PDB-8hgk: Crystal structure of human ClpP in complex with ZK53

ID or keywords:

Entry

Database: PDB / ID: 8hgk

Title

Crystal structure of human ClpP in complex with ZK53

Components

ATP-dependent Clp protease proteolytic subunit, mitochondrial

Keywords

HYDROLASE / activator / ZK53 / human ClpP

Function / homology

Function and homology information

membrane protein proteolysis / mitochondrial protein catabolic process / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / Mitochondrial protein degradation / : / peptidase activity / ATPase binding ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Yang, C.-G. / Gan, J.H. / Zhou, L.-L.

Funding support

China, 4items

Organization	Grant number	Country
National Natural Science Foundation of China (NSFC)	22037007	China
National Natural Science Foundation of China (NSFC)	21725801	China
National Natural Science Foundation of China (NSFC)	22107109	China
Ministry of Science and Technology (MoST, China)	2022YFC2804104	China

Citation

Journal: Nat Commun / Year: 2023
Title: Selective activator of human ClpP triggers cell cycle arrest to inhibit lung squamous cell carcinoma.
Authors: Zhou, L.L. / Zhang, T. / Xue, Y. / Yue, C. / Pan, Y. / Wang, P. / Yang, T. / Li, M. / Zhou, H. / Ding, K. / Gan, J. / Ji, H. / Yang, C.G.

History

Deposition	Nov 14, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 27, 2023	Provider: repository / Type: Initial release
Revision 1.1	Apr 17, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Others	Other downloads

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Validation report

Summary document	8hgk_validation.pdf.gz	3.9 MB	Display	wwPDB validaton report
Full document	8hgk_full_validation.pdf.gz	3.9 MB	Display
Data in XML	8hgk_validation.xml.gz	90.6 KB	Display
Data in CIF	8hgk_validation.cif.gz	117.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hg/8hgk ftp://data.pdbj.org/pub/pdb/validation_reports/hg/8hgk	HTTPS FTP

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Related structure data

Related structure data	1tg6S S: Starting model for refinement
Similar structure data	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: ATP-dependent Clp protease proteolytic subunit, mitochondrial

B: ATP-dependent Clp protease proteolytic subunit, mitochondrial

C: ATP-dependent Clp protease proteolytic subunit, mitochondrial

D: ATP-dependent Clp protease proteolytic subunit, mitochondrial

E: ATP-dependent Clp protease proteolytic subunit, mitochondrial

F: ATP-dependent Clp protease proteolytic subunit, mitochondrial

G: ATP-dependent Clp protease proteolytic subunit, mitochondrial

H: ATP-dependent Clp protease proteolytic subunit, mitochondrial

I: ATP-dependent Clp protease proteolytic subunit, mitochondrial

J: ATP-dependent Clp protease proteolytic subunit, mitochondrial

K: ATP-dependent Clp protease proteolytic subunit, mitochondrial

L: ATP-dependent Clp protease proteolytic subunit, mitochondrial

M: ATP-dependent Clp protease proteolytic subunit, mitochondrial

N: ATP-dependent Clp protease proteolytic subunit, mitochondrial

hetero molecules

346 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	120.310, 97.000, 123.840
Angle α, β, γ (deg.)	90.00, 93.98, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS ensembles :

#1: Protein	ATP-dependent Clp protease proteolytic subunit, mitochondrial / caseinolytic protease P / Endopeptidase Clp Mass: 24276.990 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLPP / Production host: Escherichia coli (E. coli) / References: UniProt: Q16740, endopeptidase Clp
#2: Chemical	ChemComp-ZLL / 4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide Mass: 424.282 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₁₉H₂₀BrF₂N₃O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.12 Å³/Da / Density % sol: 42.01 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.2M Magnesium acetate tetrahydrate, 20% w/v Polyethylene glycol 3350, pH7.9

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.9→20.53 Å / Num. obs: 223016 / % possible obs: 99.9 % / Redundancy: 6.9 % / R_merge(I) obs: 0.11 / Net I/σ(I): 10.4
Reflection shell	Resolution: 1.9→1.95 Å / Num. unique obs: 223016 / CC_1/2: 0.5

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Processing

Software

Name	Version	Classification
REFMAC	v5.0	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1TG6

