PDB-3m94: Complex crystal structure of Ascaris suum eIF4E-3 with m2,2,7G cap

ID or keywords:

Entry

Database: PDB / ID: 3m94

Title

Complex crystal structure of Ascaris suum eIF4E-3 with m2,2,7G cap

Components

Eukaryotic translation initiation factor 4E-binding protein 1
Translation initiation factor 4E

Keywords

TRANSLATION / eIF4E / Berkeley Structural Genomics Center / BSGC

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 4E binding / eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / mTORC1-mediated signalling / TOR signaling / translation repressor activity / negative regulation of translational initiation / translation initiation factor binding / translation initiation factor activity ...
Similarity search - Function

Biological species

Ascaris suum (pig roundworm)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Liu, W. / Berkeley Structural Genomics Center (BSGC)

Citation

Journal: Nucleic Acids Res. / Year: 2011
Title: Structural basis for nematode eIF4E binding an m2,2,7G-Cap and its implications for translation initiation.
Authors: Liu, W. / Jankowska-Anyszka, M. / Piecyk, K. / Dickson, L. / Wallace, A. / Niedzwiecka, A. / Stepinski, J. / Stolarski, R. / Darzynkiewicz, E. / Kieft, J. / Zhao, R. / Jones, D.N. / Davis, R.E.

History

Deposition	Mar 19, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 20, 2011	Provider: repository / Type: Initial release
Revision 1.1	Oct 12, 2011	Group: Database references
Revision 1.2	Dec 14, 2011	Group: Database references
Revision 1.3	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3m94.cif.gz	56.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3m94_validation.pdf.gz	700.6 KB	Display	wwPDB validaton report
Full document	3m94_full_validation.pdf.gz	701.9 KB	Display
Data in XML	3m94_validation.xml.gz	6.8 KB	Display
Data in CIF	3m94_validation.cif.gz	9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m9/3m94 ftp://data.pdbj.org/pub/pdb/validation_reports/m9/3m94	HTTPS FTP

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Related structure data

Related structure data	3m93C 2v8wS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3m93-d 5syn-2 5ubb-d 1ej4-d 1wdu-2 6zys-2 5ypi-5 6a8d-d 6ogo-2 1lm4-1 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 (10)

Deposited unit

A: Translation initiation factor 4E

C: Eukaryotic translation initiation factor 4E-binding protein 1

C: ACETYL GROUP

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	104.977, 104.977, 46.906
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	80
Space group name H-M	I4₁

#1: Protein	Translation initiation factor 4E Mass: 22169.328 Da / Num. of mol.: 1 / Fragment: UNP residues 49-236 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ascaris suum (pig roundworm) / Strain: Ascaris suum / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q6PKX2
#2: Protein/peptide	Eukaryotic translation initiation factor 4E-binding protein 1 / eIF4E-binding protein 1 / 4E-BP1 / Phosphorylated heat- and acid-stable protein regulated by ...eIF4E-binding protein 1 / 4E-BP1 / Phosphorylated heat- and acid-stable protein regulated by insulin 1 / PHAS-I Mass: 2144.564 Da / Num. of mol.: 1 / Fragment: UNP residues 51-67 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13541
#3: Chemical	ChemComp-M7M / N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate) Mass: 487.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₃H₂₃N₅O₁₁P₂
#4: Chemical	ChemComp-ACE / ACETYL GROUP Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₄O
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.66 Å³/Da / Density % sol: 53.72 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 20% MMG PEG 2000, 0.2 M (NH4)2SO4 and 100 mM Na-Critate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 27, 2009
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.05→50 Å / Num. obs: 15993 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 4.7 %

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASES		phasing
REFMAC	5.5.0072	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2v8W

2v8w

Resolution: 2.05→19.16 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.943 / SU B: 9.344 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2443	1632	10.2 %	RANDOM
R_work	0.20363	-	-	-
obs	0.20766	14361	99.03 %	-
all	-	15993	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 44.338 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.28 Å²	0 Å²	0 Å²
2-	-	-1.28 Å²	0 Å²
3-	-	-	2.56 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→19.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1558	0	34	39	1631

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.021	1632
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.266	1.957	2222
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.326	5	190
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.119	23.718	78
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.506	15	263
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.214	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	237
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	1233
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.532	1.5	959
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.99	2	1534
X-RAY DIFFRACTION	r_scbond_it	1.639	3	673
X-RAY DIFFRACTION	r_scangle_it	2.482	4.5	688
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.05→2.104 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.283	120	-
R_work	0.251	980	-
obs	-	-	94.66 %

