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- PDB-4tqc: The co-complex structure of the translation initiation factor eIF... -

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Basic information

Entry
Database: PDB / ID: 4tqc
TitleThe co-complex structure of the translation initiation factor eIF4E with the inhibitor 4EGI-1 reveals an allosteric mechanism for dissociating eIF4G
ComponentsEukaryotic translation initiation factor 4E
KeywordsPROTEIN BINDING / eIF4E / translation initiation inhibitor / allosteric / 4EGI1
Function / homology
Function and homology information


eukaryotic initiation factor 4G binding / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / chromatoid body / eukaryotic translation initiation factor 4F complex / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / mRNA cap binding / Deadenylation of mRNA / RNA 7-methylguanosine cap binding ...eukaryotic initiation factor 4G binding / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / chromatoid body / eukaryotic translation initiation factor 4F complex / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / mRNA cap binding / Deadenylation of mRNA / RNA 7-methylguanosine cap binding / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / Transport of Mature mRNA Derived from an Intronless Transcript / RISC complex / Ribosomal scanning and start codon recognition / stem cell population maintenance / Translation initiation complex formation / mTORC1-mediated signalling / negative regulation of neuron differentiation / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / 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 / neuron differentiation / ISG15 antiviral mechanism / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / G1/S transition of mitotic cell cycle / regulation of translation / DNA-binding transcription factor binding / postsynapse / negative regulation of translation / nuclear speck / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / RNA binding / extracellular exosome / 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-34J / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsPapadopoulos, E. / Jenni, S. / Wagner, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure of the eukaryotic translation initiation factor eIF4E in complex with 4EGI-1 reveals an allosteric mechanism for dissociating eIF4G.
Authors: Papadopoulos, E. / Jenni, S. / Kabha, E. / Takrouri, K.J. / Yi, T. / Salvi, N. / Luna, R.E. / Gavathiotis, E. / Mahalingam, P. / Arthanari, H. / Rodriguez-Mias, R. / Yefidoff-Freedman, R. / ...Authors: Papadopoulos, E. / Jenni, S. / Kabha, E. / Takrouri, K.J. / Yi, T. / Salvi, N. / Luna, R.E. / Gavathiotis, E. / Mahalingam, P. / Arthanari, H. / Rodriguez-Mias, R. / Yefidoff-Freedman, R. / Aktas, B.H. / Chorev, M. / Halperin, J.A. / Wagner, G.
History
DepositionJun 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Experimental preparation
Revision 1.2Oct 1, 2014Group: Database references
Revision 2.0Aug 23, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / diffrn_detector / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact / software
Item: _atom_site.id / _atom_site_anisotrop.id ..._atom_site.id / _atom_site_anisotrop.id / _citation.journal_id_CSD / _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _software.version
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9675
Polymers44,5812
Non-polymers1,3873
Water7,386410
1
A: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2183
Polymers22,2901
Non-polymers9282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7502
Polymers22,2901
Non-polymers4591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.210, 73.640, 66.980
Angle α, β, γ (deg.)90.00, 74.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Eukaryotic translation initiation factor 4E / eIF4E / eIF-4F 25 kDa subunit / mRNA cap-binding protein


Mass: 22290.334 Da / Num. of mol.: 2 / Fragment: UNP residues 28-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4E, EIF4EL1, EIF4F / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P06730
#2: Chemical ChemComp-M7G / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE


Mass: 459.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H19N5O11P2
#3: Chemical ChemComp-34J / (2S)-3-(4-amino-3-nitrophenyl)-2-{2-[4-(3,4-dichlorophenyl)-1,3-thiazol-2-yl]hydrazinyl}propanoic acid


Mass: 468.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C18H15Cl2N5O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 4000 12-20%, 100mM MES pH 8.5, 10% IPN

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.8→19.55 Å / Num. obs: 32707 / % possible obs: 93.8 % / Redundancy: 3.27 % / Net I/σ(I): 24.7

