PDB-6gkk: Translation initiation factor 4E in complex with beta-phosphoroth...

ID or keywords:

Entry

Database: PDB / ID: 6gkk

Title

Translation initiation factor 4E in complex with beta-phosphorothioate trinucleotide mRNA 5' cap diastereomer 1 (m7GppSpApG D1)

Components

Eukaryotic translation initiation factor 4E

EIF4E

Keywords

TRANSLATION /

Protein-ligand complex /

translation initiation factor /

eIF4E / mRNA 5' cap / m7GppSpApG /

phosphorothioate /

thiophosphate

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 ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.858 Å

Authors

Warminski, M. / Nowak, E. / Kowalska, J. / Jemielity, J. / Nowotny, M.

Funding support

Poland, 2items

Citation

Journal: To Be Published
Title: Translation initiation factor 4E in complex with beta-phosphorothioate trinucleotide mRNA 5' cap diastereomer 1 (m7GppSpApG D1)
Authors: Warminski, M. / Nowak, E. / Kubacka, D. / Kowalska, J. / Nowotny, M. / Jemielity, J.

History

Deposition	May 21, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 19, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6gkk.cif.gz	312.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6gkk.ent.gz	254.6 KB	Display	PDB format
PDBx/mmJSON format	6gkk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gk/6gkk ftp://data.pdbj.org/pub/pdb/validation_reports/gk/6gkk	HTTPS FTP

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Related structure data

Related structure data	5m7xS 5m7v 5m7w 5m7z 5m80 5m81 5m83 5m84 S: Starting model for refinement
Similar structure data	5j5y-1 5m7x-2 6ylt-1 6gkj-2 6u06-1 6u06-4 6ylv-4 5zk9-d 5m7x-1 4bea-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#230 - Feb 2019 Initiation Factor eIF4E similarity (17)

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

91.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Eukaryotic translation initiation factor 4E

hetero molecules

defined by author
Evidence: gel filtration
22.9 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)

3

C: Eukaryotic translation initiation factor 4E

hetero molecules

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

4

D: Eukaryotic translation initiation factor 4E

hetero molecules

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

Unit cell

Length a, b, c (Å)	38.100, 38.150, 146.910
Angle α, β, γ (deg.)	88.86, 84.64, 76.59
Int Tables number	1
Space group name H-M	P1

#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-WZO / [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl [phosphonooxy(sulfanyl)phosphoryl] hydrogen phosphate Mass: 568.307 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Formula: C₁₂H₂₁N₅O₁₃P₃S
#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.: 359 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.33 Å³/Da / Density % sol: 47.32 % / Description: thin plate
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 19% PEG 10000, 0.1M TrisHCl pH 8.0, 0.2M CH3COONH4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Feb 1, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.858→48.76 Å / Num. obs: 66480 / % possible obs: 98.3 % / Redundancy: 6.819 % / CC_1/2: 0.999 / R_merge(I) obs: 0.1 / R_rim(I) all: 0.108 / Net I/σ(I): 13.76
Reflection shell	Resolution: 1.858→1.91 Å / Redundancy: 4.216 % / R_merge(I) obs: 1.111 / Mean I/σ(I) obs: 1.21 / Num. unique obs: 4669 / CC_1/2: 0.582 / R_rim(I) all: 1.263 / % possible all: 90.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5M7X

5m7x

Resolution: 1.858→22.067 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.95 / Phase error: 25.35

	R_factor	Num. reflection	% reflection
R_free	0.2341	2449	3.69 %
R_work	0.195	-	-
obs	0.1964	66424	98.31 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.858→22.067 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5628	0	150	359	6137

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	5989
X-RAY DIFFRACTION	f_angle_d	1.223	8208
X-RAY DIFFRACTION	f_dihedral_angle_d	13.397	3446
X-RAY DIFFRACTION	f_chiral_restr	0.065	886
X-RAY DIFFRACTION	f_plane_restr	0.007	1033

