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

ID or keywords:

Entry

Database: PDB / ID: 4tqb

Title

The co-complex structure of the translation initiation factor eIF4E with the inhibitor 4EGI-1 reveals an allosteric mechanism for dissociating eIF4G

Components

Eukaryotic translation initiation factor 4E

EIF4E

Keywords

PROTEIN BINDING /

eIF4E / translation initiation inhibitor /

allosteric / 4EGI1

Function / homology

Function and homology information

Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S /

eukaryotic initiation factor 4G binding /

chromatoid body /

regulation of translation at postsynapse, modulating synaptic transmission /

RNA cap binding / eukaryotic translation initiation factor 4F complex / Transport of the SLBP independent Mature mRNA / Deadenylation of mRNA / Transport of the SLBP Dependant Mature mRNA / mRNA cap binding complex ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.59 Å

Authors

Papadopoulos, E. / Jenni, S. / Wagner, G.

Citation

Journal: 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. / ...

History

Deposition	Jun 10, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 13, 2014	Provider: repository / Type: Initial release
Revision 1.1	Oct 1, 2014	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4tqb.cif.gz	260.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4tqb.ent.gz	224.4 KB	Display	PDB format
PDBx/mmJSON format	4tqb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4tqb_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4tqb_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4tqb_validation.xml.gz	25.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tq/4tqb ftp://data.pdbj.org/pub/pdb/validation_reports/tq/4tqb	HTTPS FTP

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Related structure data

Related structure data	4tpwC 4tqcC C: citing same article (ref.)
Similar structure data	4tpw-1 7meu-1 6lxq-d 7meu-2 3hqr-d 6gkk-4 4iaw-1 5j5y-4 6ylr-1 5m7z-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#230 - Feb 2019 Initiation Factor eIF4E similarity (16) #205 - Jan 2017 Nuclear Pore Complex similarity (3) #60 - Dec 2004 Ubiquitin similarity (2) #106 - Oct 2008 Poly(A) Polymerase similarity (3) #86 - Feb 2007 Exosomes similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (2)

Deposited unit

A: Eukaryotic translation initiation factor 4E

B: Eukaryotic translation initiation factor 4E

hetero molecules

46.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Eukaryotic translation initiation factor 4E

hetero molecules

defined by author
23.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Eukaryotic translation initiation factor 4E

hetero molecules

defined by author
22.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	39.830, 73.480, 66.260
Angle α, β, γ (deg.)	90.00, 106.66, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Eukaryotic translation initiation factor 4E / EIF4E / 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-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE Mass: 539.223 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₂₀N₅O₁₄P₃
#3: Chemical	ChemComp-34K / (2E)-2-{2-[4-(4-bromophenyl)-1,3-thiazol-2-yl]hydrazinylidene}-3-(2-nitrophenyl)propanoic acid Mass: 461.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₈H₁₃BrN₄O₄S
#4: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer) Mass: 195.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 594 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.08 Å³/Da / Density % sol: 40.97 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 4000 12-20%, 100mM MES pH 6.5, 10% IPN

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Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.91956 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 2, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91956 Å / Relative weight: 1
Reflection	Resolution: 1.59→19.39 Å / Num. obs: 46347 / % possible obs: 94.1 % / Redundancy: 2.14 % / Net I/σ(I): 14.1

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Processing

Software

Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.59→19.39 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.85 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2109	2021	4.36 %
R_work	0.1819	-	-
obs	0.1832	46338	94.27 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.59→19.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3032	0	106	594	3732

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3396
X-RAY DIFFRACTION	f_angle_d	1.171	4638
X-RAY DIFFRACTION	f_dihedral_angle_d	13.48	1267
X-RAY DIFFRACTION	f_chiral_restr	0.043	482
X-RAY DIFFRACTION	f_plane_restr	0.006	582

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.59-1.6298	0.4568	138	0.3938	2744	X-RAY DIFFRACTION	82
1.6298-1.6738	0.328	137	0.3301	3092	X-RAY DIFFRACTION	93
1.6738-1.723	0.3013	143	0.2836	3108	X-RAY DIFFRACTION	94
1.723-1.7786	0.2617	145	0.2347	3164	X-RAY DIFFRACTION	95
1.7786-1.8421	0.2462	146	0.2175	3191	X-RAY DIFFRACTION	95
1.8421-1.9158	0.2679	140	0.2081	3189	X-RAY DIFFRACTION	95
1.9158-2.0029	0.2429	147	0.1945	3227	X-RAY DIFFRACTION	96
2.0029-2.1084	0.2141	144	0.1703	3227	X-RAY DIFFRACTION	96
2.1084-2.2403	0.1816	146	0.1627	3233	X-RAY DIFFRACTION	97
2.2403-2.413	0.1933	147	0.1644	3215	X-RAY DIFFRACTION	96
2.413-2.6553	0.1933	148	0.1657	3261	X-RAY DIFFRACTION	96
2.6553-3.0383	0.1736	146	0.1668	3260	X-RAY DIFFRACTION	97
3.0383-3.8231	0.1691	147	0.1544	3231	X-RAY DIFFRACTION	96
3.8231-19.3924	0.2172	147	0.1675	3175	X-RAY DIFFRACTION	93

