PDB-4zem: Crystal structure of eIF2B beta from Chaetomium thermophilum

ID or keywords:

Entry

Database: PDB / ID: 4zem

Title

Crystal structure of eIF2B beta from Chaetomium thermophilum

Components

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

Keywords

TRANSLATION / eIF2B / eIF2 / guanine nucleotide exchange factor / GEF / regulatory subcomplex / regulatory subunit / translation initiation

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: 2.55 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	Apr 20, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Sep 30, 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	4zem.cif.gz	260.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4zem.ent.gz	212.6 KB	Display	PDB format
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Validation report

Summary document	4zem_validation.pdf.gz	444.4 KB	Display	wwPDB validaton report
Full document	4zem_full_validation.pdf.gz	457.1 KB	Display
Data in XML	4zem_validation.xml.gz	23.6 KB	Display
Data in CIF	4zem_validation.cif.gz	32.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ze/4zem ftp://data.pdbj.org/pub/pdb/validation_reports/ze/4zem	HTTPS FTP

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Related structure data

Related structure data	4zeoC 5dboC 2yvkS 3ecsS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6x11-1 6vib-1 1yfu-1 4hsj-1 4l2n-2 3r84-18 6d62-1 6xb9-4 7kov-1 5d08-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

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

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

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

1

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

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

2

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

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

Unit cell

Length a, b, c (Å)	138.000, 138.000, 146.640
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

#1: Protein	Translation initiation factor eIF2b-like protein,Translation initiation factor eIF2b-like protein Mass: 42643.758 Da / Num. of mol.: 2 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) / References: UniProt: G0SEE6
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

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

Mass: 42643.758 Da / Num. of mol.: 2
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) / References: UniProt: G0SEE6

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.15 Å³/Da / Density % sol: 60.96 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 100 mM HEPES, 1.33 M tri-sodium citrate

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

BESSY

/ Beamline: 14.1 / Wavelength: 0.91841 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 12, 2012

Radiation

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

Radiation wavelength

Wavelength: 0.91841 Å / Relative weight: 1

Reflection

Resolution: 2.54→50 Å / Num. obs: 34537 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / B_iso Wilson estimate: 52.75 Å² / R_merge F obs: 0.999 / R_merge(I) obs: 0.05 / R_rim(I) all: 0.058 / Χ²: 0.963 / Net I/σ(I): 23.71 / Num. measured all: 134799

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2.54-2.63		0.764	0.584	2.62	14846	3804	3801	0.677	99.9
2.63-2.73		0.83	0.451	3.41	12719	3267	3265	0.524	99.9
2.73-2.93		0.928	0.288	5.3	20516	5257	5252	0.334	99.9
2.93-3.62		0.993	0.091	15.53	40438	10328	10320	0.106	99.9
3.62-3.95		0.998	0.035	35.64	11028	2815	2813	0.041	99.9
3.95-4.3		0.999	0.027	43.82	7780	1994	1993	0.031	99.9
4.3-4.64		0.999	0.021	53.17	5674	1453	1453	0.024	100
4.64-14		1	0.017	60.28	21151	5451	5448	0.02	99.9
14-17		1	0.01	94.59	329	90	90	0.012	100
17-50		0.999	0.014	76.38	318	111	102	0.017	91.9
	50					4

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.55 Å	46.32 Å
Translation	2.55 Å	46.32 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XSCALE		data scaling
PHASER	2.3.0	phasing
PDB_EXTRACT	3.15	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: The N-terminal domain (res. 34-134) of chain A in PDB entry 2YVK and the C-terminal domain (res. 107-305) of chain B in entry 3ECS were used.

2yvk

3ecs

Resolution: 2.55→38.458 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.19 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2038	1695	5 %
R_work	0.1757	-	-
obs	0.1771	33908	99.89 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.55→38.458 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4827	0	0	60	4887

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4941
X-RAY DIFFRACTION	f_angle_d	1.154	6701
X-RAY DIFFRACTION	f_dihedral_angle_d	14.415	1819
X-RAY DIFFRACTION	f_chiral_restr	0.05	777
X-RAY DIFFRACTION	f_plane_restr	0.005	866

