PDB-3u7x: Crystal structure of the human eIF4E-4EBP1 peptide complex without cap

ID or keywords:

Entry

Database: PDB / ID: 3u7x

Title

Crystal structure of the human eIF4E-4EBP1 peptide complex without cap

Components

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

Keywords

TRANSLATION / eIF4E / 4EBP1 / mRNA export / structural genomics consortium / SGC

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 / eukaryotic initiation factor 4E binding / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / eukaryotic translation initiation factor 4F complex / chromatoid body / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / mRNA cap binding / Deadenylation of mRNA ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.1 Å

Authors

Siddiqui, N. / Tempel, W. / Nedyalkova, L. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Borden, K.L.B. / Park, H. / Structural Genomics Consortium (SGC)

Citation

Journal: J.Mol.Biol. / Year: 2012
Title: Structural Insights into the Allosteric Effects of 4EBP1 on the Eukaryotic Translation Initiation Factor eIF4E.
Authors: Siddiqui, N. / Tempel, W. / Nedyalkova, L. / Volpon, L. / Wernimont, A.K. / Osborne, M.J. / Park, H.W. / Borden, K.L.

History

Deposition	Oct 14, 2011	Deposition site: RCSB / Processing site: RCSB
Supersession	Nov 2, 2011	ID: 3SMU
Revision 1.0	Nov 2, 2011	Provider: repository / Type: Initial release
Revision 1.1	Feb 8, 2012	Group: Database references
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.3	Sep 13, 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_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3u7x.cif.gz	186.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3u7x.ent.gz	147.9 KB	Display	PDB format
PDBx/mmJSON format	3u7x.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3u7x_validation.pdf.gz	460.9 KB	Display	wwPDB validaton report
Full document	3u7x_full_validation.pdf.gz	464.9 KB	Display
Data in XML	3u7x_validation.xml.gz	17.7 KB	Display
Data in CIF	3u7x_validation.cif.gz	24.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u7/3u7x ftp://data.pdbj.org/pub/pdb/validation_reports/u7/3u7x	HTTPS FTP

-
Related structure data

Related structure data	3tf2C 1ipbS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5zjz-d 5ev6-2 4f6h-d 4oct-2 4a6p-d 4kea-4 5wl7-d 2g1m-d 4c1r-3 5j5o-4 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

3tf2C

1ipbS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#230 - Feb 2019 Initiation Factor eIF4E similarity (19) #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

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

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

hetero molecules

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

1

A: Eukaryotic translation initiation factor 4E

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

hetero molecules

defined by author&software
27.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Eukaryotic translation initiation factor 4E

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

hetero molecules

defined by author&software
27.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

B: Eukaryotic translation initiation factor 4E

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

hetero molecules

A: Eukaryotic translation initiation factor 4E

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

hetero molecules

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

Unit cell

Length a, b, c (Å)	86.500, 38.263, 93.533
Angle α, β, γ (deg.)	90.000, 97.970, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	D
2	1	C
1	2	A
2	2	B

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	THR	THR	ARG	ARG	D	D	50 - 63	4 - 17
2	1	THR	THR	ARG	ARG	C	C	50 - 63	4 - 17
1	2	ASN	ASN	TRP	TRP	A	A	50 - 56	50 - 56
2	2	ASN	ASN	TRP	TRP	B	B	50 - 56	50 - 56

NCS ensembles :

