PDB-5k4d: Structure of eukaryotic translation initiation factor 3 subunit D...

ID or keywords:

Entry

Database: PDB / ID: 5k4d

Title

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

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: 2 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	5k4d.cif.gz	307.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5k4d.ent.gz	250.3 KB	Display	PDB format
PDBx/mmJSON format	5k4d.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5k4d_validation.pdf.gz	423 KB	Display	wwPDB validaton report
Full document	5k4d_full_validation.pdf.gz	426.6 KB	Display
Data in XML	5k4d_validation.xml.gz	33.2 KB	Display
Data in CIF	5k4d_validation.cif.gz	50.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k4/5k4d ftp://data.pdbj.org/pub/pdb/validation_reports/k4/5k4d	HTTPS FTP

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Related structure data

Related structure data	5k4bC 5k4cC C: citing same article (ref.)
Similar structure data	3wcc-5 3wce-5 3wce-3 3wca-2 3wcg-4 3wcg-5 5k4c-d 3wce-4 2q0e-1 2q0g-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: Eukaryotic translation initiation factor 3 subunit D

B: Eukaryotic translation initiation factor 3 subunit D

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

1

A: Eukaryotic translation initiation factor 3 subunit D

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

2

B: Eukaryotic translation initiation factor 3 subunit D

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)	49.975, 144.325, 55.302
Angle α, β, γ (deg.)	90.00, 109.12, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 741 / Source method: isolated from a natural source / Formula: H₂O

#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: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 741 / 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: 2.23 Å³/Da / Density % sol: 44.9 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 200 mM NaCl, 100 mM Tris 8.5, 25% PEG-3350

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Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.11587 Å / Relative weight: 1
Reflection	Resolution: 2→49.132 Å / Num. obs: 49757 / % possible obs: 99.8 % / Redundancy: 3 % / R_merge(I) obs: 0.086 / Net I/σ(I): 6.5
Reflection shell	Resolution: 2→2.05 Å / Redundancy: 2.7 % / R_merge(I) obs: 0.523 / Mean I/σ(I) obs: 1.4 / % possible all: 98.3

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2→49.132 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.03

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.208	1999	4.02 %	Random selection
R_work	0.1773	-	-	-
obs	0.1785	49707	99.77 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2→49.132 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5686	0	0	741	6427

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	5794
X-RAY DIFFRACTION	f_angle_d	0.638	7848
X-RAY DIFFRACTION	f_dihedral_angle_d	9.989	3538
X-RAY DIFFRACTION	f_chiral_restr	0.047	874
X-RAY DIFFRACTION	f_plane_restr	0.004	1020

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 (%)
2-2.05	0.3222	139	0.271	3318	X-RAY DIFFRACTION	98
2.05-2.1054	0.2685	141	0.2363	3407	X-RAY DIFFRACTION	100
2.1054-2.1674	0.2525	143	0.2123	3392	X-RAY DIFFRACTION	100
2.1674-2.2374	0.2409	144	0.1969	3410	X-RAY DIFFRACTION	100
2.2374-2.3173	0.214	142	0.1999	3399	X-RAY DIFFRACTION	100
2.3173-2.4101	0.2458	143	0.1857	3431	X-RAY DIFFRACTION	100
2.4101-2.5198	0.2404	143	0.1911	3411	X-RAY DIFFRACTION	100
2.5198-2.6526	0.2118	143	0.1858	3402	X-RAY DIFFRACTION	100
2.6526-2.8188	0.2625	143	0.1796	3406	X-RAY DIFFRACTION	100
2.8188-3.0364	0.2312	143	0.1741	3420	X-RAY DIFFRACTION	100
3.0364-3.3419	0.1747	144	0.164	3430	X-RAY DIFFRACTION	100
3.3419-3.8253	0.1748	144	0.1522	3419	X-RAY DIFFRACTION	100
3.8253-4.8189	0.1518	142	0.1407	3418	X-RAY DIFFRACTION	100
4.8189-49.1464	0.1849	145	0.1746	3445	X-RAY DIFFRACTION	99

