PDB-4ouh: Crystal structure of the FP domain of Human PI31 Proteasome Inhibitor

ID or keywords:

Entry

Database: PDB / ID: 4ouh

Title

Crystal structure of the FP domain of Human PI31 Proteasome Inhibitor

Components

Proteasome inhibitor PI31 subunit

Keywords

PROTEIN BINDING / C-terminal extention alpha Helix / Proteasome Inhibitor

Function / homology

Function and homology information

negative regulation of proteasomal protein catabolic process / Proteasome assembly / proteasome core complex / endopeptidase inhibitor activity / proteasome binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein heterodimerization activity / perinuclear region of cytoplasm / endoplasmic reticulum ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Shang, J. / Huang, X. / Du, Z.

Citation

Journal: J.Biomol.Struct.Dyn. / Year: 2015
Title: The FP domains of PI31 and Fbxo7 have the same protein fold but very different modes of protein-protein interaction.
Authors: Shang, J. / Huang, X. / Du, Z.

History

Deposition	Feb 17, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 25, 2015	Provider: repository / Type: Initial release
Revision 1.1	Mar 4, 2015	Group: Database references
Revision 1.2	Mar 18, 2015	Group: Database references
Revision 1.3	Apr 1, 2015	Group: Database references
Revision 1.4	Apr 8, 2015	Group: Database references
Revision 1.5	Apr 22, 2015	Group: Database references
Revision 1.6	Apr 29, 2015	Group: Database references
Revision 1.7	May 20, 2015	Group: Database references
Revision 1.8	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ouh.cif.gz	244.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4ouh.ent.gz	200.2 KB	Display	PDB format
PDBx/mmJSON format	4ouh.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/ou/4ouh ftp://data.pdbj.org/pub/pdb/validation_reports/ou/4ouh	HTTPS FTP

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Related structure data

Similar structure data	5nwz-d 6hze-1 2nwb-d 1o0w-d 5yym-1 3hv5-d 5iuu-d 5mi4-d 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: Proteasome inhibitor PI31 subunit

B: Proteasome inhibitor PI31 subunit

C: Proteasome inhibitor PI31 subunit

D: Proteasome inhibitor PI31 subunit

72.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

2

A: Proteasome inhibitor PI31 subunit

B: Proteasome inhibitor PI31 subunit

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

3

C: Proteasome inhibitor PI31 subunit

D: Proteasome inhibitor PI31 subunit

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

Unit cell

Length a, b, c (Å)	58.830, 97.670, 108.220
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Proteasome inhibitor PI31 subunit / hPI31 Mass: 18209.475 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HUMAN PI31, PSMF1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92530
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 494 / 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: 2.13 Å³/Da / Density % sol: 42.37 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 8000, NaAc, KBr, pH 5.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2→31.176 Å / Num. obs: 42700

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Processing

Software

Name	Version	Classification	NB
PHENIX	1.8.2_1309	refinement
PDB_EXTRACT	3.14	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→31.176 Å / FOM work R set: 0.8455 / SU ML: 0.18 / σ(F): 1.34 / Phase error: 22.2 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2385	2000	4.68 %
R_work	0.1864	-	-
obs	0.1887	42700	99.58 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 114.55 Å² / B_iso mean: 28.92 Å² / B_iso min: 5.22 Å²

Refinement step

Cycle: LAST / Resolution: 2→31.176 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4648	0	0	494	5142

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	4744
X-RAY DIFFRACTION	f_angle_d	0.877	6438
X-RAY DIFFRACTION	f_chiral_restr	0.063	723
X-RAY DIFFRACTION	f_plane_restr	0.004	827
X-RAY DIFFRACTION	f_dihedral_angle_d	12.989	1728

