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- PDB-5bxv: eIF4E complex -

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Basic information

Entry
Database: PDB / ID: 5bxv
TitleeIF4E complex
Components
  • Eukaryotic translation initiation factor 4E-binding protein 1
  • Eukaryotic translation initiation factor 4EEIF4E
KeywordsTRANSLATION / Complex
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 / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4G binding / eukaryotic initiation factor 4E 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 / TOR signaling / mTORC1-mediated signalling / negative regulation of neuron differentiation / behavioral fear response / mRNA export from nucleus / translation initiation factor binding / negative regulation of translational initiation / translation repressor activity / 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
Eukaryotic translation initiation factor 4E binding / Eukaryotic translation initiation factor 4E binding protein (EIF4EBP) / 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 / Eukaryotic translation initiation factor 4E-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSekiyama, N. / Arthanari, H. / Papdopoulos, E. / Rodriguez-Mias, R.A. / Wagner, G. / Leger-Abraham, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA68262 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM047467 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Molecular mechanism of the dual activity of 4EGI-1: Dissociating eIF4G from eIF4E but stabilizing the binding of unphosphorylated 4E-BP1.
Authors: Sekiyama, N. / Arthanari, H. / Papadopoulos, E. / Rodriguez-Mias, R.A. / Wagner, G. / Leger-Abraham, M.
History
DepositionJun 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Data collection / Other
Revision 1.2Jul 29, 2015Group: Database references
Revision 1.3Aug 5, 2015Group: Database references
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: 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-binding protein 1
C: Eukaryotic translation initiation factor 4E
D: Eukaryotic translation initiation factor 4E-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4206
Polymers54,3444
Non-polymers1,0762
Water3,927218
1
A: Eukaryotic translation initiation factor 4E
B: Eukaryotic translation initiation factor 4E-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7103
Polymers27,1722
Non-polymers5381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-18 kcal/mol
Surface area10940 Å2
MethodPISA
2
C: Eukaryotic translation initiation factor 4E
D: Eukaryotic translation initiation factor 4E-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7103
Polymers27,1722
Non-polymers5381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-18 kcal/mol
Surface area11010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.607, 67.830, 79.084
Angle α, β, γ (deg.)90.000, 112.430, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Eukaryotic translation initiation factor 4E / EIF4E / mRNA cap-binding protein / eIF-4F 25 kDa subunit


Mass: 22331.279 Da / Num. of mol.: 2 / Fragment: unp residues 33-217
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: Protein/peptide Eukaryotic translation initiation factor 4E-binding protein 1 / eIF4E-binding protein 1 / Phosphorylated heat- and acid-stable protein regulated by insulin 1 / PHAS-I


Mass: 4840.536 Da / Num. of mol.: 2 / Fragment: unp residues 50-84
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4EBP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13541
#3: Chemical ChemComp-MGP / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE


Mass: 538.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H19N5O14P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 3.32 Å3/Da / Density % sol: 62.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.4 / Details: 0.1 M Tris-HCl, and 22 % polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2012
RadiationMonochromator: Double crystal, Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 37630 / % possible obs: 96.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.8
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2 / % possible all: 92.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-2000data scaling
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
Cootmodel building
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WKW