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	5.7223	-0.1431	2.1124	2.7795	-0.3028	4.9405	-0.001	0.131	0.3153	-0.1021	-0.0512	0.1866	-0.106	-0.0981	0.0914	0.1526	-0.0039	0.0656	0.1051	0.0152	0.1143	5.9799	-4.194	-0.5025
2	5.6801	4.809	7.1753	6.8764	5.1748	9.4429	-0.1026	0.2205	0.6607	-0.0198	-0.2355	0.3075	0.1777	0.1232	0.3083	0.1229	0.0407	0.0086	0.1896	0.0122	0.1381	-0.0868	-0.6524	-4.805
3	4.5055	-0.6841	-0.4163	3.3647	-0.1613	7.5484	-0.1536	-0.0068	0.3444	-0.2347	0.0221	-0.0556	-0.3451	0.0304	0.1001	0.095	-0.0114	-0.0119	0.1046	0.0149	0.1155	11.2297	-1.9435	8.6176
4	4.0487	2.0164	1.3749	4.2105	0.8645	3.429	-0.0744	-0.2538	0.2649	-0.2799	-0.2689	1.3515	-0.2917	-0.5901	0.47	0.2497	0.1218	-0.0204	0.3095	-0.041	0.3554	-4.9527	-3.0778	9.6721
5	4.3686	0.7471	1.2826	2.5829	0.8658	5.9993	0.261	0.3601	0.2228	-0.6361	-0.146	0.2379	-0.0813	-0.2267	0.0729	0.261	0.0449	-0.02	0.1686	0.0344	0.1313	3.4565	-9.0519	-5.46
6	7.1472	-1.3756	-2.7579	5.9924	0.4347	3.1324	-0.0354	1.2764	0.1613	-1.8061	0.1826	-0.5989	-0.2585	0.8343	-0.3137	0.5871	-0.009	0.0101	0.3718	-0.0172	0.1876	8.4324	-15.9299	-14.0557
7	4.3436	-2.8154	-3.4877	5.5836	1.9119	7.5835	-0.1402	-0.4699	-0.2748	0.1108	0.1199	0.9977	-0.0655	-0.515	0.0473	0.2075	-0.0366	-0.0359	0.3267	0.0305	0.3165	-5.1745	-18.698	7.4812
8	5.2562	-0.8583	-2.4554	4.8703	0.1964	5.9879	0.0383	-0.1606	-0.1546	0.0311	0.1363	0.1485	0.319	-0.2055	-0.0941	0.114	-0.0249	-0.0242	0.1224	0.0243	0.0934	6.2701	-14.1545	9.4497
9	5.7379	-5.489	3.0548	5.257	-2.9363	2.2296	-0.1019	0.2251	-0.1849	-0.3939	-0.448	-0.6466	0.2101	1.1204	0.6426	0.2248	0.0585	0.0561	0.3138	-0.0097	0.3491	17.6837	-21.3253	0.4229
10	3.2293	-1.0507	-0.879	3.8822	-0.0035	3.8857	0.1251	0.0601	-0.2564	-0.2917	-0.1051	0.3927	0.2336	-0.3305	0.0477	0.174	-0.0313	-0.0477	0.1823	-0.0063	0.1154	-0.1916	-15.5092	0.1697
11	5.9631	2.0203	1.5784	0.6935	0.6421	4.8189	0.2653	0.2476	-0.4738	-0.8207	0.053	-0.329	-0.0327	0.4558	-0.8028	0.5376	0.1221	-0.0646	0.3455	-0.1455	0.3062	10.6597	-27.4484	-8.4593
12	7.9664	1.639	-5.3891	7.3357	0.8334	5.3398	0.0441	-0.1728	-0.4893	-0.0396	-0.1888	-0.3565	0.443	0.3998	-0.0437	0.1971	0.0055	-0.0642	0.1421	-0.0177	0.1931	9.4638	-26.0192	3.4212
13	5.0624	3.192	-4.9924	8.4207	-0.8546	7.3076	0.3493	-0.1911	-0.677	-0.1377	-0.2158	-0.0321	-0.4503	0.4362	-0.0823	0.2568	-0.0377	-0.0974	0.1783	0.0265	0.157	6.8408	-22.7756	11.8909
14	6.7214	0.2754	-2.9452	2.2728	-1.2406	7.6527	0.1173	-0.0478	-0.1724	-0.22	0.2475	0.5485	0.4555	-0.6467	-0.087	0.3154	-0.0358	-0.0621	0.1523	-0.0104	0.2132	-0.3422	-28.3811	4.7375
15	2.5103	-1.7972	3.2786	4.4975	-0.9477	5.8225	0.1561	0.3326	-0.5366	-1.1109	-0.0783	0.9874	0.4023	-0.8603	1.1467	0.5288	0.0305	-0.204	0.3238	-0.1289	0.2868	-3.4457	-22.0613	-11.5425
16	2.2032	0.9779	-1.7309	6.4286	-0.9998	9.319	-0.2802	0.4688	0.4892	-0.6585	0.0969	1.3801	-0.6442	-1.0337	0.561	0.5152	-0.0607	-0.2537	0.3274	-0.0455	0.4761	-2.8907	-27.7848	-4.5033
17	8.2158	-1.9682	1.4461	8.8245	4.29	3.5516	0.2244	0.4922	-0.7483	-0.2453	-0.1095	-0.6185	0.1415	0.1133	-0.0216	0.1888	0.0162	0.0669	0.2283	0.0309	0.2178	21.4461	-22.347	15.194
