PDB-4jne: Allosteric opening of the polypeptide-binding site when an Hsp70 ...

ID or keywords:

Entry

Database: PDB / ID: 4jne

Title

Allosteric opening of the polypeptide-binding site when an Hsp70 binds ATP

Components

Hsp70 CHAPERONE DnaK

Keywords

CHAPERONE /

DnaK / 70kDa heat shock protein (Hsp70) / ATP-binding / Nucleotide binding domain (NBD) / substructure binding domain (SBD) / allosteric coupling

Function / homology

Function and homology information

stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein /

inclusion body / protein folding chaperone /

heat shock protein binding /

ADP binding / ATP-dependent protein folding chaperone ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.96 Å

Authors

Qi, R. / Sarbeng, E.B. / Liu, Q. / Le, K.Q. / Xu, X. / Xu, H. / Yang, J. / Wong, J.L. / Vorvis, C. / Hendrickson, W.A. ...

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Allosteric opening of the polypeptide-binding site when an Hsp70 binds ATP.
Authors: Qi, R. / Sarbeng, E.B. / Liu, Q. / Le, K.Q. / Xu, X. / Xu, H. / Yang, J. / Wong, J.L. / Vorvis, C. / Hendrickson, W.A. / Zhou, L. / Liu, Q.

History

Deposition	Mar 15, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 29, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jul 10, 2013	Group: Database references
Revision 1.2	Aug 7, 2013	Group: Database references
Revision 1.3	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.4	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4jne.cif.gz	496.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4jne.ent.gz	408 KB	Display	PDB format
PDBx/mmJSON format	4jne.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jn/4jne ftp://data.pdbj.org/pub/pdb/validation_reports/jn/4jne	HTTPS FTP

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Related structure data

Related structure data	4jn4C 4jnfC C: citing same article (ref.)
Similar structure data	4jn4-d 1xo0-d 1pvp-d 1pvr-d 6j5a-d 1pvq-d 5eqj-1 3tvw-2 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 (11)

Deposited unit

A: Hsp70 CHAPERONE DnaK

B: Hsp70 CHAPERONE DnaK

hetero molecules

134 kDa, 2 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)	290.678, 290.678, 99.317
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	97
Space group name H-M	I422

Components on special symmetry positions

ID	Model	Components
1	1	A-1338- HOH
2	1	A-1385- HOH
3	1	A-1733- HOH
4	1	B-1302- HOH
5	1	B-1367- HOH
6	1	B-1515- HOH
7	1	B-1685- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	Hsp70 CHAPERONE DnaK Mass: 65893.344 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-610 / Mutation: N432M,Q433G,S434G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pSMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6Y8

#1: Protein

Hsp70 CHAPERONE DnaK

Mass: 65893.344 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-610 / Mutation: N432M,Q433G,S434G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: K12 / Plasmid: pSMT / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6Y8

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Non-polymers , 5 types, 1416 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1397 / 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: 3.98 Å³/Da / Density % sol: 69.09 %
Crystal grow	Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.8-2.0 M ammonium sulfate, 0.1 M Hepes-NaOH, 2-3% PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97915 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 16, 2011
Radiation	Monochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97915 Å / Relative weight: 1
Reflection	Resolution: 1.96→40 Å / Num. all: 150467 / Num. obs: 150467 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 1.96→2.01 Å / % possible all: 97.4

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Processing

Software

Name	Version	Classification
MAR345		data collection
MOLREP		phasing
PHENIX	(phenix.refine: 1.7_650)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.96→29.966 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 17.61 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2007	7542	5.01 %	Random
R_work	0.1728	-	-	-
obs	0.1742	150429	99.78 %	-
all	-	150429	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 46.38 Å² / k_sol: 0.37 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.6767 Å²	-0 Å²	0 Å²
2-	-	2.6767 Å²	0 Å²
3-	-	-	-5.3534 Å²

Refinement step

Cycle: LAST / Resolution: 1.96→29.966 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9100	0	143	1397	10640

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	9338
X-RAY DIFFRACTION	f_angle_d	0.916	12630
X-RAY DIFFRACTION	f_dihedral_angle_d	13.944	3548
X-RAY DIFFRACTION	f_chiral_restr	0.057	1466
X-RAY DIFFRACTION	f_plane_restr	0.004	1652