1wkw


Resolution: 2.1→38.6 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1948 1893 5.03 %Random selection
Rwork0.1617 35727 --
obs0.1634 37620 96.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 244.49 Å2 / Biso mean: 52.4418 Å2 / Biso min: 20.36 Å2
Refinement stepCycle: final / Resolution: 2.1→38.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 66 218 3770
Biso mean--55.21 45.06 -
Num. residues----423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123645
X-RAY DIFFRACTIONf_angle_d1.3034954
X-RAY DIFFRACTIONf_chiral_restr0.051526
X-RAY DIFFRACTIONf_plane_restr0.007616
X-RAY DIFFRACTIONf_dihedral_angle_d19.0581363
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.097-2.14950.26111020.21212345244789
2.1495-2.20760.2071320.19592577270998
2.2076-2.27250.23321520.18122569272198
2.2725-2.34590.22851580.18082570272898
2.3459-2.42970.21641320.18482565269798
2.4297-2.5270.24791340.18462591272598
2.527-2.64190.26231300.1862559268997
2.6419-2.78120.23511480.18012557270597
2.7812-2.95540.21371250.18192546267196
2.9554-3.18350.22621410.16962549269097
3.1835-3.50370.181200.15662550267096
3.5037-4.01020.1741320.14382549268196
4.0102-5.05060.15831630.13022525268896
5.0506-38.62490.17081240.15832675279997
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)
12.1302-1.1188-1.66021.02810.18422.11490.09380.1401-0.21180.0105-0.23940.112-0.1806-0.37140.02660.25790.01620.01760.3057-0.03250.2962-30.0266-8.7685-4.8117
28.81062.5049-0.41826.79110.3442.2486-0.26971.2087-0.2729-0.5122-0.2759-0.53480.09230.37970.35090.52960.09980.04750.49980.00790.3181-14.2234-14.5976-25.2563
32.42290.6613-0.54352.6263-0.42171.1607-0.0390.16040.0289-0.25360.01650.04170.0125-0.07380.02080.28280.0144-0.02610.28180.00090.2574-21.6037-12.7733-11.5527
43.03740.4426-0.03153.6972-1.0072.34480.17820.07270.35970.2403-0.4916-0.4715-0.06410.52470.10820.2591-0.00670.00830.33760.04480.3426-7.6697-5.7125-9.0727
58.13390.442.29982.96651.98385.91370.24-0.6732-1.38710.35710.2499-0.62921.62880.41810.06690.83230.1842-0.12530.38030.02850.6841-6.0027-26.6077-4.8154
62.50710.453-0.05133.13870.73524.0145-0.0003-0.18370.02910.1852-0.0397-0.1559-0.0923-0.03460.00250.2263-0.0034-0.01160.26230.02570.2525-15.2392-10.0942-2.8986
71.99550.0917-0.01345.06281.37043.85460.08860.04030.33250.2317-0.1753-0.733-0.39820.4203-0.03350.3018-0.039-0.0210.29060.05580.408-8.0483-2.5546-5.4649
82.6586-0.13760.91884.5135-2.79733.53120.0353-0.16020.02590.0712-0.294-0.59780.01380.47480.2890.2917-0.0112-0.05920.35970.04550.4163-4.8208-7.8494-2.9456
96.2987-0.90110.66927.85420.41784.39510.0272-0.6229-0.08641.1282-0.10790.16460.076-0.29710.14640.36760.03970.01530.404-0.00140.2572-25.9606-9.02996.4454
108.766-0.20311.59274.83871.96222.0281-0.2056-1.1294-0.96560.3449-0.7498-0.08510.4922-0.41380.85270.4166-0.07650.09310.53340.05340.5747-33.3536-20.57060.694
117.65343.2542-4.91986.2309-0.08794.28021.06090.37010.7188-0.282-0.3321.2372-0.412-0.994-0.50960.35430.0508-0.06140.46610.03460.5466-33.7204-18.2172-14.361
126.4509-1.0449-0.15035.31410.25917.1655-0.0546-0.06480.0069-0.52030.00050.13950.5738-0.5540.10520.3427-0.0521-0.01260.26610.01660.3647-26.0535-23.8538-16.5426