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
RefinementResolution: 1.8→19.5 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1941 1432 4.38 %
Rwork0.161 --
obs0.1625 32700 93.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2940 0 88 410 3438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043105
X-RAY DIFFRACTIONf_angle_d0.794210
X-RAY DIFFRACTIONf_dihedral_angle_d15.0541130
X-RAY DIFFRACTIONf_chiral_restr0.03436
X-RAY DIFFRACTIONf_plane_restr0.002522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.86750.251870.2222191X-RAY DIFFRACTION66
1.8675-1.94220.24981550.20043135X-RAY DIFFRACTION95
1.9422-2.03060.19611430.18963250X-RAY DIFFRACTION98
2.0306-2.13750.20291500.17363266X-RAY DIFFRACTION98
2.1375-2.27120.22061450.16873222X-RAY DIFFRACTION98
2.2712-2.44630.19871450.16173258X-RAY DIFFRACTION98
2.4463-2.69190.18821590.16573257X-RAY DIFFRACTION98
2.6919-3.08010.18991430.15883242X-RAY DIFFRACTION97
3.0801-3.87570.20481520.14283218X-RAY DIFFRACTION97
3.8757-19.55270.16691530.15343229X-RAY DIFFRACTION95
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)
14.3805-0.54842.68481.2346-0.19536.6808-0.0577-0.06670.1955-0.1554-0.07360.1231-0.4877-0.36610.03790.33710.00240.02270.16270.01410.27423.8209-4.2503-1.5714
25.61610.54124.43813.94591.49757.7146-0.43520.47440.8275-0.6436-0.2176-0.0746-0.9719-0.1673-0.26980.45740.0872-0.05920.24250.02340.2658-0.5487-0.3336-4.7139
32.47560.1742-0.31352.3382-0.46534.8785-0.36690.04680.3734-0.21830.2494-0.0769-0.6060.1881-0.09450.3677-0.031-0.04480.17330.00650.212410.1155-1.66979.3183
49.37142.65552.79557.6633-3.21763.1643-0.57550.5642-0.6461.0230.0181.0757-0.7823-2.19950.21760.55720.2049-0.01530.8428-0.12360.7796-4.0918-2.456110.1045
54.94330.65791.7615.43250.1797.1303-0.0060.26070.133-0.25720.00750.2386-0.6891-0.32370.07980.30410.0517-0.01130.21020.04020.20193.4423-8.5521-5.3825
64.0325-1.0433-0.03612.17512.71257.53380.25450.45950.272-1.22310.0485-0.2607-0.01651.25860.41540.50180.03770.03070.3805-0.03280.26498.9708-15.0014-13.6227
73.1494-0.47141.67786.32170.36083.61260.0733-0.7908-0.01770.20190.08541.27730.3351-1.40650.46710.2693-0.07190.01060.59630.03860.4742-5.0523-19.39196.3617
84.75220.1294-0.19474.2654-0.86586.9089-0.0185-0.21830.18050.180.2320.28030.0883-0.32320.20480.17530.00790.02520.13470.02820.17145.8425-14.15789.4443
94.2899-3.540.22267.56740.8994.5358-0.05310.3828-0.2549-0.61410.1526-0.5039-0.14741.58960.34330.2760.03330.07640.4751-0.11160.358917.7205-20.27170.81
103.4867-0.85621.46623.61860.3024.00840.0161-0.2018-0.1613-0.08850.12110.38790.0328-0.62320.24190.18250.0067-0.00730.25210.0450.1934-0.0646-15.4197-0.2515
116.3099-2.5061-0.19265.9143-3.27682.28470.70921.0032-0.9688-1.6522-0.0638-0.22581.39110.53030.80240.85180.2544-0.04840.4273-0.16690.375611.866-26.6389-8.9098