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 (%)
1.858-1.8959	0.3317	134	0.3133	3494	X-RAY DIFFRACTION	89
1.8959-1.9371	0.3117	141	0.2772	3693	X-RAY DIFFRACTION	97
1.9371-1.9821	0.2816	144	0.2589	3763	X-RAY DIFFRACTION	98
1.9821-2.0317	0.3048	145	0.2387	3764	X-RAY DIFFRACTION	99
2.0317-2.0866	0.2866	144	0.2335	3762	X-RAY DIFFRACTION	99
2.0866-2.1479	0.2708	145	0.2232	3795	X-RAY DIFFRACTION	98
2.1479-2.2172	0.2647	144	0.2146	3765	X-RAY DIFFRACTION	99
2.2172-2.2963	0.2307	144	0.2155	3755	X-RAY DIFFRACTION	99
2.2963-2.3882	0.272	149	0.2094	3902	X-RAY DIFFRACTION	99
2.3882-2.4967	0.2853	143	0.2082	3738	X-RAY DIFFRACTION	99
2.4967-2.6281	0.2699	145	0.207	3780	X-RAY DIFFRACTION	100
2.6281-2.7925	0.2243	145	0.2019	3798	X-RAY DIFFRACTION	100
2.7925-3.0076	0.2514	145	0.199	3799	X-RAY DIFFRACTION	99
3.0076-3.3094	0.2258	145	0.1827	3775	X-RAY DIFFRACTION	99
3.3094-3.7862	0.1943	147	0.1662	3844	X-RAY DIFFRACTION	100
3.7862-4.7623	0.1899	147	0.1619	3831	X-RAY DIFFRACTION	100
4.7623-22.0681	0.216	142	0.1801	3717	X-RAY DIFFRACTION	98