ID
1
2

#1: Protein	Eukaryotic translation initiation factor 4E / eIF-4E / eIF4E / eIF-4F 25 kDa subunit / mRNA cap-binding protein Mass: 25130.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4E, EIF4EL1, EIF4F / Plasmid: pT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06730
#2: Protein/peptide	Eukaryotic translation initiation factor 4E-binding protein 1 / 4E-BP1 / eIF4E-binding protein 1 / Phosphorylated heat- and acid-stable protein regulated by ...4E-BP1 / eIF4E-binding protein 1 / Phosphorylated heat- and acid-stable protein regulated by insulin 1 / PHAS-I Mass: 2357.755 Da / Num. of mol.: 2 / Fragment: UNP residues 46-66 / Source method: obtained synthetically Details: Fmoc solid-phase peptide synthesis (Sheldon Biotechnology Center) Source: (synth.) Homo sapiens (human) / References: UniProt: Q13541
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-UNX / UNKNOWN ATOM OR ION Num. of mol.: 20 / Source method: obtained synthetically
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.79 Å³/Da / Density % sol: 55.89 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1:1 of (protein stock: 0.0004 M eif4e, 0.001 M 4epb1, 0.004 M ribavirin, 0.02 HEPES, 0.1 M potassium chloride, 0.001 tcep, ph 7.3):(reservoir: 2 M ammonium sulfate, 2% Peg-400, 0.1 M sodium ...Details: 1:1 of (protein stock: 0.0004 M eif4e, 0.001 M 4epb1, 0.004 M ribavirin, 0.02 HEPES, 0.1 M potassium chloride, 0.001 tcep, ph 7.3):(reservoir: 2 M ammonium sulfate, 2% Peg-400, 0.1 M sodium HEPES), vapor diffusion, sitting drop, temperature 291K

Crystal

Density Matthews: 2.79 Å³/Da / Density % sol: 55.89 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1:1 of (protein stock: 0.0004 M eif4e, 0.001 M 4epb1, 0.004 M ribavirin, 0.02 HEPES, 0.1 M potassium chloride, 0.001 tcep, ph 7.3):(reservoir: 2 M ammonium sulfate, 2% Peg-400, 0.1 M sodium ...

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97924 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2010

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97924 Å / Relative weight: 1

Reflection

Resolution: 2.1→50 Å / Num. obs: 35859 / % possible obs: 99.7 % / Redundancy: 3.6 % / R_merge(I) obs: 0.089 / Χ²: 1.282 / Net I/σ(I): 7.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.1-2.14	3.4	0.64	1728	1.036	1	96.9
2.14-2.18	3.5	0.571	1703	1.056	1	98.7
2.18-2.22	3.6	0.481	1800	1.155	1	99.4
2.22-2.26	3.6	0.486	1766	2.18	1	99.4
2.26-2.31	3.7	0.457	1769	1.305	1	99.7
2.31-2.37	3.7	0.373	1784	1.155	1	99.9
2.37-2.42	3.7	0.318	1786	1.142	1	99.9
2.42-2.49	3.7	0.307	1768	1.155	1	100
2.49-2.56	3.7	0.268	1818	1.183	1	100
2.56-2.65	3.7	0.223	1748	1.121	1	100
2.65-2.74	3.7	0.188	1801	1.154	1	99.8
2.74-2.85	3.7	0.145	1760	1.142	1	100
2.85-2.98	3.7	0.113	1820	1.132	1	100
2.98-3.14	3.7	0.083	1810	1.168	1	100
3.14-3.33	3.7	0.066	1787	1.198	1	100
3.33-3.59	3.7	0.054	1828	1.343	1	100
3.59-3.95	3.7	0.054	1791	1.727	1	99.7
3.95-4.52	3.6	0.047	1827	1.832	1	100
4.52-5.7	3.5	0.037	1836	1.299	1	100
5.7-50	3.5	0.031	1929	1.139	1	99.8

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
REFMAC	5.5.0109	refinement
PDB_EXTRACT	3.11	data extraction
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IPB

1ipb

Resolution: 2.1→30 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.928 / WR_factor R_free: 0.21 / WR_factor R_work: 0.186 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 9.957 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. AMINO ACID RESIDUES 51 THROUGH 58 ARE POORLY DEFINED BY ELECTRON DENSITY. FO-FC DENSITY SUGGESTS AN ALTERNATE ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2239	1503	4.211 %	THIN SHELLS (SFTOOLS)
R_work	0.1982	-	-	-
obs	0.199	35692	98.947 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso max: 114.74 Å² / B_iso mean: 41.169 Å² / B_iso min: 27.09 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.746 Å²	0 Å²	2.148 Å²
2-	-	-0.441 Å²	0 Å²
3-	-	-	0.29 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3205	0	40	123	3368