125.21110.4766-1.77855.03531.05463.2754-0.04320.058-0.6499-0.1056-0.1414-0.15860.83410.02720.17260.26580.0239-0.00060.1676-0.03050.208410.054-25.53942.9629
135.84365.6257-2.30816.00440.13179.96190.19130.774-0.75081.0343-0.03-0.53060.0560.4698-0.01630.258-0.0123-0.01340.32040.02080.23216.517-23.678311.6083
142.643-1.0725-1.21891.4401-1.25343.86290.5033-0.0941-0.78820.66810.03321.030.2875-0.45110.30890.6428-0.1776-0.1060.25760.08170.56650.6556-28.96023.4096
155.9419-0.76052.58416.85372.03394.4639-0.0755-0.1295-0.5801-0.4848-0.00930.35520.5468-0.8834-0.1420.4933-0.071-0.06530.3223-0.00980.209-2.3921-21.3934-12.3004
162.3603-0.6003-2.44253.19980.22452.5950.21420.381-0.6042-0.4-0.02830.45060.8518-0.58910.20130.7048-0.1355-0.25770.2603-0.05320.40470.5867-28.9498-6.0029
177.5812-0.54050.47633.77293.53444.1790.10180.4026-0.3501-0.01770.1793-0.53050.17980.7544-0.0120.2610.03230.01290.27150.00710.284320.9955-21.817715.6612
187.4722-0.9759-1.02114.5408-0.05444.6719-0.2044-0.0871-0.23810.39820.05670.02170.6358-0.49740.11160.2434-0.0101-0.01280.1671-0.00150.2112.3442-18.691132.0796
192.79061.30252.52370.68051.59345.238-0.0091-0.72-0.06830.80910.25031.0397-0.5087-2.0539-0.16760.63690.09980.25811.17890.21540.62091.7942-16.987847.4252
201.31630.22820.82761.12460.78044.65310.0855-0.0929-0.12320.1796-0.0435-0.03420.4869-0.11170.06820.2204-0.01810.02640.13420.02620.192511.1308-20.838127.9992
214.4138-0.5707-3.01623.23852.68578.97940.1027-0.2137-0.50520.6113-0.36751.94620.5069-0.07450.77720.5883-0.15390.07690.3906-0.10570.52971.2149-19.471424.8705
221.7527-0.0349-0.34344.2132-0.25535.85840.1113-0.1218-0.1570.3969-0.09570.42870.2987-0.48950.04530.2806-0.0510.01960.19550.02190.2579.2055-14.532134.4644
232.84460.1566-1.86342.41150.23241.6073-0.2741-0.6194-0.1446-0.59440.2894-0.37150.220.14370.32840.2869-0.0261-0.03810.26360.07440.265521.6316-11.538840.4811
243.77531.0474-0.9274.3097-0.19244.331-0.18690.08480.46560.2338-0.01940.5876-0.2666-0.9561-0.08160.27530.05410.06540.3164-0.01490.27354.91-2.903730.7696
255.525-0.468-0.73512.131-0.6523.8321-0.0934-0.01740.11170.07360.11440.1191-0.1635-0.08720.07080.1890.0040.00350.1320.01920.201110.8192-8.740722.0108
263.77274.5485-4.37755.8467-3.98022.0024-0.85631.4378-0.3153-0.92070.2793-1.37931.1950.7237-0.39720.3972-0.08740.1150.52320.00920.451825.8795-4.635523.3833
271.97940.8840.78383.58350.32333.4086-0.015-0.32250.20020.3135-0.01560.1412-0.1324-0.3031-0.03680.2350.01960.01540.19480.01980.213910.8184-6.314433.6101
287.22621.5454-1.5394.7223-2.26481.1971-0.34050.26580.7140.3681-0.1974-0.4804-0.8630.9417-0.49260.296-0.0796-0.03170.24590.03130.324723.25532.776829.515