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 (%)
1.96-1.9813	0.2532	229	0.2355	4427	X-RAY DIFFRACTION	94
1.9813-2.0046	0.2555	233	0.2295	4741	X-RAY DIFFRACTION	100
2.0046-2.0291	0.2538	242	0.2152	4759	X-RAY DIFFRACTION	100
2.0291-2.0547	0.2336	277	0.2094	4686	X-RAY DIFFRACTION	100
2.0547-2.0818	0.2577	267	0.2045	4718	X-RAY DIFFRACTION	100
2.0818-2.1103	0.2259	233	0.1944	4760	X-RAY DIFFRACTION	100
2.1103-2.1404	0.1963	245	0.1815	4708	X-RAY DIFFRACTION	100
2.1404-2.1724	0.2154	272	0.1808	4724	X-RAY DIFFRACTION	100
2.1724-2.2063	0.2034	253	0.1768	4757	X-RAY DIFFRACTION	100
2.2063-2.2425	0.2287	231	0.1767	4733	X-RAY DIFFRACTION	100
2.2425-2.2811	0.2116	236	0.1747	4732	X-RAY DIFFRACTION	100
2.2811-2.3226	0.2098	256	0.1803	4764	X-RAY DIFFRACTION	100
2.3226-2.3672	0.2153	228	0.1783	4759	X-RAY DIFFRACTION	100
2.3672-2.4155	0.2148	266	0.1787	4727	X-RAY DIFFRACTION	100
2.4155-2.468	0.2121	269	0.1716	4701	X-RAY DIFFRACTION	100
2.468-2.5254	0.1911	262	0.1754	4761	X-RAY DIFFRACTION	100
2.5254-2.5885	0.2335	255	0.17	4758	X-RAY DIFFRACTION	100
2.5885-2.6585	0.206	229	0.1773	4756	X-RAY DIFFRACTION	100
2.6585-2.7367	0.2192	256	0.1735	4763	X-RAY DIFFRACTION	100
2.7367-2.8249	0.2003	251	0.1748	4796	X-RAY DIFFRACTION	100
2.8249-2.9258	0.2062	242	0.1796	4776	X-RAY DIFFRACTION	100
2.9258-3.0428	0.216	233	0.1741	4776	X-RAY DIFFRACTION	100
3.0428-3.1812	0.2003	260	0.1811	4779	X-RAY DIFFRACTION	100
3.1812-3.3487	0.2117	270	0.181	4779	X-RAY DIFFRACTION	100
3.3487-3.5582	0.1886	265	0.1702	4797	X-RAY DIFFRACTION	100
3.5582-3.8324	0.1759	261	0.1538	4805	X-RAY DIFFRACTION	100
3.8324-4.2171	0.1647	246	0.1413	4834	X-RAY DIFFRACTION	100
4.2171-4.8252	0.1521	260	0.1359	4841	X-RAY DIFFRACTION	100
4.8252-6.0709	0.1972	261	0.1651	4906	X-RAY DIFFRACTION	100
6.0709-29.9697	0.2019	254	0.191	5064	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	0.1976	-0.0296	-0.1235	0.3509	-0.1315	0.2152	-0.0728	0.1608	0.0087	-0.0681	-0.0228	-0.0971	0.0409	-0.0442	0.0471	0.1293	0.0036	-0.0011	0.1299	0.0036	0.1411	19.2775	72.2392	15.7921
2	0.1979	-0.1898	-0.063	0.3381	0.0583	0.1399	-0.0304	-0.0418	0.2703	0.0232	0.0242	-0.2653	-0.1108	-0.0029	0.0079	0.1352	0.0353	-0.0651	0.1451	-0.0115	0.256	11.5787	90.6004	21.6951
3	0.2188	-0.0668	-0.0494	0.182	-0.1232	0.3471	-0.089	0.1369	0.0284	-0.0404	0.0558	0.0138	0.0603	-0.0445	0.0051	0.1085	-0.0159	-0.0154	0.1642	0.0003	0.1214	8.9235	72.8001	16.3369
4	0.0016	0.001	-0.0028	0.0013	-0.001	0.0065	0.0052	0.0015	-0.0005	-0.0062	-0.0122	-0.0256	0.0213	0.0002	0.0023	0.5282	0.0706	0.0568	0.3299	0.0978	0.3622	11.2845	50.9867	34.4008