1tg6

Resolution: 1.9→20.53 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.954 / SU B: 10.638 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22106	10975	4.9 %	RANDOM
R_work	0.18565	-	-	-
obs	0.1874	212014	99.84 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 33.321 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.25 Å²	-0 Å²	2.52 Å²
2-	-	0.64 Å²	-0 Å²
3-	-	-	-2.22 Å²

Refinement step

Cycle: 1 / Resolution: 1.9→20.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18933	0	369	478	19780

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	19727
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	18585
X-RAY DIFFRACTION	r_angle_refined_deg	1.329	2	26776
X-RAY DIFFRACTION	r_angle_other_deg	0.939	3	43069
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.861	5	2465
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.283	24.157	712
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.342	15	3339
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.187	15	96
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	3110
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	21368
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3556
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	3.201	3.073	9932
X-RAY DIFFRACTION	r_mcbond_other	3.201	3.072	9931
X-RAY DIFFRACTION	r_mcangle_it	3.957	4.577	12352
X-RAY DIFFRACTION	r_mcangle_other	3.957	4.577	12353
X-RAY DIFFRACTION	r_scbond_it	3.604	3.698	9795
X-RAY DIFFRACTION	r_scbond_other	3.601	3.697	9794
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.17	5.358	14418
X-RAY DIFFRACTION	r_long_range_B_refined	4.931	36.942	20739
X-RAY DIFFRACTION	r_long_range_B_other	4.908	36.852	20680
X-RAY DIFFRACTION	r_rigid_bond_restr	2.346	3	38312
X-RAY DIFFRACTION	r_sphericity_free	39.777	5	257
X-RAY DIFFRACTION	r_sphericity_bonded	11.527	5	38166