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 (%)
2.5501-2.6251	0.3415	141	0.2949	2690	X-RAY DIFFRACTION	100
2.6251-2.7098	0.2895	142	0.2635	2688	X-RAY DIFFRACTION	100
2.7098-2.8067	0.2811	141	0.2422	2685	X-RAY DIFFRACTION	100
2.8067-2.919	0.2797	142	0.2351	2703	X-RAY DIFFRACTION	100
2.919-3.0518	0.2494	140	0.2128	2657	X-RAY DIFFRACTION	100
3.0518-3.2126	0.258	142	0.2047	2694	X-RAY DIFFRACTION	100
3.2126-3.4138	0.2308	141	0.1867	2686	X-RAY DIFFRACTION	100
3.4138-3.6772	0.2127	141	0.1749	2667	X-RAY DIFFRACTION	100
3.6772-4.0468	0.179	142	0.1562	2709	X-RAY DIFFRACTION	100
4.0468-4.6316	0.1602	141	0.1404	2674	X-RAY DIFFRACTION	100
4.6316-5.832	0.1787	141	0.1552	2690	X-RAY DIFFRACTION	100
5.832-38.4627	0.1628	141	0.1508	2670	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	4.1364	-0.5652	-0.3	5.8115	1.2935	6.0352	0.1294	-0.7533	-0.1794	0.7645	-0.174	0.2704	0.2066	-0.111	0.0419	0.5885	-0.2292	-0.067	0.75	-0.0296	0.3785	28.6508	7.209	-16.156
2	3.1958	1.5321	1.887	6.9537	0.473	1.8022	-0.8613	0.7191	-0.1592	-0.9834	0.0992	0.937	-0.3897	-0.93	0.5075	0.589	0.0131	-0.2869	0.564	-0.0644	0.804	32.8601	35.687	-12.9501
3	3.2866	2.3389	1.5729	4.1587	2.1082	2.9447	0.149	0.0736	-0.1736	0.2207	-0.1603	-0.0638	0.121	0.1098	0.0242	0.2697	-0.0011	0.0193	0.4271	0.0128	0.2907	22.865	-5.2787	-39.7128
4	4.0549	-0.1855	-2.2009	7.3121	2.973	4.1195	-0.0386	-0.3519	-0.7414	1.4048	-0.0128	-0.9649	0.6939	0.8647	0.0806	0.5366	0.0389	-0.2066	0.6793	0.0518	0.6477	37.414	-5.5754	-32.9614
5	3.3289	0.9639	0.6449	2.684	0.9432	5.4633	0.0985	-0.129	0.0732	0.2766	0.0247	-0.4502	-0.2657	0.8327	-0.1491	0.3592	-0.0806	-0.0044	0.5644	-0.0206	0.4276	36.7556	6.3101	-35.6619
6	6.4076	1.4273	-0.0753	4.858	-1.3009	4.5715	-0.599	1.1526	1.3269	-0.3746	0.3918	-0.9413	-0.8343	1.0944	0.2628	1.0095	-0.1172	0.2122	1.0708	0.4134	1.6667	38.0261	39.434	-62.2442
7	5.6454	0.6298	-0.2063	4.4451	-0.4948	6.3515	-0.0114	-0.2813	1.9918	0.0056	-0.0262	-0.7665	-1.2181	0.695	0.138	0.7414	-0.1719	-0.0598	0.5904	0.0119	1.6489	30.8072	39.833	-50.9134
8	3.6222	-1.2106	-0.7126	6.5897	0.1765	2.9239	-0.171	-0.333	1.2039	0.6303	0.2435	-1.1947	-0.4475	0.5726	-0.0552	0.4191	-0.0602	-0.0851	0.6199	-0.0381	0.8721	32.2967	27.0046	-48.4953
9	6.476	-0.8009	-1.4599	5.4706	2.7925	4.4022	0.248	1.0344	0.3005	-0.7333	-0.2139	-0.2158	-0.0991	0.099	-0.0125	0.6049	0.1482	0.1587	0.7295	0.0469	0.4751	34.1874	5.0392	-68.2331
10	5.4076	-2.1473	-0.9535	6.1592	1.7292	4.7218	0.1465	0.9144	-0.1668	-0.5915	-0.3255	0.1508	-0.1237	-0.2832	0.1501	0.3078	0.0563	0.0113	0.5285	0.031	0.3571	19.094	14.22	-58.9092

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 10 through 104 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 105 through 179 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 180 through 330 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 331 through 382 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 383 through 417 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 10 through 41 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 42 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 279 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 280 through 419 )

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