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	0.6529	-0.0114	-0.298	0.0802	-0.0645	0.2455	-0.115	-0.0629	-0.3541	-0.0314	0.0372	-0.2502	0.3147	0.4682	-0.1888	0.168	0.0698	-0.051	0.3295	0.0003	0.2148	34.2198	38.7174	-0.6033
2	0.2466	-0.147	-0.3472	0.477	-0.0578	0.9044	0.0353	0.0104	0.042	0.0728	-0.0013	0.0732	-0.0361	0.0205	0.0002	0.1024	-0.0011	-0.01	0.1215	-0.0081	0.1272	16.0892	55.3633	-3.2915
3	0.1397	-0.1758	-0.1591	0.2265	0.2256	0.2156	0.1587	-0.094	-0.0189	-0.0185	0.029	-0.1255	-0.2337	0.0019	0.2385	0.1601	-0.0287	-0.0222	0.1551	-0.0178	0.0879	27.0535	52.8799	-1.8317
4	0.3181	0.0004	-0.1729	0.6972	-0.1001	0.9885	0.0239	0.0138	0.0079	0.0151	0.0375	0.0322	0.0141	-0.0157	0.1902	0.0579	0.0112	-0.0041	0.0923	-0.0065	0.0789	17.4578	51.9808	-10.577
5	0.1822	0.0586	0.0018	0.1685	0.1486	0.4611	0.0518	-0.0364	0.0311	0.0258	-0.1625	0.0387	-0.1333	0.0144	-0.0869	0.181	0.0338	-0.0131	0.1308	-0.0457	0.1687	24.1857	29.268	-27.3287
6	0.3162	0.0341	-0.0478	0.8428	0.1921	0.2974	0.002	0.0228	-0.0535	0.0444	-0.1591	0.1393	-0.0276	-0.0917	-0.0527	0.128	0.0164	0.0125	0.1426	-0.0294	0.144	25.7361	13.6992	-31.1245
7	0.0466	-0.0132	-0.062	0.4624	0.0095	0.1685	-0.0229	-0.1317	0.2934	-0.2397	-0.2026	0.1795	-0.0486	-0.6452	-0.0501	0.2218	0.0032	-0.0866	0.3248	-0.1185	0.2686	13.9637	16.8695	-45.4814
8	0.0997	-0.1503	-0.0362	0.1658	0.0921	0.1923	0.01	-0.1523	-0.062	-0.0214	-0.1172	0.0617	0.3192	-0.1972	-0.0237	0.1411	0.0028	0.0151	0.1522	-0.0092	0.18	27.9367	4.0774	-40.1261
9	0.1642	-0.0879	0.0169	0.0707	-0.0393	0.0717	-0.1004	-0.116	-0.0165	0.3121	0.0831	-0.1085	0.0408	0.0595	-0.0064	0.2531	0.009	0.0264	0.1626	0.0082	0.1776	31.8638	9.1696	-23.7217
10	0.0636	0.0162	-0.0547	0.2367	-0.161	0.1415	0.008	-0.0414	0.0127	0.0208	-0.006	-0.0951	-0.0123	0.0664	-0	0.1316	0.005	0.0106	0.1308	-0.0167	0.1616	36.0268	14.7046	-32.0078
11	0.3745	-0.152	-0.0748	0.3235	0.2201	0.1456	0.1353	0.2977	0.5106	-0.5344	0.1561	0.1628	-0.3006	-0.2241	0.0381	0.3257	0.0293	0.0322	0.3434	0.111	0.2406	27.0682	15.149	-59.9543
12	0.4349	0.1043	0.356	0.0457	0.0665	0.3345	-0.0663	-0.0874	0.128	-0.0942	-0.0913	0.069	-0.1532	-0.1295	-0.0338	0.1628	0.0313	-0.0161	0.0737	-0.0166	0.1795	29.2722	20.6977	-44.2599
13	0.2264	0.189	-0.1327	0.3843	0.0988	0.3002	-0.0146	0.0463	0.0121	-0.1584	-0.0481	-0.0255	-0.1516	-0.0064	-0.0054	0.1707	0.016	0.0069	0.1345	-0.0135	0.1703	30.1402	19.2131	-40.8284
14	0.3132	0.4339	-0.0839	0.723	-0.1859	0.1264	0.2755	-0.0082	0.1148	0.1092	-0.1667	0.6116	-0.1529	-0.3269	0.0087	0.2095	0.1348	-0.0085	0.3887	-0.1446	0.5078	10.483	29.2828	-26.8728

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 172 through 192 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 193 through 283 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 284 through 303 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 304 through 536 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 178 through 209 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 210 through 290 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 291 through 319 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 320 through 347 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 348 through 374 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 375 through 408 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 409 through 426 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 427 through 452 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 453 through 509 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 510 through 534 )

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