PDB-5sv7: The Crystal structure of a chaperone

ID or keywords:

Entry

Database: PDB / ID: 5sv7

Title

The Crystal structure of a chaperone

Components

Eukaryotic translation initiation factor 2-alpha kinase 3

Keywords

TRANSLATION / chaperone

Function / homology

Function and homology information

regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of translation initiation in response to endoplasmic reticulum stress / chondrocyte development / response to manganese-induced endoplasmic reticulum stress / negative regulation of translation in response to stress / negative regulation of translational initiation in response to stress / PERK-mediated unfolded protein response / negative regulation of myelination / PERK regulates gene expression / mitochondria-associated endoplasmic reticulum membrane contact site ...regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of translation initiation in response to endoplasmic reticulum stress / chondrocyte development / response to manganese-induced endoplasmic reticulum stress / negative regulation of translation in response to stress / negative regulation of translational initiation in response to stress / PERK-mediated unfolded protein response / negative regulation of myelination / PERK regulates gene expression / mitochondria-associated endoplasmic reticulum membrane contact site / endocrine pancreas development / misfolded protein binding / ALK mutants bind TKIs / endoplasmic reticulum organization / Modulation of host responses by IFN-stimulated genes / regulation of translational initiation / ER overload response / cellular response to cold / bone mineralization / positive regulation of transcription by RNA polymerase I / positive regulation of vascular endothelial growth factor production / endoplasmic reticulum unfolded protein response / cellular response to glucose starvation / translation regulator activity / negative regulation of translational initiation / ossification / cellular response to amino acid starvation / insulin-like growth factor receptor signaling pathway / response to endoplasmic reticulum stress / skeletal system development / non-specific protein-tyrosine kinase / Hsp90 protein binding / eukaryotic translation initiation factor 2alpha kinase activity / calcium-mediated signaling / positive regulation of protein localization to nucleus / KEAP1-NFE2L2 pathway / Signaling by ALK fusions and activated point mutants / protein tyrosine kinase activity / angiogenesis / protein phosphatase binding / non-specific serine/threonine protein kinase / protein kinase activity / negative regulation of translation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of gene expression / endoplasmic reticulum membrane / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / ATP binding / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.209 Å

Authors

Wang, P. / Li, J. / Sha, B.

Funding support

United States, 1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2016
Title: The ER stress sensor PERK luminal domain functions as a molecular chaperone to interact with misfolded proteins.
Authors: Wang, P. / Li, J. / Sha, B.

History

Deposition	Aug 4, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 1, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Apr 13, 2022	Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.3	Oct 4, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5sv7.cif.gz	343.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5sv7.ent.gz	278.9 KB	Display	PDB format
PDBx/mmJSON format	5sv7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5sv7_validation.pdf.gz	467.8 KB	Display	wwPDB validaton report
Full document	5sv7_full_validation.pdf.gz	505.1 KB	Display
Data in XML	5sv7_validation.xml.gz	35.6 KB	Display
Data in CIF	5sv7_validation.cif.gz	48 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sv/5sv7 ftp://data.pdbj.org/pub/pdb/validation_reports/sv/5sv7	HTTPS FTP

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Related structure data

Related structure data	4yzsS S: Starting model for refinement
Similar structure data	4yzs-1 2r7o-d 2g2r-d 5lfk-1 5nj8-d 4zws-d 4rjw-1 5ak0-1 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	#32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: Eukaryotic translation initiation factor 2-alpha kinase 3

B: Eukaryotic translation initiation factor 2-alpha kinase 3

C: Eukaryotic translation initiation factor 2-alpha kinase 3

D: Eukaryotic translation initiation factor 2-alpha kinase 3

146 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)	163.913, 163.913, 63.076
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	145
Space group name H-M	P3₂

#1: Protein	Eukaryotic translation initiation factor 2-alpha kinase 3 / PRKR-like endoplasmic reticulum kinase / Pancreatic eIF2-alpha kinase / HsPEK Mass: 36524.777 Da / Num. of mol.: 4 / Fragment: UNP residues 95-420 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2AK3, PEK, PERK / Production host: Bacteria (eubacteria) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS References: UniProt: Q9NZJ5, non-specific serine/threonine protein kinase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.35 Å³/Da / Density % sol: 63.27 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: MES 0.1M, PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 5, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.2→37.851 Å / Num. obs: 30419 / % possible obs: 99 % / Redundancy: 9.4 % / Net I/σ(I): 40.4

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Processing

Software

Name	Version	Classification
PHENIX	1.10.1_2155	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4YZS

4yzs

Resolution: 3.209→37.851 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.08