18	7.1722	-1.7766	-3.1119	4.3111	0.7725	7.2438	-0.0943	-0.0453	-0.413	0.4186	-0.0251	-0.0562	0.3165	-0.2499	0.0998	0.1266	-0.0249	-0.0402	0.0806	0.017	0.1304	14.4894	-19.044	31.3903
19	2.5414	1.9019	4.1238	4.0442	3.6241	6.8018	-0.2026	-1.044	-0.4428	0.3895	0.54	0.8546	-0.4862	-0.6026	-0.5788	0.7279	0.0687	0.1255	0.8179	0.1947	0.51	3.7887	-16.8638	47.4778
20	1.7803	0.5179	-1.2459	1.8128	-0.5214	5.5115	0.0074	-0.0765	-0.157	0.2339	-0.0462	-0.098	0.1202	-0.0517	-0.0305	0.1101	-0.0207	-0.0075	0.0987	0.0165	0.1308	12.2681	-20.7683	28.4075
21	8.1127	-5.9786	-4.2794	5.9361	2.7439	5.5406	-0.1469	0.1063	-0.338	0.4718	-0.1749	0.7661	0.8002	-0.7635	0.2782	0.2161	-0.1063	0.0278	0.2567	-0.0246	0.2184	1.8166	-18.6231	25.6333
22	2.9828	-0.5336	0.3102	3.1931	0.0804	3.2555	0.0394	-0.2559	-0.3298	0.4967	-0.0781	0.1996	0.0441	-0.3154	-0.0341	0.1618	-0.0346	0.0179	0.1376	0.0254	0.1348	10.9576	-14.2423	34.246
23	0.8672	-0.7884	-0.9714	0.8271	1.5458	5.2379	0.0927	-0.6345	-0.2934	0.0735	0.1439	-0.2151	0.3375	0.4474	1.3958	0.2511	-0.0594	-0.3185	0.2485	0.1702	0.1812	23.8917	-11.5973	39.6096
24	6.3557	0.5524	2.3414	3.2447	0.1088	4.2201	0.0909	-0.2414	0.0099	0.2695	-0.054	0.4439	-0.0154	-0.5063	0.0246	0.1715	-0.0193	0.0204	0.1459	-0.0023	0.1473	7.253	-1.6225	30.3694
25	3.7045	-1.0016	-0.7575	3.866	-0.0837	3.6455	0.0044	0.0148	0.0331	0.0392	-0.03	0.1108	-0.0303	-0.1163	0.0155	0.0562	-0.0094	0.0079	0.1049	0.0084	0.0854	12.1471	-8.684	21.6539
26	5.9868	4.163	0.2678	6.0032	-0.4232	7.3296	-0.0071	0.6404	-0.4226	-0.2849	0.1431	-0.9678	0.1459	1.2264	0.1459	0.137	-0.0094	-0.0142	0.2984	-0.0043	0.2929	27.3551	-5.3641	22.1282
27	5.134	0.6907	-0.0808	3.4247	-0.2039	3.1433	-0.0429	-0.2369	0.1897	0.364	-0.0223	-0.0095	-0.1433	-0.115	-0.0214	0.1483	-0.0059	-0.0143	0.0995	0.0024	0.0807	13.3859	-5.9213	33.2917
28	8.1064	-0.5217	1.4583	3.885	-2.2123	1.4452	-0.0098	0.1649	0.426	0.3496	-0.2294	-0.5848	-0.4777	0.4489	0.1314	0.1957	-0.048	-0.0089	0.1653	0.0192	0.1863	25.394	2.4575	27.997
29	2.3677	-3.515	-2.3718	6.5261	4.9166	3.8911	-0.032	0.0376	0.3853	-0.646	-0.0949	-0.2035	-0.5846	0.0292	0.1255	0.1495	-0.0125	-0.0212	0.1207	0.0157	0.1315	15.3494	1.4157	20.4241
30	0.8578	1.4884	0.4393	2.815	1.6525	4.0007	-0.0371	-0.0587	0.284	0.0916	-0.2158	0.3028	-0.4154	-0.3377	0.21	0.1299	0.0207	0.0004	0.1553	-0.0156	0.1377	10.5635	5.5123	25.4199
31	7.101	5.6653	1.8394	6.3505	-1.2342	4.4814	0.265	-0.7182	0.7376	1.0497	-0.2893	0.5578	-0.7342	-0.3859	0.8653	0.4357	-0.1002	-0.0264	0.2788	-0.0253	0.1767	16.7203	-0.384	42.8573
32	5.8004	-0.0952	-0.1665	5.3453	-2.1763	7.6105	0.1457	-1.2403	-0.1053	1.2069	0.0793	0.075	-0.4462	-0.5216	-0.0901	0.5028	-0.0105	-0.0579	0.3593	-0.0012	0.2552	15.3755	5.9803	38.3048
33	1.0673	-1.0509	-0.2179	1.1718	-0.0492	0.5523	0.1672	-0.3704	-0.4209	0.1558	-0.2861	0.8878	0.195	-1.0465	-0.0412	0.4531	-0.0281	-0.1	0.4459	-0.0573	0.3678	-7.3876	-14.2448	-6.9007
34	1.2678	2.4815	-0.1157	4.9888	-0.2736	0.0352	0.073	-0.3476	0.3936	0.3344	-0.1192	0.7792	-0.1525	-0.5956	-0.0257	0.3692	-0.0539	0.0108	0.3256	-0.0028	0.2122	9.4619	-7.1835	43.0566
35	0.1347	0.0435	-0.0935	0.0852	-0.0171	0.072	-0.583	0.115	0.2532	0.1232	0.0211	0.2059	0.3948	0.456	0.0017	0.5469	0.0726	-0.0623	0.3332	-0.0184	0.4627	-4.0189	2.4081	0.9273

