PDB-5wb5: Leishmania IF4E-1 bound to Leishmania 4E-IP1

ID or keywords:

Entry

Database: PDB / ID: 5wb5

Title

Leishmania IF4E-1 bound to Leishmania 4E-IP1

Components

Putative eukaryotic translation initiation factor eIF-4E
Uncharacterized protein

Keywords

TRANSLATION /

initiation factors /

leishmania /

parasites / cap

Function / homology

Function and homology information

RNA cap 4 binding / nuclear stress granule / eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / translation regulator activity /

translation initiation factor activity /

P-body / cytoplasmic stress granule /

regulation of translation /

cytoplasm
Similarity search - Function

Biological species

Leishmania major (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Leger-Abraham, M. / Meleppattu, S. / Arthanari, H. / Zinoviev, A. / Boeszoermenyi, A. / Wagner, G. / Shapira, M.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R01-AI108718	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	R01-CA200913	United States

Citation

Journal: Nucleic Acids Res. / Year: 2018
Title: Structural basis for LeishIF4E-1 modulation by an interacting protein in the human parasite Leishmania major.
Authors: Meleppattu, S. / Arthanari, H. / Zinoviev, A. / Boeszoermenyi, A. / Wagner, G. / Shapira, M. / Leger-Abraham, M.

History

Deposition	Jun 27, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 14, 2018	Provider: repository / Type: Initial release
Revision 1.1	Apr 4, 2018	Group: Data collection / Database references / Category: citation / diffrn_radiation_wavelength Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_radiation_wavelength.wavelength
Revision 1.2	Jun 20, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Feb 20, 2019	Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5wb5.cif.gz	136.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5wb5.ent.gz	107.1 KB	Display	PDB format
PDBx/mmJSON format	5wb5.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/wb/5wb5 ftp://data.pdbj.org/pub/pdb/validation_reports/wb/5wb5	HTTPS FTP

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Related structure data

Related structure data	1wkwS S: Starting model for refinement
Similar structure data	6bju-2 6bju-1 6ozg-2 4ued-d 6ykh-d 4ira-d 6orr-3 6h2z-d 6d63-3 6gxe-d 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 (3)

Deposited unit

A: Putative eukaryotic translation initiation factor eIF-4E

B: Uncharacterized protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, isothermal titration calorimetry, immunoprecipitation

Unit cell

Length a, b, c (Å)	68.220, 68.220, 220.200
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	180
Space group name H-M	P6₂22

#1: Protein	Putative eukaryotic translation initiation factor eIF-4E Mass: 24276.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The side chain of residue K17, Y32 and M39 could not be built for poor density and were assigned as alanine. However, all these residues are solvent exposed and are not interacting with Leishmania 4E-IP1 Source: (gene. exp.) Leishmania major (eukaryote) / Gene: EIF4E1, LMJF_27_1620 / Production host: Escherichia coli (E. coli) / References: UniProt: E9ADE1
#2: Protein	Uncharacterized protein Mass: 5907.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_35_3980 / Production host: Escherichia coli (E. coli) / References: UniProt: E9AFM3
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.49 Å³/Da / Density % sol: 50.59 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.1 M Tris-HCl 3 % polyethylene glycol 400 2.125-2.175 M of ammonium sulfate.

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
3	100	1
4	100	1
5	100	1
6	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	ALS	8.2.2	1	0.999909
SYNCHROTRON	ALS	8.2.2	2	0.999925
SYNCHROTRON	ALS	8.2.2	3	0.999893
SYNCHROTRON	ALS	8.2.2	4	0.999887
SYNCHROTRON	ALS	8.2.2	5	0.999925
SYNCHROTRON	ALS	8.2.2	6	0.999887

Detector

Type	ID	Detector	Date
ADSC QUANTUM 315r	1	CCD	Apr 19, 2013
ADSC QUANTUM 315r	2	CCD	Apr 19, 2013
ADSC QUANTUM 315r	3	CCD	Apr 19, 2013
ADSC QUANTUM 315r	4	CCD	Apr 19, 2013
ADSC QUANTUM 315r	5	CCD	Apr 19, 2013
ADSC QUANTUM 315r	6	CCD	Apr 19, 2013

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	2
3	SINGLE WAVELENGTH	M	x-ray	3
4	SINGLE WAVELENGTH	M	x-ray	4
5	SINGLE WAVELENGTH	M	x-ray	5
6	SINGLE WAVELENGTH	M	x-ray	6

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.999909	1
2	0.999925	1
3	0.999893	1
4	0.999887	1
5		1
6		1

Reflection

Resolution: 2.7→36.7 Å / Num. obs: 9019 / % possible obs: 99.8 % / Redundancy: 64.813 % / CC_1/2: 0.999 / R_merge(I) obs: 0.133 / R_rim(I) all: 0.134 / Χ²: 1.024 / Net I/σ(I): 37.1 / Num. measured all: 584551 / Scaling rejects: 17959

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.7-2.77	70.79	0.474	14.68	44739	632	632	0.996	0.477	100
2.77-2.85	69.363	0.438	15.55	45086	650	650	0.996	0.441	100
2.85-2.93	69.995	0.386	17.33	41017	586	586	0.995	0.389	100
2.93-3.02	69.822	0.389	17.39	41614	599	596	0.995	0.392	99.5
3.02-3.12	68.668	0.292	21.36	40995	597	597	0.997	0.294	100
3.12-3.23	69.916	0.242	25.7	38174	546	546	0.998	0.244	100
3.23-3.35	68.052	0.196	29.64	36612	540	538	0.994	0.198	99.6
3.35-3.49	66.487	0.175	32.86	35105	529	528	0.999	0.177	99.8
3.49-3.64	66.423	0.164	34.12	32813	498	494	0.998	0.166	99.2
3.64-3.82	58.135	0.139	40.34	28951	498	498	0.999	0.14	100
3.82-4.02	63.675	0.113	47.45	29800	468	468	0.999	0.114	100
4.02-4.27	62.93	0.096	55.83	28067	446	446	0.999	0.097	100
4.27-4.56	62.15	0.089	57.33	26041	419	419	1	0.089	100
4.56-4.93	60.855	0.084	62.89	23916	393	393	1	0.085	100
4.93-5.4	59.978	0.089	57.02	21652	361	361	1	0.09	100
5.4-6.04	58.306	0.097	53.9	19824	340	340	0.999	0.097	100
6.04-6.97	56.146	0.09	54.26	17293	308	308	0.999	0.091	100
6.97-8.54	56.119	0.071	68.59	15096	269	269	1	0.072	100
8.54-12.07	54.634	0.056	82.64	11637	214	213	1	0.057	99.5
12.07-36.7	44.664	0.06	74.32	6119	143	137	0.999	0.061	95.8

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Processing

Software

Name	Version	Classification
PHENIX	1.12_2829	refinement
XSCALE		data scaling
PDB_EXTRACT	3.22	data extraction
TRUNCATE		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: TRUNCATED VERSION OF AN EIF4E, M7GTP, 4E-BP1 COMPLEX WITH PDB ID 1WKW

1wkw

Resolution: 2.7→36.7 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.21 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2827	439	4.87 %
R_work	0.24	8576	-
obs	0.2421	9015	99.83 %

Solvent computation

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

Displacement parameters

B_iso max: 170.08 Å² / B_iso mean: 66.2755 Å² / B_iso min: 17.58 Å²

Refinement step

Cycle: final / Resolution: 2.7→36.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1650	0	17	21	1688
B_iso mean	-	-	67.59	37.4	-
Num. residues	-	-	-	-	207

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	1694
X-RAY DIFFRACTION	f_angle_d	0.484	2294
X-RAY DIFFRACTION	f_chiral_restr	0.041	260
X-RAY DIFFRACTION	f_plane_restr	0.002	282
X-RAY DIFFRACTION	f_dihedral_angle_d	6.935	1011

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
2.6999-3.0904	0.3267	168	0.2957	2733	2901
3.0904-3.8929	0.3254	123	0.2533	2809	2932
3.8929-36.7034	0.2428	148	0.2136	3034	3182

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	0.0872	-0.0144	0.0643	0.0723	-0.0684	0.1236	0.0563	0.0306	-0.174	-0.2512	0.026	0.1179	-0.0879	-0.056	0.1384	0.6653	0.1699	-0.094	0.0898	-0.0329	0.2626	-15.9926	3.9075	12.5704
2	0.2942	-0.1487	0.1823	0.0788	-0.0996	0.1159	0.1608	0.0017	-0.1995	-0.2834	-0.0637	0.1227	-0.0201	-0.1019	0.074	0.5498	0.4354	-0.4283	-0.1905	0.2834	-0.0813	-13.1057	5.2776	14.9495
3	0.0235	-0.0449	0.0154	0.1914	0.0036	0.0125	0.0337	0.033	0.0119	-0.0402	0.0289	-0.0672	-0.0698	-0.0622	0.1955	0.4866	0.2419	0.023	0.1559	0.0425	0.3294	-13.0751	17.0571	17.6427
4	0.012	-0.0254	0.0002	0.0526	0.0114	0.0242	0.0435	0.0154	0.0186	-0.0969	0.0032	-0.005	0.0094	-0.026	0.1404	0.5328	0.1749	0.0049	-0.018	0.0111	0.2136	-14.8307	11.5978	26.4832
5	0.0261	-0.0054	0.0725	0.0922	-0.0721	0.2147	0.0983	-0.0031	0.0063	-0.0602	0.1148	-0.0604	0.0133	0.004	0.1105	0.4637	0.0684	-0.0155	0.0888	0.0062	0.2173	-11.4399	17.58	13.7048
6	0.0439	0.0492	-0.0215	0.06	-0.0193	0.0191	0.0414	-0.0285	0.0206	-0.0257	0.0175	0.1883	0.0284	-0.018	0.1345	0.7108	0.3448	-0.0596	0.2255	-0.0484	0.3306	-22.2023	19.815	23.2256
7	0.0247	0.0109	0.0019	0.0102	-0.0065	0.0153	0.0263	0.018	0.0452	-0.0853	0.0098	0.1085	-0.0237	-0.0252	-0.0053	0.3726	0.257	0.0293	0.2073	0.0081	0.3437	-17.4173	22.3564	21.1115
8	0.0015	-0.0029	0.005	0.0108	-0.0136	0.0171	-0.0126	-0.0083	-0.001	0.0023	-0.0049	0.0098	0.0053	-0.0158	-0.0043	0.3161	0.1835	-0.0612	0.2655	0.1047	0.1977	-21.3106	4.4972	34.3674
9	0.0055	-0.0056	-0.001	0.0042	0.0047	0.0091	-0.009	-0.0284	0.0167	0.0046	-0.0015	-0.0442	-0.0255	-0.0159	-0.0017	0.4572	0.2495	0.0366	0.3246	0.0336	0.2711	-7.5089	1.2112	33.7067
10	0.0122	-0.0062	-0.0059	0.0226	-0.0006	0.0028	-0.0013	0.0131	-0.0207	-0.0122	0.008	0.0221	0.0094	-0.0095	0.0097	0.6545	0.1757	-0.1663	0.1301	-0.1566	0.3379	-7.0174	-6.7139	14.4714
11	0.008	-0.0029	0.007	0.0025	-0.001	0.0307	0.0063	0.0115	-0.027	-0.022	0.0149	0.0017	-0.018	0.0236	-0.0012	0.6923	0.1028	0.0626	0.1944	-0.0427	0.232	1.4975	9.1868	6.0519

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 13 through 37 )	A	13 - 37
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 38 through 85 )	A	38 - 85
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 86 through 127 )	A	86 - 127
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 128 through 158 )	A	128 - 158
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 159 through 170 )	A	159 - 170
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 171 through 194 )	A	171 - 194
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 195 through 210 )	A	195 - 210
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 4 through 9 )	B	4 - 9
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 10 through 22 )	B	10 - 22
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 23 through 33 )	B	23 - 33
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 34 through 43 )	B	34 - 43

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