5	0.5759	0.1266	-0.0737	0.3384	-0.2716	0.2189	-0.1429	-0.1155	-0.0706	0.0329	0.0029	-0.0173	0.0518	-0.012	0.0974	0.1832	0.0201	0.0374	0.1659	0.0116	0.1193	6.5044	62.612	34.4405
6	0.2599	0.1515	0.0986	0.2742	0.3173	0.5016	-0.1228	-0.1509	0.0653	0.0702	0.0626	-0.0134	0.0837	-0.0956	0.0441	0.1357	0.0579	-0.0188	0.1434	-0.0311	0.1477	11.8807	78.7383	35.271
7	0.964	0.1959	-0.3167	0.3328	0.1566	0.5415	0.1068	0.0047	0.1093	0.0409	0.0091	0.003	-0.0227	0.112	-0.111	0.2574	0.0425	-0.024	0.2746	-0.1488	0.3916	26.6859	101.9181	38.5911
8	0.4374	0.0833	-0.1313	0.0897	0.0034	0.0888	0.0173	-0.0233	0.2813	0.1619	0.2248	-0.169	0.1047	0.1023	-0.0083	0.0915	0.057	-0.121	0.1839	-0.1341	0.253	28.0271	90.1741	36.5937
9	0.4694	-0.0603	0.0227	0.0893	-0.0107	0.279	-0.1314	-0.1624	-0.0641	0.1382	0.0719	0.0242	0.1343	-0.0378	0.0472	0.1836	0.0483	0.0159	0.1509	-0.0074	0.1084	8.0604	66.4768	35.6083
10	0.0725	-0.0399	0.0252	0.1853	-0.0452	0.1001	-0.1131	-0.0229	0.0546	-0.0224	0.0703	0.0682	0.0029	-0.1368	0.0371	0.1038	-0.0286	-0.0192	0.2587	-0.0124	0.1683	-18.2388	76.8828	22.9622
11	0.4631	-0.0134	-0.064	0.1139	0.1152	0.1286	0.0218	0.1689	-0.0349	-0.1402	-0.0162	-0.0001	-0.1249	0.1551	0.0031	0.203	-0.0342	-0.05	0.3119	0.0281	0.1669	5.1325	83.1025	4.5987
12	0.04	0.052	0.1077	0.8804	0.2292	0.299	0.1074	-0.0281	-0.0271	0.0343	0.1431	-0.1536	-0.006	-0.3272	-0.1473	0.1872	-0.02	-0.0306	0.2983	0.0669	0.1705	39.93	81.3229	-5.192
13	0.1183	-0.2739	-0.1521	0.7052	0.4165	0.6219	0.2969	0.0168	0.1909	-0.0948	-0.0347	-0.4763	-0.2265	-0.0406	-0.2517	0.3433	-0.0442	0.0045	0.212	0.0729	0.3765	45.7491	88.997	-11.1965
14	0.1436	-0.1201	0.0701	0.1601	-0.1414	0.157	0.1815	0.0062	0.0738	-0.1169	0.0446	-0.4335	-0.1373	-0.0054	-0.2087	0.5411	-0.0148	0.0704	0.3342	-0.0666	0.5875	51.9524	80.3933	-23.5057
15	0.1439	-0.084	0.0008	0.0583	-0.0272	0.303	-0.1391	-0.0898	0.0181	0.1401	0.0015	-0.0138	-0.1959	-0.053	0.0479	0.1702	0.0017	-0.0193	0.0792	-0.012	0.1286	36.9707	64.2669	33.6202
16	0.0043	0.0054	-0.0047	0.0186	-0.0191	0.0209	-0.1343	0.106	0.0588	0.1117	-0.0722	-0.0483	-0.4534	0.1837	0.0159	0.1055	-0.2747	-0.2205	-0.0259	-0.0305	0.1174	55.1436	72.3914	28.3814
17	0.2227	-0.0417	-0.004	0.1085	-0.0757	0.1676	-0.0984	-0.0049	-0.0211	0.1057	0.0274	-0.0351	-0.1203	-0.0191	-0.0048	0.1159	0.0052	-0.0164	0.0829	0.0051	0.092	44.8863	57.4005	33.325
18	0.0135	0.0121	0.0011	0.0133	0.0064	0.0118	-0.0045	0.0027	0.0055	0.0006	-0.0005	0.0024	0.0017	0.0055	0.0026	0.3212	-0.19	-0.0407	0.4637	-0.1663	0.3456	26.7022	45.3439	18.8051
19	0.6566	0.1813	0.3358	0.0517	0.0791	0.2202	-0.0051	0.0865	-0.0864	0.0535	-0.0155	-0.0336	0.0637	-0.0158	0.0199	0.125	-0.0404	-0.0004	0.1156	-0.0086	0.1349	40.1653	51.3601	13.6821