	R_factor	Num. reflection	% reflection
R_free	0.3218	1572	5.17 %
R_work	0.2705	-	-
obs	0.2732	30419	98.03 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.209→37.851 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6573	0	0	29	6602

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	6688
X-RAY DIFFRACTION	f_angle_d	1.699	9029
X-RAY DIFFRACTION	f_dihedral_angle_d	15.025	3956
X-RAY DIFFRACTION	f_chiral_restr	0.085	1029
X-RAY DIFFRACTION	f_plane_restr	0.009	1113

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 (%)
3.2085-3.312	0.3369	132	0.255	2308	X-RAY DIFFRACTION	85
3.312-3.4303	0.292	158	0.2393	2627	X-RAY DIFFRACTION	100
3.4303-3.5676	0.2855	139	0.2196	2644	X-RAY DIFFRACTION	99
3.5676-3.7298	0.3088	136	0.2286	2704	X-RAY DIFFRACTION	100
3.7298-3.9263	0.291	150	0.2399	2657	X-RAY DIFFRACTION	100
3.9263-4.172	0.3316	148	0.2626	2661	X-RAY DIFFRACTION	100
4.172-4.4936	0.3399	175	0.2527	2655	X-RAY DIFFRACTION	100
4.4936-4.9449	0.2782	137	0.2665	2628	X-RAY DIFFRACTION	100
4.9449-5.6584	0.3503	143	0.3171	2695	X-RAY DIFFRACTION	100
5.6584-7.1213	0.3355	152	0.34	2664	X-RAY DIFFRACTION	100
7.1213-37.8536	0.3897	102	0.3321	2604	X-RAY DIFFRACTION	96