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2-2.05	0.2825	139	0.2086	2837	2976	99
2.05-2.1054	0.2675	141	0.2085	2865	3006	99
2.1054-2.1674	0.2325	139	0.1956	2845	2984	100
2.1674-2.2373	0.283	141	0.1841	2870	3011	99
2.2373-2.3172	0.2334	142	0.1901	2865	3007	99
2.3172-2.41	0.263	141	0.186	2873	3014	100
2.41-2.5196	0.2342	142	0.1959	2891	3033	100
2.5196-2.6524	0.253	141	0.1873	2891	3032	100
2.6524-2.8185	0.2354	143	0.1985	2895	3038	100
2.8185-3.0359	0.2825	143	0.1935	2904	3047	100
3.0359-3.3411	0.2528	143	0.1923	2935	3078	100
3.3411-3.8239	0.2375	146	0.1685	2951	3097	100
3.8239-4.8148	0.1906	145	0.1582	2972	3117	100
4.8148-31.1802	0.2145	154	0.1997	3106	3260	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	0.0276	-0.0085	0.023	0.0034	-0.0056	0.0179	0.0004	-0.0598	0.0195	-0.0681	0.0252	0.0154	0.022	-0.0154	0.001	0.0777	0.0023	0.0062	0.0602	-0.0101	0.0635	11.8145	8.9478	106.7208
2	0.0101	0.0001	0.0008	0.0057	-0.0003	0.0052	-0.012	-0.0463	0.0399	0.027	0.0379	-0.0259	-0.0286	-0.0235	0.0087	0.106	0.0114	0.0095	0.0858	-0.0324	0.1118	16.337	18.8823	112.3778
3	0.04	-0.0115	0.0316	0.0068	-0.0074	0.0214	0.0046	-0.0421	-0.0437	0.0466	-0.0078	-0.0207	0.0669	-0.0305	0.0075	0.0921	0.0068	-0.0104	0.0622	-0.106	-0.0133	22.0278	7.4637	111.9241
4	0.0156	-0.0052	0.0016	0.0025	0.0009	0.0034	-0.0421	0.0232	-0.0722	-0.0524	-0.0166	0.0187	-0.0229	-0.0139	-0.0041	0.1339	0.011	-0.0152	0.0766	-0.0068	0.1106	14.5666	1.792	98.4153
5	0.0015	0.0006	0.0021	0.0002	0.0002	0.002	0.0058	0.0183	0.0165	0.0461	0.0011	0.0006	0.0085	-0.0037	0	0.2855	0.0003	-0.0866	0.2533	0.0577	0.2506	19.1125	-1.9529	123.7039
6	0.0082	0.0043	-0.0008	0.0028	0.0024	0.0071	-0.0176	-0.0309	-0.0252	-0.0047	-0.0233	0.0163	0.0299	-0.0027	-0.0041	0.1016	0.0186	0.0004	0.105	-0.0151	0.0961	-3.3199	13.2445	109.8963
7	0.0396	0.0612	0.0136	0.0979	0.0239	0.0058	-0.0779	0.0282	0.0202	-0.0231	-0.0303	0.0298	-0.0003	0.049	-0.0404	0.115	-0.0091	-0.0011	0.062	-0.0084	0.0428	-9.7983	8.4196	102.3261
8	0.0014	0.0021	0.0017	0.0045	0.0002	0.0071	0.0032	0.0221	-0.0413	-0.0061	0.0207	-0.0304	0.0147	0.0055	0.0053	0.0886	0.0256	-0.0273	0.0751	-0.0952	0.0907	-9.7898	0.5804	100.1921
9	0.0135	-0.0149	0.0065	0.0198	-0.0111	0.019	-0.0067	-0.0327	0.0222	0.011	-0.0032	0.0142	-0.0093	-0.0246	0.0112	0.0325	0.0282	0.0584	0.0654	-0.1318	0.1222	-19.9056	4.9716	106.8123