20	0.7428	0.8396	-0.2564	1.3626	-0.8455	1.4061	0.0471	0.0023	-0.4599	0.0325	-0.0283	0.002	0.3572	-0.0814	-0.0288	0.5704	-0.2139	0.0665	0.3354	-0.0684	0.4518	31.9824	34.9602	20.7083
21	0.1103	-0.0927	0.0211	0.1073	0.0631	0.1048	-0.0681	0.1039	0.0043	-0.0001	-0.0161	0.0382	-0.0494	0.124	-0.0026	0.1358	-0.0609	-0.0623	0.1252	0.0679	0.1	48.5952	69.1498	12.8605
22	0.0326	0.0286	0.0273	0.0973	0.0187	-0.0081	-0.1458	0.002	0.0464	0.19	-0.1865	-0.0258	-0.3205	0.1336	0.0159	0.2903	-0.4237	-0.1572	-0.7164	0.0955	0.1465	44.8629	87.7591	15.0624
23	0.1248	0.0166	0.0348	0.0838	0.0135	0.0945	-0.0409	0.0489	-0.027	0.0127	-0.0197	0.016	-0.0325	0.0154	-0.0038	0.1038	-0.0189	-0.0062	0.0955	-0.002	0.1157	39.7592	59.2798	9.151
24	0.5626	-0.1898	0.1339	0.2486	0.0634	0.1318	0.0003	0.1318	0.0204	0.0082	-0.0075	0.0025	0.1588	0.0643	-0.0179	0.1375	0.031	-0.0103	0.1494	0.0303	0.1461	63.3003	41.316	26.0871
25	0.2471	0.0976	0.0745	0.1413	-0.1355	0.2915	0.0015	-0.0761	-0.0221	0.077	-0.0711	-0.0013	-0.3165	0.0111	0.0508	0.2715	-0.0139	-0.0693	0.188	0.0388	0.1818	57.3016	60.7801	42.6981
26	0.1327	0.2325	-0.0819	0.7161	-0.3412	0.1865	0.1403	0.0783	0.018	0.1001	0.0777	0.0992	0.1194	0.1911	-0.0945	0.4196	0.1854	-0.1266	0.3086	-0.07	0.1837	29.5119	86.0686	54.4906
27	0.5252	0.5852	-0.1224	0.734	-0.0795	1.0954	0.2188	-0.127	0.284	-0.0978	0.0113	0.1955	-0.2389	0.1961	-0.2139	0.3539	-0.0993	0.0223	0.2794	-0.0838	0.3532	30.8028	95.753	60.2969
28	0.4122	-0.0024	-0.2009	0.1351	0.24	0.5215	0.2717	-0.0201	0.1034	-0.1011	-0.0673	0.3352	-0.1166	0.0091	-0.1921	0.7128	-0.0808	0.283	0.7029	-0.0269	0.8886	20.585	93.5168	72.4597

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:51)
2	X-RAY DIFFRACTION	2	(chain A and resid 52:105)
3	X-RAY DIFFRACTION	3	(chain A and resid 106:181)
4	X-RAY DIFFRACTION	4	(chain A and resid 182:188)
5	X-RAY DIFFRACTION	5	(chain A and resid 189:213)
6	X-RAY DIFFRACTION	6	(chain A and resid 214:241)
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8	X-RAY DIFFRACTION	8	(chain A and resid 254:315)
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10	X-RAY DIFFRACTION	10	(chain A and resid 405:505)
11	X-RAY DIFFRACTION	11	(chain A and resid 506:525)
12	X-RAY DIFFRACTION	12	(chain A and resid 526:554)
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17	X-RAY DIFFRACTION	17	(chain B and resid 108:180)
18	X-RAY DIFFRACTION	18	(chain B and resid 181:186)
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20	X-RAY DIFFRACTION	20	(chain B and resid 209:214)
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27	X-RAY DIFFRACTION	27	(chain B and resid 555:595)
28	X-RAY DIFFRACTION	28	(chain B and resid 596:604)

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