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	1.2933	-0.1329	-0.2334	1.5058	-0.4384	0.1851	-0.0013	-0.2948	-0.0105	0.0723	-0.0794	-0.2236	0.08	0.1016	0.0313	0.2197	-0.0385	-0.1153	0.4877	0.0916	0.3273	-5.4844	-40.6363	22.1937
2	0.8526	-0.0431	0.1281	1.1089	-0.2605	1.1053	0.0849	0.1449	-0.0977	-0.1515	0.0781	-0.1141	0.0251	0.1128	-0.035	0.3527	-0.2118	-0.0698	0.6101	0.0633	0.3727	-14.6424	-32.3783	-1.4894
3	0.5251	0.1846	0.4872	0.3689	0.3906	0.9039	0.0745	-0.089	-0.2036	0.0933	-0.0383	-0.2146	0.0851	-0.0425	-0.1141	0.2384	-0.1695	-0.1058	0.5989	0.0534	0.2457	-22.7299	-46.3583	10.2312
4	0.4375	0.0291	0.5162	0.4109	0.4516	1.4274	-0.0272	-0.0659	0.1081	-0.0595	0.0706	-0.1721	-0.0123	0.0703	-0.0448	0.1995	-0.2233	-0.0659	0.5154	0.0164	0.2969	-16.5081	-40.1136	5.4496
5	0.3749	0.2214	0.0838	0.3486	-0.2627	0.7179	0.0703	-0.0693	0.1696	0.0118	0.0858	0.0962	0.0219	-0.0219	-0.1056	0.2491	0.048	0.0035	0.5321	-0.0195	0.2515	-7.624	-32.0855	20.2868
6	2.2272	0.9053	0.1079	3.5129	1.4272	1.8901	-0.0246	-0.0565	-0.012	0.2271	0.0228	-0.2643	0.0506	0.0423	-0.0228	0.3459	-0.2662	-0.0403	0.4882	-0.0448	0.3609	-13.2152	-15.6071	9.4551
7	2.1255	1.2508	0.9704	2.6126	-0.3531	2.7325	-0.111	0.039	-0.118	0.0117	-0.0687	-0.2188	0.1367	0.2081	0.0205	0.2213	-0.1398	0.0026	0.4988	-0.065	0.2775	-9.4645	-32.3684	2.7113
8	1.0387	0.2177	0.5738	0.2941	0.0907	0.5266	0.0497	0.1375	-0.2407	-0.0146	0.1071	-0.1482	0.3287	0.2913	-0.1505	0.4035	-0.1671	-0.0579	0.3206	-0.0323	0.3828	-42.0693	-62.4415	-9.386
9	0.6976	0.12	0.1398	0.7674	0.076	1.0105	0.0332	0.1117	-0.122	0.0626	-0.0718	0.0247	-0.0074	0.0419	0.0752	0.2686	-0.1157	0.0113	0.3499	-0.0312	0.2224	-37.0761	-50.0435	4.3159
10	0.7974	0.213	-0.1268	0.2775	-0.0626	0.9362	-0.0253	-0.2104	-0.0755	0.0459	-0.0526	-0.014	0.042	0.0156	-0.1116	0.2359	-0.2602	0.0726	0.5689	-0.106	0.2681	-34.2364	-51.6823	6.1193
11	0.9379	0.0781	0.6963	0.7584	-0.1309	0.6553	0.0242	-0.1777	0.0121	0.0871	-0.0096	-0.0099	-0.0307	-0.113	-0.0682	0.2292	-0.1484	0.0047	0.3437	-0.1295	0.3348	-51.4065	-57.1155	-10.8426
12	0.9058	0.645	0.3051	0.8228	0.4445	0.4287	-0.0563	0.0757	0.0263	-0.1789	0.045	0.1326	0.0411	-0.0504	0.0088	0.2389	-0.1442	-0.1893	0.1713	0.0001	0.4045	-53.8529	-60.7326	-12.4525
13	0.4444	0.1399	-0.0705	0.6162	0.0839	0.4959	-0.0018	-0.038	0.0628	-0.0548	-0.0356	0.0896	-0.0158	-0.0912	0.0924	0.3655	-0.2732	0.0631	0.395	-0.1212	0.3209	-54.3497	-49.2374	-2.8119
14	0.6205	0.0538	0.1152	0.6331	0.1823	0.4282	0.0783	0.0264	0.1661	-0.0622	-0.0162	-0.1056	-0.088	-0.0264	-0.0134	0.245	-0.1919	0.0426	0.1744	0.0985	0.3488	-31.4144	-0.9755	-8.9205
15	1.2837	-0.6034	-0.0885	1.8696	-1.3552	1.7739	0.007	-0.1085	-0.023	0.1503	0.0189	-0.0325	-0.0787	0.0093	-0.0194	0.2663	-0.1059	-0.0475	0.4131	0.1857	0.1631	-25.8739	-14.5499	13.06
16	0.5655	-0.3766	-0.2947	0.3028	0.1128	0.2924	0.0327	-0.1391	-0.0133	0.146	-0.0943	-0.132	0.0032	0.1229	0.033	0.3675	-0.2063	-0.1779	0.3647	0.0731	0.356	-26.7479	-20.2351	15.3323
17	0.2834	0.2268	-0.1183	0.3398	0.0012	0.1578	-0.041	0.2263	0.1609	-0.3208	0.0764	0.0269	-0.1062	-0.0493	0.1168	0.007	-0.3416	0.0056	0.108	0.0513	0.0902	-43.3761	-9.5253	-4.6042
18	0.6637	-0.0816	-0.1299	0.5613	-0.0032	0.2556	0.0386	-0.0094	0.1694	-0.1536	-0.1049	-0.1052	-0.0013	0.019	-0.0393	0.1882	-0.1805	0.0616	0.2035	0.0153	0.05	-27.7239	-7.245	-4.0634
19	2.8756	-1.7274	-0.5719	2.3252	0.663	1.3642	0.1077	0.0294	0.0783	-0.0422	0.0047	-0.2877	-0.14	0.0976	-0.0544	0.2233	-0.12	-0.0575	0.264	-0.034	0.2972	-17.7617	-13.0363	3.1633
20	0.7003	-0.1809	-0.6013	0.6021	0.0889	1.1196	-0.0584	0.3568	-0.0248	-0.1928	-0.108	0.251	0.0502	-0.1813	0.0319	0.1167	0.0204	-0.0143	0.4644	-0.0353	0.1616	-58.731	-27.1642	5.2411
21	0.8475	0.0445	0.0602	0.6899	-0.1601	1.7358	-0.2205	-0.0441	0.2969	0.1121	-0.105	0.1008	-0.1661	-0.086	0.0268	0.0935	-0.0705	-0.0188	0.3159	-0.0599	0.2109	-52.2978	-16.1295	9.73
22	0.4467	-0.0543	0.2345	0.7742	0.4329	0.756	-0.0092	-0.2179	-0.2008	0.0095	-0.1266	0.2473	0.0648	-0.1831	0.1399	0.1795	-0.1198	0.0313	0.2952	-0.0149	0.1926	-63.2994	-35.1186	13.9646

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 104 through 128 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 129 through 173 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 174 through 236 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 237 through 318 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 319 through 376 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 377 through 386 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 387 through 400 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 104 through 140 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 141 through 235 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 236 through 268 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 269 through 317 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 318 through 344 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 345 through 400 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 104 through 140 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 141 through 164 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 165 through 192 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 193 through 248 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 249 through 374 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 375 through 401 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 104 through 192 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 193 through 268 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 269 through 400 )

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