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	10954	0.02
1	2	B	10954	0.02
2	1	A	10918	0.06
2	2	C	10918	0.06
3	1	A	10920	0.06
3	2	D	10920	0.06
4	1	A	11164	0.05
4	2	E	11164	0.05
5	1	A	10922	0.07
5	2	F	10922	0.07
6	1	A	10972	0.05
6	2	G	10972	0.05
7	1	A	10732	0.05
7	2	H	10732	0.05
8	1	A	10896	0.07
8	2	I	10896	0.07
9	1	A	10856	0.05
9	2	J	10856	0.05
10	1	A	10928	0.06
10	2	K	10928	0.06
11	1	A	10962	0.05
11	2	L	10962	0.05
12	1	A	11026	0.05
12	2	M	11026	0.05
13	1	A	10954	0.06
13	2	N	10954	0.06
14	1	B	10874	0.06
14	2	C	10874	0.06
15	1	B	10856	0.05
15	2	D	10856	0.05
16	1	B	10888	0.04
16	2	E	10888	0.04
17	1	B	10830	0.06
17	2	F	10830	0.06
18	1	B	10862	0.05
18	2	G	10862	0.05
19	1	B	10732	0.06
19	2	H	10732	0.06
20	1	B	10784	0.07
20	2	I	10784	0.07
21	1	B	10794	0.04
21	2	J	10794	0.04
22	1	B	10852	0.06
22	2	K	10852	0.06
23	1	B	10864	0.05
23	2	L	10864	0.05
24	1	B	10802	0.05
24	2	M	10802	0.05
25	1	B	10894	0.05
25	2	N	10894	0.05
26	1	C	10822	0.05
26	2	D	10822	0.05
27	1	C	10884	0.05
27	2	E	10884	0.05
28	1	C	10850	0.06
28	2	F	10850	0.06
29	1	C	10888	0.05
29	2	G	10888	0.05
30	1	C	10818	0.06
30	2	H	10818	0.06
31	1	C	10886	0.05
31	2	I	10886	0.05
32	1	C	10778	0.05
32	2	J	10778	0.05
33	1	C	10792	0.05
33	2	K	10792	0.05
34	1	C	10806	0.07
34	2	L	10806	0.07
35	1	C	10870	0.04
35	2	M	10870	0.04
36	1	C	10838	0.06
36	2	N	10838	0.06
37	1	D	10888	0.05
37	2	E	10888	0.05
38	1	D	10850	0.06
38	2	F	10850	0.06
39	1	D	10904	0.05
39	2	G	10904	0.05
40	1	D	10716	0.06
40	2	H	10716	0.06
41	1	D	10822	0.07
41	2	I	10822	0.07
42	1	D	10752	0.05
42	2	J	10752	0.05
43	1	D	10892	0.05
43	2	K	10892	0.05
44	1	D	10870	0.08
44	2	L	10870	0.08
45	1	D	10804	0.04
45	2	M	10804	0.04
46	1	D	10830	0.06
46	2	N	10830	0.06
47	1	E	10974	0.06
47	2	F	10974	0.06
48	1	E	10948	0.06
48	2	G	10948	0.06
49	1	E	10726	0.06
49	2	H	10726	0.06
50	1	E	10970	0.06
50	2	I	10970	0.06
51	1	E	10846	0.05
51	2	J	10846	0.05
52	1	E	10952	0.05
52	2	K	10952	0.05
53	1	E	10964	0.06
53	2	L	10964	0.06
54	1	E	11086	0.05
54	2	M	11086	0.05
55	1	E	10994	0.04
55	2	N	10994	0.04
56	1	F	10896	0.06
56	2	G	10896	0.06
57	1	F	10800	0.06
57	2	H	10800	0.06
58	1	F	10904	0.06
58	2	I	10904	0.06
59	1	F	10818	0.06
59	2	J	10818	0.06
60	1	F	10962	0.06
60	2	K	10962	0.06
61	1	F	10872	0.07
61	2	L	10872	0.07
62	1	F	10858	0.05
62	2	M	10858	0.05
63	1	F	10906	0.07
63	2	N	10906	0.07
64	1	G	10750	0.06
64	2	H	10750	0.06
65	1	G	10868	0.06
65	2	I	10868	0.06
66	1	G	10802	0.04
66	2	J	10802	0.04
67	1	G	11006	0.05
67	2	K	11006	0.05
68	1	G	10930	0.07
68	2	L	10930	0.07
69	1	G	10888	0.05
69	2	M	10888	0.05
70	1	G	10944	0.06
70	2	N	10944	0.06
71	1	H	10768	0.07
71	2	I	10768	0.07
72	1	H	10736	0.06
72	2	J	10736	0.06
73	1	H	10704	0.06
73	2	K	10704	0.06
74	1	H	10664	0.07
74	2	L	10664	0.07
75	1	H	10744	0.05
75	2	M	10744	0.05
76	1	H	10656	0.06
76	2	N	10656	0.06
77	1	I	10742	0.06
77	2	J	10742	0.06
78	1	I	10830	0.06
78	2	K	10830	0.06
79	1	I	10776	0.07
79	2	L	10776	0.07
80	1	I	10906	0.06
80	2	M	10906	0.06
81	1	I	10846	0.06
81	2	N	10846	0.06
82	1	J	10754	0.05
82	2	K	10754	0.05
83	1	J	10712	0.06
83	2	L	10712	0.06
84	1	J	10678	0.04
84	2	M	10678	0.04
85	1	J	10684	0.06
85	2	N	10684	0.06
86	1	K	10886	0.07
86	2	L	10886	0.07
87	1	K	10850	0.05
87	2	M	10850	0.05
88	1	K	10964	0.05
88	2	N	10964	0.05
89	1	L	10862	0.07
89	2	M	10862	0.07
90	1	L	10910	0.06
90	2	N	10910	0.06
91	1	M	10864	0.06
91	2	N	10864	0.06

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.368	823	-
R_work	0.343	15499	-
obs	-	-	99.99 %