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	2.9018	-2.6338	-2.6045	2.9678	0.8921	7.6313	0.0259	0.094	-0.0768	0.1704	-0.0132	0.2205	0.0575	-0.2981	-0.0128	0.263	0.0078	0.077	0.15	-0.0424	0.2217	-17.3442	31.1416	21.2971
2	5.1529	-1.5646	-1.6813	7.0516	4.4347	6.0217	-0.0109	0.3446	-0.2618	-0.0538	0.1747	0.0003	0.2077	0.0797	-0.1638	0.1304	0.0115	-0.0545	0.1826	-0.0641	0.1093	-8.585	20.3185	7.5596
3	1.4833	-0.1726	-2.2494	5.6227	4.08	9.4305	0.1151	0.7174	-0.1191	-0.8883	-0.0477	-0.0441	-0.1021	0.0724	-0.0674	0.5062	0.1369	0.0362	0.8037	-0.1725	0.311	-4.8953	13.9831	-3.0611
4	1.3571	0.1489	-0.1757	5.0508	1.9425	2.7252	0.1908	0.0945	-0.053	0.1742	-0.0391	-0.0719	0.144	-0.1481	-0.1516	0.0872	-0.0116	-0.0548	0.1296	-0.0367	0.1671	-13.9631	18.6478	15.9373
5	3.7236	-0.2989	0.8907	7.912	-0.1115	4.3436	0.2014	0.3023	-0.56	-0.3359	0.0553	0.055	0.4495	0.3715	-0.2567	0.1318	0.0771	-0.0606	0.1318	-0.1524	0.2107	-3.6359	13.4879	8.664
6	7.3454	-3.0246	-6.888	4.5724	1.2919	9.4645	0.1747	0.802	0.3012	-0.5204	-0.0573	-0.2368	0.1577	-0.0573	-0.1174	0.1366	0.021	0.0042	0.4669	-0.002	0.1792	-3.435	26.7541	4.0054
7	9.9506	-1.8807	3.7641	8.7322	-4.2673	7.6093	0.1604	0.93	0.5859	-0.2795	0.0704	-0.3266	-0.1812	0.2116	-0.2308	0.1559	-0.0246	0.0938	0.2741	-0.0637	0.1846	3.3979	29.0722	3.3609
8	3.4716	3.2566	-1.6164	9.3254	-2.5391	4.8702	-0.1655	-0.2881	-0.6877	0.0121	0.269	-0.3346	0.8764	0.3866	-0.1035	0.2283	0.1094	-0.1088	0.2302	-0.0581	0.388	6.0959	11.3354	18.2919
9	2.8396	0.0497	0.9283	5.8788	0.8958	2.7236	0.1967	-0.0632	-0.0731	0.1914	-0.0476	-0.2384	0.0378	0.271	-0.1491	0.0968	0.0036	-0.0314	0.1777	-0.0689	0.1726	-2.2618	23.5019	20.9465
10	4.1511	0.3454	1.2562	0.094	-0.3326	3.3909	0.2469	0.3214	-0.2599	0.0029	-0.038	-0.0233	0.1304	0.6291	-0.2089	0.1167	0.0481	0.0446	0.2573	-0.182	0.2997	2.1328	19.5347	11.4618
11	4.9571	2.5005	0.8261	5.6772	-0.2834	3.8077	-0.0163	0.5189	0.4593	-0.272	0.1914	-0.1913	-0.273	0.7491	-0.1751	0.0755	-0.0237	0.0419	0.2969	-0.1177	0.2331	7.2245	29.2759	12.0646
12	6.1306	3.9274	-0.6978	8.5059	-2.7854	4.9128	0.2446	-0.4837	-0.0782	0.5476	-0.017	-0.2004	-0.0282	0.0697	-0.2276	0.0957	0.0134	-0.06	0.2038	-0.1127	0.15	6.4469	25.5101	23.7943
13	5.2389	-1.3188	1.4209	4.579	-3.6971	9.613	0.0899	0.017	-0.3307	-0.172	-0.0466	-0.386	0.7574	0.4722	-0.0433	0.147	0.0289	-0.0179	0.2235	-0.1028	0.287	12.1174	20.2939	16.9283
14	7.5387	-3.9791	-7.1793	4.09	6.146	9.8317	0.1343	-0.1251	0.4991	-0.3184	0.0422	-0.2647	-0.2726	0.283	-0.1764	0.278	0.1168	0.1652	0.4316	0.1155	0.6217	17.8339	23.5461	10.397

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	35 - 40
2	X-RAY DIFFRACTION	2	A	41 - 51
3	X-RAY DIFFRACTION	3	A	52 - 61
4	X-RAY DIFFRACTION	4	A	62 - 84
5	X-RAY DIFFRACTION	5	A	85 - 94
6	X-RAY DIFFRACTION	6	A	95 - 102
7	X-RAY DIFFRACTION	7	A	103 - 112
8	X-RAY DIFFRACTION	8	A	113 - 125
9	X-RAY DIFFRACTION	9	A	126 - 145
10	X-RAY DIFFRACTION	10	A	146 - 161
11	X-RAY DIFFRACTION	11	A	162 - 176
12	X-RAY DIFFRACTION	12	A	177 - 188
13	X-RAY DIFFRACTION	13	A	189 - 200
14	X-RAY DIFFRACTION	14	A	201 - 219

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