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 33:57)
2	X-RAY DIFFRACTION	2	(chain A and resid 58:64)
3	X-RAY DIFFRACTION	3	(chain A and resid 65:78)
4	X-RAY DIFFRACTION	4	(chain A and resid 79:87)
5	X-RAY DIFFRACTION	5	(chain A and resid 88:104)
6	X-RAY DIFFRACTION	6	(chain A and resid 105:109)
7	X-RAY DIFFRACTION	7	(chain A and resid 110:124)
8	X-RAY DIFFRACTION	8	(chain A and resid 125:141)
9	X-RAY DIFFRACTION	9	(chain A and resid 142:147)
10	X-RAY DIFFRACTION	10	(chain A and resid 148:168)
11	X-RAY DIFFRACTION	11	(chain A and resid 169:174)
12	X-RAY DIFFRACTION	12	(chain A and resid 175:184)
13	X-RAY DIFFRACTION	13	(chain A and resid 185:189)
14	X-RAY DIFFRACTION	14	(chain A and resid 190:198)
15	X-RAY DIFFRACTION	15	(chain A and resid 199:206)
16	X-RAY DIFFRACTION	16	(chain A and resid 207:217)
17	X-RAY DIFFRACTION	17	(chain B and resid 35:40)
18	X-RAY DIFFRACTION	18	(chain B and resid 41:49)
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33	X-RAY DIFFRACTION	33	(chain A and resid 301)
34	X-RAY DIFFRACTION	34	(chain B and resid 1000)
35	X-RAY DIFFRACTION	35	(chain A and resid 302)

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