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.021	3391
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2319
X-RAY DIFFRACTION	r_angle_refined_deg	1.316	1.936	4615
X-RAY DIFFRACTION	r_angle_other_deg	0.894	3	5588
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.494	5	423
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.033	22.848	165
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.499	15	562
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.783	15	31
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	494
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	3810
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	763
X-RAY DIFFRACTION	r_mcbond_it	0.688	1.5	2043
X-RAY DIFFRACTION	r_mcbond_other	0.147	1.5	831
X-RAY DIFFRACTION	r_mcangle_it	1.257	2	3278
X-RAY DIFFRACTION	r_scbond_it	1.902	3	1348
X-RAY DIFFRACTION	r_scangle_it	3.024	4.5	1326

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	D	81	MEDIUM POSITIONAL	0.29	0.5
1	D	89	LOOSE POSITIONAL	0.22	5
1	D	81	MEDIUM THERMAL	0.19	2
1	D	89	LOOSE THERMAL	0.24	10
2	A	42	MEDIUM POSITIONAL	0.12	0.5
2	A	15	LOOSE POSITIONAL	0.21	5
2	A	42	MEDIUM THERMAL	0.16	2
2	A	15	LOOSE THERMAL	0.33	10

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.1-2.154		0	0.274	2382	2624	90.777
2.154-2.213	0.294	169	0.241	2365	2551	99.334
2.213-2.277	0.297	152	0.236	2348	2515	99.404
2.277-2.346		0	0.21	2410	2417	99.71
2.346-2.423	0.251	139	0.197	2200	2343	99.829
2.423-2.507	0.234	140	0.193	2108	2257	99.601
2.507-2.601	0.216	114	0.195	2088	2207	99.773
2.601-2.707	0.233	101	0.206	2013	2128	99.342
2.707-2.826		0	0.193	2016	2024	99.605
2.826-2.963	0.247	96	0.185	1884	1986	99.698
2.963-3.121	0.224	87	0.184	1739	1833	99.618
3.121-3.308	0.198	74	0.193	1661	1747	99.313
3.308-3.534	0.176	65	0.193	1603	1671	99.82
3.534-3.812	0.198	83	0.185	1480	1569	99.618
3.812-4.169	0.202	88	0.178	1324	1423	99.227
4.169-4.65	0.177	49	0.166	1254	1308	99.618
4.65-5.348	0.199	57	0.176	1102	1162	99.742
5.348-6.499	0.26	40	0.229	964	1007	99.702
6.499-8.983	0.32	28	0.223	757	788	99.619
8.983-30	0.257	21	0.232	491	512	100

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	2.0686	0.2282	-1.4839	2.1662	-0.6502	5.0628	0.0068	-0.0791	-0.0832	-0.0212	0.0138	-0.0917	0.1495	0.0776	-0.0206	0.0681	-0.0252	-0.0153	0.0112	-0.0012	0.0139	38.1223	-7.2829	18.1657
2	4.5964	-1.0078	-0.4728	2.3514	0.4552	1.4817	-0.0394	0.1048	-0.0225	-0.1162	-0.0431	0.0613	-0.0172	-0.1111	0.0825	0.0204	-0.0012	-0.0265	0.0155	-0.0243	0.0596	61.3098	0.4823	47.2028
3	4.7394	5.3656	0.8119	14.2984	2.9601	7.6677	0.1171	0.783	0.173	-1.0067	-0.2905	0.2583	0.0499	-0.3301	0.1733	0.2401	0.0435	-0.0478	0.4519	0.0796	0.2478	28.4804	-2.1964	4.6319
4	8.7345	5.2802	0.4468	17.1965	3.3278	8.721	-0.0609	-0.6796	-0.0342	0.3767	-0.2368	-0.7951	-0.1019	0.8658	0.2977	0.1614	0.0999	-0.0535	0.3781	0.0635	0.1954	72.6173	-4.1235	59.3549

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	31 - 217
2	X-RAY DIFFRACTION	2	B	31 - 217
3	X-RAY DIFFRACTION	3	C	50 - 63
4	X-RAY DIFFRACTION	4	D	50 - 63

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi