PDB-5dbo: Crystal structure of the tetrameric eIF2B-beta2-delta2 complex fr...

ID or keywords:

Entry

Database: PDB / ID: 5dbo

Title

Crystal structure of the tetrameric eIF2B-beta2-delta2 complex from C. thermophilum

Components

Translation initiation factor eIF2b-like protein,Translation initiation factor eIF2b-like protein
Translation initiation factor eif-2b-like protein

Keywords

TRANSLATION / Translation initiation / translational regulation / eIF2B / exchange factor / eIF2 / complex

Function / homology

Function and homology information

translation initiation factor activity
Similarity search - Function

Biological species

Chaetomium thermophilum (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3 Å

Authors

Kuhle, B. / Ficner, R.

Citation

Journal: Nucleic Acids Res. / Year: 2015
Title: Architecture of the eIF2B regulatory subcomplex and its implications for the regulation of guanine nucleotide exchange on eIF2.
Authors: Kuhle, B. / Eulig, N.K. / Ficner, R.

History

Deposition	Aug 21, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Oct 7, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 25, 2015	Group: Database references
Revision 1.2	Jan 10, 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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PDBx/mmCIF format	5dbo.cif.gz	491.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5dbo.ent.gz	405.5 KB	Display	PDB format
PDBx/mmJSON format	5dbo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5dbo_validation.pdf.gz	471.2 KB	Display	wwPDB validaton report
Full document	5dbo_full_validation.pdf.gz	502.4 KB	Display
Data in XML	5dbo_validation.xml.gz	45.2 KB	Display
Data in CIF	5dbo_validation.cif.gz	61 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/db/5dbo ftp://data.pdbj.org/pub/pdb/validation_reports/db/5dbo	HTTPS FTP

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Related structure data

Related structure data	4zemSC 4zeoSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4ddw-d 4ddv-2 4ddx-1 4ddv-1 4ddx-2 4ddt-d 1gku-d 4ddu-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

Deposited unit

A: Translation initiation factor eif-2b-like protein

B: Translation initiation factor eIF2b-like protein,Translation initiation factor eIF2b-like protein

C: Translation initiation factor eif-2b-like protein

D: Translation initiation factor eIF2b-like protein,Translation initiation factor eIF2b-like protein

190 kDa, 4 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)	109.430, 109.430, 219.060
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	Translation initiation factor eif-2b-like protein Mass: 49742.598 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0028980 / Plasmid: pGEX-6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: G0S811
#2: Protein	Translation initiation factor eIF2b-like protein,Translation initiation factor eIF2b-like protein Mass: 45348.828 Da / Num. of mol.: 2 / Fragment: UNP residues 1-92,UNP residues 118-388 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0063470 / Plasmid: pGEX-6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: G0SEE6

#1: Protein

Translation initiation factor eif-2b-like protein

Mass: 49742.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0028980 / Plasmid: pGEX-6P1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: G0S811

#2: Protein

Translation initiation factor eIF2b-like protein,Translation initiation factor eIF2b-like protein

Mass: 45348.828 Da / Num. of mol.: 2 / Fragment: UNP residues 1-92,UNP residues 118-388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Chaetomium thermophilum (fungus) / Gene: CTHT_0063470 / Plasmid: pGEX-6P1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: G0SEE6

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.99 Å³/Da / Density % sol: 38.22 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: MES (pH 6.0), pentaerythritol propoxylate (5/4 PO/OH), NaCl

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.85506 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.85506 Å / Relative weight: 1
Reflection	Resolution: 3→50 Å / Num. obs: 31063 / % possible obs: 99.6 % / Redundancy: 8.21 % / R_sym value: 0.107 / Net I/σ(I): 14.73
Reflection shell	Resolution: 3→3.18 Å / Mean I/σ(I) obs: 2.8 / Num. unique all: 4881 / CC_1/2: 0.841 / R_sym value: 0.69 / % possible all: 98.3

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	7.63 Å	48.95 Å
Translation	7.63 Å	48.95 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
PHASER	2.5.7	phasing
PDB_EXTRACT	3.15	data extraction
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4ZEM and 4ZEO

4zem

4zeo

Resolution: 3→48.948 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.61 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2546	1554	5 %
R_work	0.2082	-	-
obs	0.2105	31060	99.66 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3→48.948 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9377	0	0	0	9377

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	9564
X-RAY DIFFRACTION	f_angle_d	1.316	12970
X-RAY DIFFRACTION	f_dihedral_angle_d	14.257	3538
X-RAY DIFFRACTION	f_chiral_restr	0.053	1506
X-RAY DIFFRACTION	f_plane_restr	0.007	1688

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 (%)
3.0002-3.097	0.3521	136	0.3134	2579	X-RAY DIFFRACTION	97
3.097-3.2077	0.3263	139	0.2924	2644	X-RAY DIFFRACTION	100
3.2077-3.3361	0.2842	139	0.2595	2627	X-RAY DIFFRACTION	100
3.3361-3.4879	0.2764	140	0.2491	2668	X-RAY DIFFRACTION	100
3.4879-3.6717	0.2845	140	0.2313	2657	X-RAY DIFFRACTION	100
3.6717-3.9016	0.279	140	0.2209	2659	X-RAY DIFFRACTION	100
3.9016-4.2027	0.2597	141	0.2028	2672	X-RAY DIFFRACTION	100
4.2027-4.6254	0.2224	141	0.1753	2682	X-RAY DIFFRACTION	100
4.6254-5.294	0.1995	142	0.1762	2702	X-RAY DIFFRACTION	100
5.294-6.6672	0.2783	144	0.2108	2736	X-RAY DIFFRACTION	100
6.6672-48.954	0.2381	152	0.1836	2880	X-RAY DIFFRACTION	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	2.3762	2.3059	0.6207	5.0495	2.2413	0.9058	-0.1371	-0.1389	-0.6759	0.7903	0.2249	-0.7782	0.2733	0.6638	-0.0814	0.6188	-0.0607	-0.1188	0.6167	0.0234	1.3198	42.2395	-22.9009	-14.5994
2	4.9852	0.1616	-0.0775	3.7003	-0.9301	3.8513	-0.4148	0.6413	-0.4896	-0.9613	0.4292	-0.6834	-0.1944	0.1602	-0.0616	0.6593	-0.2517	0.1561	0.5338	-0.1081	0.7147	30.273	-27.3796	-28.7194
3	4.5242	1.0851	0.1163	6.3136	-1.3373	4.616	0.1993	-0.4179	-0.7391	-0.0841	-0.0197	-0.1085	0.4691	-0.0607	-0.2077	0.5807	-0.1627	-0.0885	0.428	-0.0026	0.6792	21.7839	-36.6115	-22.1169
4	1.8852	2.4183	-0.5185	4.0463	0.3095	1.9016	0.0666	-0.0402	0.0046	-0.368	0.0177	0.684	-0.001	0.0121	-0.044	0.4737	-0.1369	-0.0459	0.5227	0.0189	0.5142	17.3518	-6.501	-33.9093
5	2.9591	0.1198	0.2513	3.5522	0.6073	2.1674	-0.151	0.5044	-0.2877	-0.6437	0.2568	-0.3454	-0.1755	0.3036	-0.1583	0.5226	-0.2488	0.0376	0.7099	-0.0132	0.4945	28.0505	1.7435	-33.1546
6	2.5775	0.683	1.1069	1.7774	-0.2632	1.7376	0.1104	0.0744	-0.3914	0.2281	-0.1141	-0.1838	0.1187	-0.0514	-0.0298	0.4851	-0.0952	-0.0253	0.4543	-0.0196	0.3958	24.849	-8.4738	-17.5472
7	4.4643	0.0793	2.1278	2.9596	0.936	4.6419	-0.2607	1.2844	-0.0579	-0.662	0.4026	-0.6446	0.347	0.4867	-0.1859	0.7557	-0.2198	0.0927	0.9957	0.0334	0.7521	56.1602	32.2566	-26.4899
8	2.0772	2.2009	-1.3019	4.9063	-3.6065	2.4373	0.302	0.2876	0.483	0.9028	0.1756	-0.0712	-0.485	-0.1748	-0.1432	0.7148	-0.1767	0.0711	0.6576	-0.0628	1.1042	52.1638	33.7991	-12.9229
9	3.3178	-0.0704	0.9057	4.3817	-0.7102	2.2941	0.0576	0.2072	-0.0595	-0.0916	-0.1063	-0.105	-0.1041	0.1743	0.0848	0.4825	-0.2195	-0.0214	0.6081	-0.0237	0.4674	41.818	9.7799	-12.0953
10	8.1897	3.7356	1.629	5.5069	1.301	2.8534	1.3316	-0.265	3.2769	1.6755	-0.8542	0.7172	-1.4932	-0.3595	-0.3132	0.9935	-0.009	0.3435	0.7332	-0.0151	0.9551	38.432	25.9436	-5.9999
11	0.3736	-0.9839	-0.4013	2.9848	0.8216	0.0497	0.1811	-0.4802	0.016	0.6358	-0.2672	-0.1274	0.0464	0.3134	0.1593	0.9588	-0.3632	-0.214	0.8074	0.0578	0.7019	42.2864	19.54	25.8275
12	5.1901	5.6362	2.4432	7.9774	3.0832	1.7242	0.9321	-0.4768	-0.0598	0.6845	-0.5518	-0.6971	0.555	0.0624	-0.2924	0.9542	-0.3782	-0.1385	0.7475	0.0233	1.1914	51.79	31.2101	24.23
13	5.1682	1.9095	0.4487	1.498	-0.5761	0.9281	0.2223	-0.011	1.1285	0.1756	-0.1176	0.2062	-0.4131	0.1501	-0.0987	1.0481	-0.2845	0.0055	0.6056	-0.0631	0.6178	37.072	38.2578	19.259
14	3.1639	-0.6962	-1.0095	2.52	1.2604	1.965	0.0352	-0.051	0.046	0.2187	0.1165	-0.1393	-0.2076	0.1239	-0.1857	0.718	-0.1389	-0.0651	0.4031	0.0141	0.3535	21.3895	16.8908	15.9664
15	0.4702	0.2805	0.2967	0.1566	0.1889	0.2821	0.0077	-0.6749	-0.6437	0.6359	2.1051	-0.918	-0.2117	-0.6988	0.2068	1.8244	-0.1494	0.5018	1.4152	0.1072	1.5433	10.3512	-31.5283	29.2436
16	1.0125	1.0155	1.2904	3.5583	1.6959	1.7456	-0.5866	-1.3028	-0.9947	0.5398	-0.288	-0.2762	-0.0792	-0.7321	0.4893	2.1208	-0.6814	1.4501	1.1628	-0.0515	0.741	6.0294	-21.1754	27.4379
17	2.1785	-2.2559	-0.3637	8.5977	0.8431	8.2044	-0.3201	-0.177	-0.9671	1.2349	0.3997	1.6628	0.1424	-0.2677	0.0875	1.1045	-0.3374	0.162	0.7925	0.0163	1.0618	-1.4529	-28.635	18.9489
18	3.8965	3.8743	3.702	4.8569	5.0584	5.6114	0.1902	1.2356	0.0755	0.8375	0.1786	1.4129	-0.2358	-0.569	0.368	1.5131	-0.3339	0.2778	0.6552	0.0061	1.7232	-0.129	-26.5247	9.9665
19	1.9996	0.488	-1.5662	3.3662	-0.3236	2.2518	-0.2197	-0.0063	-0.5592	0.3195	0.0929	0.0379	0.4175	-0.0024	0.003	0.6535	-0.1147	-0.0658	0.4295	0.0696	0.541	23.3378	-13.9664	10.2697
20	2.5519	0.4374	-0.6036	3.3569	-0.3203	4.797	0.3285	-0.5522	-0.6309	0.3553	-0.8489	1.9555	-0.1295	-0.7848	0.1451	0.694	-0.1997	0.2427	0.651	-0.0802	1.1469	10.8893	-7.5021	7.8257
21	3.0992	-1.4353	-0.689	1.1816	-0.2129	6.2123	-0.7109	0.6077	-0.3369	-2.3799	1.1729	3.643	0.5808	-0.8492	-0.4595	0.903	-0.2408	-0.2442	0.7796	0.0784	1.3284	12.5338	-14.4197	-0.9227

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 127 through 156 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 157 through 190 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 191 through 264 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 265 through 304 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 305 through 353 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 354 through 443 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 10 through 82 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 83 through 214 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 215 through 382 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 383 through 406 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 127 through 191 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 192 through 223 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 224 through 279 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 280 through 441 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 10 through 23 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 24 through 41 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 42 through 82 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 83 through 181 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 182 through 322 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 323 through 378 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 379 through 406 )

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