PDB-5k4b: Structure of eukaryotic translation initiation factor 3 subunit D...

ID or keywords:

Entry

Database: PDB / ID: 5k4b

Title

Structure of eukaryotic translation initiation factor 3 subunit D (eIF3d) cap binding domain from Nasonia vitripennis, Crystal form 1

Components

Eukaryotic translation initiation factor 3 subunit D

Keywords

TRANSLATION / Eukaryotic translation initiation factor 3 / cap-binding domain

Function / homology

Function and homology information

cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / mRNA cap binding / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / translation initiation factor activity
Similarity search - Function

Biological species

Nasonia vitripennis (jewel wasp)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.399 Å

Authors

Kranzusch, P.J. / Lee, A.S.Y. / Doudna, J.A. / Cate, J.H.D.

Funding support

United States, 2items

Citation

Journal: Nature / Year: 2016
Title: eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation.
Authors: Lee, A.S. / Kranzusch, P.J. / Doudna, J.A. / Cate, J.H.

History

Deposition	May 20, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 27, 2016	Provider: repository / Type: Initial release
Revision 1.1	Aug 10, 2016	Group: Database references
Revision 1.2	Aug 17, 2016	Group: Database references
Revision 1.3	Sep 20, 2017	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Nov 20, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5k4b.cif.gz	317.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5k4b_validation.pdf.gz	435.1 KB	Display	wwPDB validaton report
Full document	5k4b_full_validation.pdf.gz	441.4 KB	Display
Data in XML	5k4b_validation.xml.gz	36.3 KB	Display
Data in CIF	5k4b_validation.cif.gz	56.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k4/5k4b ftp://data.pdbj.org/pub/pdb/validation_reports/k4/5k4b	HTTPS FTP

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Related structure data

Related structure data	5k4cC 5k4dC C: citing same article (ref.)
Similar structure data	3cex-2 5iqb-2 5c7q-d 3cex-1 1u5q-2 4x90-4 5b3t-1 2vut-6 5c8l-d 6cav-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) 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: Eukaryotic translation initiation factor 3 subunit D

B: Eukaryotic translation initiation factor 3 subunit D

hetero molecules

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

1

A: Eukaryotic translation initiation factor 3 subunit D

hetero molecules

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

2

B: Eukaryotic translation initiation factor 3 subunit D

hetero molecules

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

Unit cell

Length a, b, c (Å)	61.832, 62.909, 192.112
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Eukaryotic translation initiation factor 3 subunit D / eIF3d / Eukaryotic translation initiation factor 3 subunit 7 Mass: 42203.555 Da / Num. of mol.: 2 / Fragment: unp residues 172-537 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nasonia vitripennis (jewel wasp) / Gene: LOC100122367 / Production host: Escherichia coli (E. coli) / References: UniProt: K7IM66
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 910 / 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: 2.21 Å³/Da / Density % sol: 44.43 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 200 mM (NH4)2SO4, 100 mM Bis-Tris 6.5, 23-27% PEG-3350

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Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11586 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.11586 Å / Relative weight: 1
Reflection	Resolution: 1.399→48.06 Å / Num. obs: 148455 / % possible obs: 100 % / Redundancy: 15.8 % / R_merge(I) obs: 0.026 / Net I/σ(I): 12.9
Reflection shell	Resolution: 1.399→1.42 Å / Redundancy: 10.1 % / R_merge(I) obs: 0.453 / Mean I/σ(I) obs: 1.5 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.399→48.028 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.16

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1931	2359	1.59 %	Random selection
R_work	0.1745	-	-	-
obs	0.1748	148311	99.87 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.399→48.028 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5837	0	3	910	6750

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5949
X-RAY DIFFRACTION	f_angle_d	1.167	8062
X-RAY DIFFRACTION	f_dihedral_angle_d	12.414	2248
X-RAY DIFFRACTION	f_chiral_restr	0.05	896
X-RAY DIFFRACTION	f_plane_restr	0.006	1053