297.9942-2.49061.60562.8082-1.38856.1539-0.05640.31020.6151-0.91460.03840.0456-0.23490.3880.14160.3271-0.02350.00090.15970.0080.230613.85481.47821.285
300.9857-0.5044-0.61924.99911.97891.14490.0093-0.03510.016-0.3651-0.21920.1926-0.153-0.386-0.13870.29340.02020.00140.16420.00090.2378.70095.496126.178
314.6667-0.4347-1.18747.56030.42332.2887-0.1135-0.48640.61571.1592-0.02530.2532-0.4898-0.2613-0.25190.4411-0.0085-0.03610.2742-0.03510.245114.0128-0.811243.6848
324.61651.04822.47740.3790.9572.8621-0.381-0.82010.38921.32920.0329-0.1384-0.6425-0.4876-0.03460.68230.0467-0.08380.2919-0.05670.302314.91756.243537.2059
330.8074-0.04940.30440.16270.09870.1975-1.2059-0.5676-0.039-0.09620.61820.74981.2266-1.0394-0.0120.49790.0491-0.03810.58750.00720.3994-6.602-13.5637-8.1004
341.20330.2071-0.00080.46950.64840.9806-0.8716-0.19990.70110.90620.84561.0568-1.4332-0.722-0.04620.47870.03650.08990.46430.0670.48757.3352-8.200743.2362
358.51744.84421.79683.99612.78363.12360.28580.2627-0.7920.8757-0.00520.3830.38821.311-0.13960.61090.0098-0.08550.4870.01410.5872-5.0882.59681.825
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 35:57)
2X-RAY DIFFRACTION2(chain A and resid 58:64)
3X-RAY DIFFRACTION3(chain A and resid 65:78)
4X-RAY DIFFRACTION4(chain A and resid 79:87)
5X-RAY DIFFRACTION5(chain A and resid 88:104)
6X-RAY DIFFRACTION6(chain A and resid 105:109)
7X-RAY DIFFRACTION7(chain A and resid 110:124)
8X-RAY DIFFRACTION8(chain A and resid 125:141)
9X-RAY DIFFRACTION9(chain A and resid 142:147)
10X-RAY DIFFRACTION10(chain A and resid 148:168)
11X-RAY DIFFRACTION11(chain A and resid 169:174)
12X-RAY DIFFRACTION12(chain A and resid 175:184)
13X-RAY DIFFRACTION13(chain A and resid 185:189)
14X-RAY DIFFRACTION14(chain A and resid 190:198)
15X-RAY DIFFRACTION15(chain A and resid 199:206)
16X-RAY DIFFRACTION16(chain A and resid 207:217)
17X-RAY DIFFRACTION17(chain B and resid 35:40)
18X-RAY DIFFRACTION18(chain B and resid 41:49)
19X-RAY DIFFRACTION19(chain B and resid 50:55)
20X-RAY DIFFRACTION20(chain B and resid 56:77)
21X-RAY DIFFRACTION21(chain B and resid 78:82)
22X-RAY DIFFRACTION22(chain B and resid 83:102)
23X-RAY DIFFRACTION23(chain B and resid 103:107)
24X-RAY DIFFRACTION24(chain B and resid 108:125)
25X-RAY DIFFRACTION25(chain B and resid 126:142)
26X-RAY DIFFRACTION26(chain B and resid 143:147)
27X-RAY DIFFRACTION27(chain B and resid 148:170)
28X-RAY DIFFRACTION28(chain B and resid 171:180)
29X-RAY DIFFRACTION29(chain B and resid 181:186)
30X-RAY DIFFRACTION30(chain B and resid 187:197)
31X-RAY DIFFRACTION31(chain B and resid 198:206)
32X-RAY DIFFRACTION32(chain B and resid 207:217)
33X-RAY DIFFRACTION33(chain A and resid 301)
34X-RAY DIFFRACTION34(chain B and resid 1000)
35X-RAY DIFFRACTION35(chain A and resid 302)

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