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	0.8563	-0.2673	-0.127	0.1153	-0.0529	0.5878	0.0522	-0.018	0.1481	-0.0103	0.0023	-0.0477	-0.107	0.1631	-0.0545	0.0911	-0.1065	-0.0423	0.1683	-0.0234	0.2165	378.9896	45.7176	520.116
2	0.4255	-0.1287	-0.1419	0.5889	-0.0005	0.3012	0.0197	-0.0546	-0.0072	0.01	0.0503	-0.1066	-0.0403	0.1357	-0.0701	0.0591	-0.0648	-0.0682	0.2254	-0.0334	0.1788	391.3083	23.5014	528.3851
3	0.1814	0.1295	-0.1055	0.4694	0.2434	0.6856	0.0166	-0.0358	-0.0951	-0.0101	0.0543	-0.0803	-0.0139	0.1666	-0.0709	0.0319	0.0208	-0.067	0.1834	-0.0011	0.2154	386.068	-1.9415	521.1099
4	0.861	-0.0009	-0.4838	0.1185	-0.0553	0.733	0.0118	0.0489	-0.1753	-0.0099	-0.0278	0.0088	0.0065	0.0665	0.016	0.0319	0.0258	-0.0628	0.0607	-0.0352	0.2055	367.3164	-11.1008	504.4048
5	0.6253	-0.0536	-0.1701	0.4417	-0.2035	0.167	0.0376	0.2043	-0.0483	0.0127	-0.0516	-0.0033	-0.0095	-0.0288	0.0139	0.0557	0.0055	-0.079	0.1312	-0.0299	0.1357	348.9366	2.8501	490.6066
6	0.4607	-0.027	-0.0843	0.319	0.231	0.2044	0.048	0.1146	0.0574	0.0146	-0.0658	-0.0427	-0.0095	-0.0166	0.0177	0.0505	0.0145	-0.0637	0.1361	0.0858	0.17	344.5909	29.4173	490.4163
7	0.8701	0.1008	-0.2151	0.3084	0.313	0.6304	0.1536	0.0916	0.1801	-0.0074	-0.0138	-0.0856	-0.1573	0.0326	-0.1398	0.0807	-0.0288	-0.0112	0.0547	0.0743	0.2604	358.2724	48.3226	503.413
8	0.8469	-0.0232	-0.3231	0.8006	-0.2394	0.4731	-0.007	-0.2794	0.0103	0.1	-0.0322	0.0039	-0.0726	0.1295	0.0392	0.0859	-0.0549	-0.0673	0.3043	-0.0222	0.0884	363.4055	25.3327	560.5055
9	0.7313	-0.0595	-0.1102	0.2212	-0.2173	0.3592	0.0084	-0.1914	0.1105	0.0323	0.0204	0.0135	-0.0643	0.0262	-0.0288	0.1056	-0.0602	-0.015	0.1413	-0.1038	0.1587	347.8269	44.7733	550.3213
10	0.5557	0.2093	0.0997	0.1213	-0.01	0.2947	0.044	-0.0758	0.1195	0.02	-0.0108	0.0657	-0.0573	-0.0035	-0.0332	0.0963	-0.0021	-0.0129	0.0271	-0.0355	0.1972	327.4148	42.6438	532.7991
11	0.3957	0.0055	-0.2217	0.3211	-0.0552	0.3508	0.0314	0.017	0.0096	0.0251	-0.0125	0.0326	-0.0223	-0.0486	-0.019	0.0605	-0.0028	-0.0638	0.0733	0.0099	0.1678	316.7587	20.4857	521.9779
12	0.2107	-0.1256	-0.155	0.3743	-0.0274	0.3811	-0.0081	0.0155	-0.1061	0.0636	-0.0118	0.0601	-0.0378	0.0193	0.0199	0.078	-0.0331	-0.0708	0.0555	0.0034	0.1753	324.3166	-5.1414	525.3928
13	0.8477	0.0304	-0.2255	0.1301	0.2108	0.5772	-0.0247	-0.0986	-0.1985	0.0297	-0.0205	-0.0328	0.0148	0.0061	0.0452	0.0815	0.0095	-0.0662	0.0603	0.0819	0.2079	343.8356	-14.5579	540.9927
14	1.037	0.2901	-0.3131	0.6132	0.3096	0.513	0.0462	-0.3169	-0.1429	0.0691	-0.0453	-0.0662	0.0118	0.0959	-0.0009	0.0752	0.0133	-0.0754	0.2554	0.1031	0.1392	361.2221	-1.2575	556.6046

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	57 - 249
2	X-RAY DIFFRACTION	2	B	58 - 249
3	X-RAY DIFFRACTION	3	C	58 - 249
4	X-RAY DIFFRACTION	4	D	58 - 249
5	X-RAY DIFFRACTION	5	E	58 - 249
6	X-RAY DIFFRACTION	6	F	58 - 249
7	X-RAY DIFFRACTION	7	G	58 - 249
8	X-RAY DIFFRACTION	8	H	58 - 249
9	X-RAY DIFFRACTION	9	I	58 - 249
10	X-RAY DIFFRACTION	10	J	57 - 249
11	X-RAY DIFFRACTION	11	K	58 - 249
12	X-RAY DIFFRACTION	12	L	58 - 249
13	X-RAY DIFFRACTION	13	M	58 - 249
14	X-RAY DIFFRACTION	14	N	58 - 249

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