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	6.6206	3.6148	5.8061	5.0229	3.0135	5.6286	-0.06	0.3273	-0.2216	0.1088	0.2706	-0.9948	-0.1684	0.8509	-0.3388	0.2425	-0.0214	0.0003	0.3102	-0.0803	0.6182	-45.6688	78.9738	-1.454
2	7.4051	1.1279	1.547	0.4935	0.1797	0.592	-0.0798	-0.2877	0.1552	-0.0659	0.0018	0.3365	-0.017	-0.1265	0.0715	0.2088	-0.0082	0.0187	0.1482	-0.0306	0.3388	-73.6233	70.196	-7.6337
3	7.2815	4.2932	1.7117	4.0084	2.2626	1.4534	-0.0287	-0.0856	0.9781	-0.1391	-0.07	0.2911	-0.19	-0.0997	0.1558	0.2098	0.0184	0.0172	0.1723	-0.0432	0.3828	-68.5818	74.881	-5.2409
4	2.4949	-0.322	1.7586	2.3549	-0.1205	3.691	-0.0408	0.0069	0.0956	-0.0722	0.0379	-0.0727	-0.0991	-0.0405	0.0318	0.1409	0.0007	0.0499	0.1124	-0.0405	0.2368	-63.2152	70.4841	-8.0393
5	0.7612	-0.4706	0.3391	2.9109	-0.0909	2.507	-0.0748	0.0119	-0.2356	-0.3475	-0.0128	-0.2687	0.3345	0.0131	0.0799	0.2356	-0.0218	0.0987	0.1572	-0.0563	0.3606	-58.7353	60.1909	-13.4043
6	3.6394	0.2455	-2.7898	2.3813	-2.4483	5.8874	-0.0936	0.2178	-0.0029	-0.4339	0.0914	-0.449	-0.0881	-0.0309	0.0255	0.259	-0.0326	0.0589	0.151	-0.0605	0.3151	-60.9267	69.0331	-19.3554
7	2.7102	-2.3291	0.3902	4.229	0.2252	3.4573	-0.002	0.4226	-0.0867	-0.7611	0.0015	-0.3326	0.2164	0.0297	-0.0019	0.3756	-0.072	0.1479	0.2455	-0.0792	0.2672	-58.2513	63.9224	-25.5863
8	3.9146	2.0879	-4.3204	1.3031	-2.4057	4.9904	0.3114	0.3323	0.4882	0.3543	-0.1729	-0.1325	-0.8566	0.2416	-0.3856	0.3222	-0.0471	0.0647	0.438	0.0577	0.5345	-29.5077	63.9912	-61.6299
9	4.2883	4.588	-1.388	5.7142	-1.8118	0.7399	-0.188	0.1568	-0.224	-0.2029	0.1668	-0.0477	0.1403	-0.0652	0.0184	0.1832	0.014	0.0522	0.2105	-0.0465	0.328	-43.354	39.5232	-55.1877
10	1.2838	-0.1099	0.0918	1.7096	-0.2805	2.5032	-0.0436	-0.0548	-0.0634	0.0853	-0.0279	0.2385	0.0417	-0.1673	0.0692	0.1504	0.0022	0.062	0.1595	-0.0578	0.2729	-46.7667	51.1359	-51.5245
11	2.8883	-1.3165	0.2251	1.633	0.152	3.161	-0.1554	-0.5239	0.036	0.6174	0.0828	0.2527	0.0993	-0.1009	0.045	0.3134	0.0118	0.1172	0.2512	-0.0505	0.2387	-46.4504	52.8894	-38.9314
12	3.2684	1.2231	0.4271	3.8305	-3.9022	5.5566	-0.0169	-0.0805	0.0592	0.7437	0.208	-0.3223	-0.545	-0.5959	-0.2023	0.5217	0.0397	0.0211	0.1878	-0.0523	0.2878	-64.4216	63.529	9.6604
13	4.4902	0.1632	0.9923	0.3637	-0.9825	4.435	0.1664	0.2588	-0.9633	0.2826	-0.0545	-0.7267	0.3658	1.0094	-0.1752	0.5441	0.0011	-0.3628	0.3887	-0.0581	0.9096	-44.399	44.7453	16.1776
14	1.8398	-1.0807	0.8371	0.6496	-0.5599	0.6773	0.1043	0.0339	-0.365	0.4718	0.0999	-0.927	0.0604	0.1828	-0.183	0.5262	-0.0977	-0.2444	0.3146	0.0019	0.8408	-46.6057	50.2287	13.1328
15	0.7443	-0.2681	0.9589	0.1245	-0.4079	1.5272	0.2934	-0.141	-0.2763	0.8718	-0.1451	-0.8937	0.0955	0.1218	-0.1074	0.6214	-0.1023	-0.3195	0.2386	0.0176	0.6072	-53.1431	48.686	16.2198
16	0.5045	-0.2956	0.2285	0.1812	-0.1668	0.3172	0.3433	-0.3981	-0.4471	1.4215	-0.174	-0.0297	0.285	-0.1951	-0.1581	0.951	-0.1822	-0.2149	0.2853	0.0422	0.4375	-61.6066	41.5743	21.9523
17	1.6677	0.5837	0.3077	2.216	0.4742	0.8283	0.412	-0.4044	-0.0596	0.6569	-0.1028	-0.1294	-0.0838	-0.003	0.801	1.0189	-0.3043	-0.4773	0.2768	-0.0178	0.4993	-58.0994	52.2214	26.2959
18	3.0098	0.4361	0.3723	0.8957	0.6584	0.5137	0.2487	-0.7236	-0.2589	1.0878	-0.3179	-0.247	0.0717	0.109	-0.1681	1.2011	-0.1766	-0.2521	0.4589	0.0743	0.3584	-58.6847	46.8045	29.9192
19	1.4983	-1.2594	0.1737	1.1972	-0.5387	4.1754	-0.2369	-0.7261	-0.6128	0.5235	0.0793	0.0108	0.5947	-0.2661	0.129	1.3213	-0.3815	-0.2217	0.6956	0.2023	0.4941	-58.3413	42.1147	34.9538
20	4.6632	-1.4149	1.9933	7.7214	-5.7374	4.7877	0.004	0.881	0.1023	-0.4914	0.089	-0.2723	0.5518	0.1374	-0.1439	0.282	0.0923	-0.015	0.6417	-0.0677	0.2395	-50.2559	49.0864	-71.802
21	0.9731	0.9312	1.284	5.2629	-1.6993	3.6804	0.2437	0.7828	1.3924	-0.0996	0.0327	0.2081	-0.8612	-0.1041	-0.2021	0.3773	0.0543	0.1152	0.6564	0.354	0.85	-63.3043	71.9955	-77.901
22	3.2844	-0.1304	-0.6163	2.6659	-0.3696	2.4792	0.0109	0.8992	0.8928	0.1453	0.1825	0.1043	-0.3665	-0.1202	-0.1639	0.1951	0.0113	0.0305	0.5122	0.1273	0.3571	-63.2034	62.0909	-73.5715
23	0.5929	-0.1166	0.258	0.5292	0.168	0.198	0.1022	1.0697	0.7503	-0.3008	-0.1459	0.1435	-0.4449	-0.0989	-0.104	0.1852	0.0289	0.0649	1.5223	0.4166	0.5987	-67.0636	64.2833	-86.4761
24	3.4366	-0.0192	-1.9496	4.2948	-0.5741	4.6868	0.2813	1.6095	0.017	-0.3791	-0.2115	-0.1642	0.4988	0.2403	-0.0115	0.3027	0.0009	-0.0146	1.0506	-0.0141	0.2495	-63.0782	54.8254	-83.9116
25	0.8568	-0.1753	-1.4144	2.1367	0.503	2.4152	-0.1842	1.3308	0.0243	-0.864	0.0028	0.3379	0.0199	-0.0966	-0.0646	0.4891	0.0126	-0.0792	1.7282	0.1074	0.2872	-67.0981	58.4013	-93.3075

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 30 through 42 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 43 through 56 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 57 through 66 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 67 through 110 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 111 through 142 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 143 through 172 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 173 through 217 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 28 through 42 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 43 through 66 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 67 through 142 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 143 through 217 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 31 through 42 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 43 through 56 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 57 through 66 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 67 through 110 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 111 through 142 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 143 through 156 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 157 through 187 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 188 through 217 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 32 through 42 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 43 through 56 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 57 through 95 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 96 through 125 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 126 through 155 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 156 through 217 )

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