134.2995-0.73391.38162.7604-0.70811.1684-0.3204-0.03240.60620.10820.0679-0.3121-0.16150.06510.1440.2809-0.00280.01810.2709-0.04860.3037-8.7831-36.9609-11.4418
143.5712-4.53250.39975.8673-0.3072.28620.04750.1927-0.2666-0.5137-0.24052.2142-0.0184-0.780.18520.34480.0476-0.06740.451-0.08520.7731-33.8521-31.9885-19.4109
152.716-0.3030.2182.3193-0.28792.3897-0.0014-0.09560.115-0.03250.00580.1551-0.0346-0.1437-0.00420.2387-0.01310.02020.2818-0.0090.263-19.7071-38.2349-14.6634
164.194-0.8781.53718.5632.2211.37810.07811.05670.5675-1.30480.43630.0679-1.5880.7911-0.42150.741-0.00150.04750.56910.12650.3329-16.3068-31.4297-32.8924
173.5196-0.32760.19124.2488-0.29485.459-0.03020.2729-1.0019-0.26680.0040.7580.7604-0.5954-0.13010.4251-0.052-0.09040.4466-0.02230.5609-26.4354-51.7932-23.6784
184.1095-0.15610.95753.53580.08144.1540.18190.3603-0.2233-0.2671-0.07370.03220.20680.1228-0.07290.3330.0128-0.02360.2864-0.0380.2609-17.0524-45.2923-23.2995
193.73031.6177-1.97733.32360.1083.58540.10540.7594-0.4139-0.8220.2747-0.51640.52190.4172-0.30220.46220.0807-0.0110.5318-0.11660.3544-11.7328-50.0838-31.4928
203.16680.4751-0.39441.97991.86242.10320.35990.6842-0.3414-0.3338-0.13130.19020.1119-0.2041-0.25420.61970.0809-0.08790.6365-0.10680.3405-22.3145-46.8007-36.149
216.26372.4766-1.8986.3208-0.35136.52550.1687-0.0929-0.2596-0.12140.0134-0.06160.45570.2629-0.20920.27160.0459-0.04230.31080.01710.4102-4.5436-48.4847-13.3022
222.1395-2.35271.63439.1296-0.22511.8938-0.22870.4127-0.0264-0.81280.1573-0.11041.5759-0.12550.16060.57950.040.02380.56780.04760.3367-8.2666-45.0236-0.7093
233.5133-4.44943.50035.8297-4.75613.9848-0.1634-0.39310.67480.9636-0.2351-0.8248-0.76820.9665-0.00710.5580.044-0.04890.6201-0.07710.4905-14.8795-35.945-0.6262
248.24215.49931.93046.21352.65212.74010.9801-1.17030.64060.8862-0.84510.35880.0693-0.2015-0.00980.4198-0.06860.12310.4476-0.01960.4355-25.951-35.891-4.622
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 33:47)A33 - 47
2X-RAY DIFFRACTION2(chain A and resid 48:60)A48 - 60
3X-RAY DIFFRACTION3(chain A and resid 61:105)A61 - 105
4X-RAY DIFFRACTION4(chain A and resid 106:118)A106 - 118
5X-RAY DIFFRACTION5(chain A and resid 119:123)A119 - 123
6X-RAY DIFFRACTION6(chain A and resid 124:158)A124 - 158
7X-RAY DIFFRACTION7(chain A and resid 159:179)A159 - 179
8X-RAY DIFFRACTION8(chain A and resid 180:206)A180 - 206
9X-RAY DIFFRACTION9(chain B and resid 50:62)B50 - 62
10X-RAY DIFFRACTION10(chain B and resid 63:69)B63 - 69
11X-RAY DIFFRACTION11(chain B and resid 70:77)B70 - 77
12X-RAY DIFFRACTION12(chain B and resid 78:84)B78 - 84
13X-RAY DIFFRACTION13(chain C and resid 33:47)C33 - 47
14X-RAY DIFFRACTION14(chain C and resid 48:59)C48 - 59
15X-RAY DIFFRACTION15(chain C and resid 60:104)C60 - 104
16X-RAY DIFFRACTION16(chain C and resid 105:110)C105 - 110
17X-RAY DIFFRACTION17(chain C and resid 111:123)C111 - 123
18X-RAY DIFFRACTION18(chain C and resid 124:170)C124 - 170
19X-RAY DIFFRACTION19(chain C and resid 171:190)C171 - 190
20X-RAY DIFFRACTION20(chain C and resid 191:217)C191 - 217
21X-RAY DIFFRACTION21(chain D and resid 51:63)D51 - 63
22X-RAY DIFFRACTION22(chain D and resid 64:68)D64 - 68
23X-RAY DIFFRACTION23(chain D and resid 69:74)D69 - 74
24X-RAY DIFFRACTION24(chain D and resid 75:83)D75 - 83

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