.14571.04480.316-0.0042-0.56390.7550.105-0.97320.66090.3063-0.43410.6845-0.0772-0.36330.3092-0.0620.7066-45.585544.622915.5397
230.27310.63790.15411.51530.31910.43970.2076-0.0778-0.24310.3325-0.0211-0.55330.08290.1293-0.09920.5037-0.0918-0.19480.1443-0.02040.4068-54.836346.951711.8423
240.0341-0.02790.09910.0214-0.07670.28380.1033-0.0547-0.12810.3161-0.127-0.28610.12530.0855-0.09120.9526-0.2769-0.36920.37990.10120.4954-54.063143.127724.6076
252.87840.49230.71422.32910.31031.16330.1831-0.22960.13430.3228-0.0893-0.0153-0.0711-0.04450.18370.7796-0.2354-0.17180.2375-0.00220.2676-61.782848.515321.9462
260.85-0.08840.34950.29320.30920.63140.1337-0.1866-0.03590.4836-0.1489-0.09940.1281-0.1265-0.04661.0954-0.3516-0.23830.4380.11330.342-60.272445.679729.8387
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 138 )
6X-RAY DIFFRACTION6chain 'A' and (resid 139 through 155 )
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 186 )
8X-RAY DIFFRACTION8chain 'A' and (resid 187 through 194 )
9X-RAY DIFFRACTION9chain 'A' and (resid 195 through 217 )
10X-RAY DIFFRACTION10chain 'B' and (resid 32 through 42 )
11X-RAY DIFFRACTION11chain 'B' and (resid 43 through 56 )
12X-RAY DIFFRACTION12chain 'B' and (resid 57 through 78 )
13X-RAY DIFFRACTION13chain 'B' and (resid 79 through 172 )
14X-RAY DIFFRACTION14chain 'B' and (resid 173 through 217 )
15X-RAY DIFFRACTION15chain 'C' and (resid 32 through 42 )
16X-RAY DIFFRACTION16chain 'C' and (resid 43 through 66 )
17X-RAY DIFFRACTION17chain 'C' and (resid 67 through 118 )
18X-RAY DIFFRACTION18chain 'C' and (resid 119 through 138 )
19X-RAY DIFFRACTION19chain 'C' and (resid 139 through 156 )
20X-RAY DIFFRACTION20chain 'C' and (resid 157 through 191 )
21X-RAY DIFFRACTION21chain 'D' and (resid 33 through 42 )
22X-RAY DIFFRACTION22chain 'D' and (resid 43 through 56 )
23X-RAY DIFFRACTION23chain 'D' and (resid 57 through 95 )
24X-RAY DIFFRACTION24chain 'D' and (resid 96 through 125 )
25X-RAY DIFFRACTION25chain 'D' and (resid 126 through 156 )
26X-RAY DIFFRACTION26chain 'D' and (resid 157 through 190 )

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