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 (%)
1.3987-1.4272	0.3088	134	0.3072	8301	X-RAY DIFFRACTION	98
1.4272-1.4582	0.3119	135	0.2608	8461	X-RAY DIFFRACTION	100
1.4582-1.4922	0.2253	148	0.2306	8538	X-RAY DIFFRACTION	100
1.4922-1.5295	0.2502	128	0.2082	8487	X-RAY DIFFRACTION	100
1.5295-1.5708	0.2194	138	0.1954	8522	X-RAY DIFFRACTION	100
1.5708-1.6171	0.215	140	0.188	8507	X-RAY DIFFRACTION	100
1.6171-1.6693	0.1975	136	0.1862	8566	X-RAY DIFFRACTION	100
1.6693-1.7289	0.2251	136	0.1882	8509	X-RAY DIFFRACTION	100
1.7289-1.7982	0.2032	140	0.1871	8570	X-RAY DIFFRACTION	100
1.7982-1.88	0.2016	141	0.1826	8551	X-RAY DIFFRACTION	100
1.88-1.9791	0.2188	139	0.175	8569	X-RAY DIFFRACTION	100
1.9791-2.1031	0.1735	136	0.1684	8600	X-RAY DIFFRACTION	100
2.1031-2.2655	0.19	139	0.1682	8617	X-RAY DIFFRACTION	100
2.2655-2.4935	0.2073	143	0.1707	8621	X-RAY DIFFRACTION	100
2.4935-2.8542	0.1795	139	0.1768	8694	X-RAY DIFFRACTION	100
2.8542-3.5959	0.1672	142	0.1634	8740	X-RAY DIFFRACTION	100
3.5959-48.0563	0.1726	145	0.1505	9099	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	1.1781	-0.127	0.1385	0.225	0.2562	0.5416	-0.0837	0.0834	0.1787	-0.0214	0.012	0.0464	-0.0041	0.0476	-0.0845	0.0854	-0.0108	-0.0124	0.0424	0.0434	0.1052	41.9965	32.0335	56.1115
2	0.664	0.2013	0.1864	0.5768	0.0697	0.3102	-0.0139	-0.0276	-0.0035	0.0249	0.0389	-0.0576	0.0629	0.0598	-0.0045	0.0968	0.0074	0.0073	0.0633	-0.0016	0.1029	50.8246	25.0464	57.5209
3	0.5312	-0.3958	-0.1451	0.3104	-0.0071	0.4942	0.0347	-0.2352	0.0272	0.1378	-0.054	-0.1195	-0.058	0.0619	-0.0038	0.1366	-0.0159	-0.0168	0.129	-0.0324	0.1409	39.432	37.7134	71.6956
4	0.6292	0.0101	0.5121	0.3188	0.1657	0.3668	0.0034	0.0629	-0.1072	-0.0481	-0.0244	0.0538	0.0835	-0.0111	-0.0034	0.1094	-0.0052	0.0111	0.0555	-0.0099	0.1102	38.6259	17.1405	53.7256
5	0.3636	-0.1686	0.2053	0.2342	-0.2284	0.1677	-0.1288	-0.0453	0.0737	0.0375	0.0742	0.1697	-0.0036	0.0479	0.0031	0.092	-0.003	-0.0069	0.0787	-0.0267	0.1379	30.6475	35.6918	62.5818
6	0.1361	0.0396	-0.2978	0.0466	-0.0994	0.8011	0.0973	0.1869	0.171	-0.0427	-0.054	-0.0581	-0.1923	-0.2961	0.0431	0.1464	0.0602	-0.0261	0.0983	-0.0534	0.2377	27.6523	46.503	62.9644
7	1.0752	0.0985	0.2775	0.1048	0.0478	0.1525	-0.0269	0.0269	0.1705	-0.0247	0.0023	0.0159	-0.0474	0.0119	-0.0819	0.1004	-0.0069	0.0045	0.048	0.0082	0.1107	38.1603	35.7472	55.8904
8	0.4105	-0.0214	0.383	0.2378	0.0269	0.4203	-0.0417	0.164	0.0941	0.2032	-0.0278	-0.0633	0.0169	0.3128	-0.0473	0.111	0.0024	0.0032	0.118	-0.0108	0.1653	63.5003	33.7177	58.8467
9	0.5897	-0.155	0.2115	0.1591	0.2612	0.4615	-0.0673	-0.1015	-0.0309	0.0563	0.0503	0.0268	0.0078	-0.0635	-0	0.2098	0.0085	0.0121	0.2156	-0.0095	0.1308	48.0672	16.0014	90.6325
10	0.824	-0.0997	0.2334	0.1155	0.039	0.4514	0.0085	0.0609	-0.0201	0.0149	-0.0139	0.0116	0.0704	0.0292	0	0.1332	0.0145	0.0137	0.1634	-0.0122	0.1215	53.1643	11.0627	76.5137
11	0.538	-0.3878	-0.0338	0.321	-0.1054	0.2927	0.0243	0.0546	0.071	-0.0367	-0.1002	-0.0235	-0.1481	0.1424	-0.0037	0.1515	-0.0009	0.006	0.1906	0.0066	0.0787	69.1858	18.1199	75.795
12	0.4395	0.1363	0.4754	0.292	0.0148	0.3279	0.0416	0.0182	-0.124	-0.0256	0.0282	0.0706	0.1651	-0.0239	0.0002	0.1863	0.0028	0.0119	0.1446	-0.0246	0.1536	48.6334	1.0159	71.7503
13	0.5648	-0.404	-0.0347	0.5685	0.046	0.7079	-0.0301	-0.1048	-0.0773	0.0326	-0.0069	-0.0194	0.0938	0.2023	0.0011	0.151	0.022	0.0015	0.1827	-0.0017	0.0906	66.0003	6.8001	82.8223
14	0.0239	-0.088	-0.0006	0.2874	-0.1554	0.1462	-0.1065	-0.1143	0.1439	0.0774	0.0177	-0.0202	-0.2118	-0.0887	-0.0008	0.1464	0.0329	-0.0177	0.2236	-0.035	0.1495	47.0678	27.3512	88.4986

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 172 through 229 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 230 through 300 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 301 through 337 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 338 through 387 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 388 through 418 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 419 through 437 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 438 through 510 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 511 through 537 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 173 through 209 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 210 through 300 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 301 through 337 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 338 through 398 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 399 through 510 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 511 through 537 )

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