10	0.0015	0.0008	-0.0024	0.0006	-0.0019	0.0046	-0.0163	-0.0209	-0.0109	-0.004	0.0108	0.0073	0.0078	-0.0105	-0.0002	0.1227	-0.0182	0.0354	0.1198	-0.0424	0.0657	-18.907	8.8021	117.1315
11	0.0617	-0.0199	0.0235	0.0137	-0.0054	0.0095	-0.0839	-0.067	0.0088	0.0287	-0.0062	-0.0101	0.0012	-0.0018	-0.0236	0.1417	0.0108	0.0047	0.1155	-0.0144	0.0705	-9.2629	12.7609	118.9538
12	0.0013	0.0001	-0.0029	0.0001	0.0003	0.006	0.0008	0.0213	-0.0081	-0.0077	-0.008	-0.0052	0.0276	-0.0031	0.0003	0.2257	-0.0387	0.0479	0.1236	-0.0213	0.2872	-12.7312	-10.6932	108.943
13	0.0562	0.0248	-0.0033	0.0108	0.0004	0.0008	0.0147	-0.036	-0.0521	-0.0095	0.0222	0.0232	0.0252	-0.037	0.0159	0.0598	-0.0548	0.004	0.1532	0.2544	0.211	-2.9144	28.4893	79.6155
14	0.0027	0.0022	0.0038	0.0011	0.0007	0.0043	0.0131	-0.0197	-0.0188	-0.0079	0.01	0.0043	0.0157	0.0216	0.042	0.1161	0.0063	-0.0139	0.3007	0.2119	0.2416	1.6259	21.1727	88.329
15	0.0014	-0.0027	0.0015	0.002	-0.0026	0.003	0.0122	-0.0334	-0.054	-0.0136	0.0187	0.0458	0.0108	-0.0184	0.0261	0.107	-0.0128	-0.0169	0.1214	0.1658	0.1904	6.3513	21.2842	78.8736
16	0.0009	-0.0006	0.0012	0.0006	-0.0023	0.0073	0.0058	0.0071	0.0053	-0.008	-0.0073	-0.0039	0.0108	0.022	0.0057	0.0958	-0.0233	0.0072	0.118	0.0812	0.1044	10.2666	30.0705	73.0373
17	0.0109	0.0042	-0.0026	0.0068	0.0034	0.0066	-0.0045	-0.057	0.0273	-0.0211	0.014	0.009	-0.0244	-0.0288	-0.0031	0.1572	0.0291	0.0194	0.1449	0.0646	0.1619	-1.1875	41.931	78.3129
18	0	-0.0003	-0.0007	0.0024	0.003	0.0048	0.0067	0.0022	-0.0018	-0.018	0.0046	0.0008	0.0041	-0.0028	0.0079	0.1127	-0.0373	-0.0035	0.1415	0.1597	0.1742	1.9431	31.2302	67.4492
19	0.0025	-0.001	0.0005	0.0058	0.0005	-0.0002	-0.0113	0.0131	-0.0061	-0.0082	-0.0027	-0.0006	0.0142	-0.0008	-0.0002	0.3968	-0.0041	0.0349	0.2804	0.0115	0.4068	4.4969	14.6998	66.1533
20	0.0273	-0.0046	0.0192	0.0021	-0.009	0.0685	-0.0276	-0.0314	0.0109	0.0052	-0.035	-0.0078	-0.0168	-0.0018	-0.0281	0.0777	-0.0223	-0.0269	0.1502	0.0901	0.1833	-18.177	24.8301	84.2547
21	0.0376	-0.0208	0.0339	0.0315	-0.016	0.0307	-0.002	-0.1253	-0.0395	0.0621	0.0052	-0.0018	-0.0053	-0.0188	-0.0095	0.0933	-0.0421	-0.0058	0.1523	0.1588	0.1704	-24.5072	32.9696	80.0785
22	0.0166	0.0061	0.0012	0.0101	-0.0064	0.0071	0.0212	-0.0095	-0.0037	-0.0214	-0.0039	-0.0234	0.0075	-0.0084	0.0228	0.1305	-0.0285	0.0161	0.1133	0.133	0.1617	-24.456	36.5717	72.8014
23	0.014	-0.005	-0.0055	0.0027	0.0048	0.007	-0.0183	-0.0331	-0.0424	-0.0025	0.0149	0.0261	0.0023	-0.0034	-0.0069	0.0721	-0.0308	0.0003	0.1788	0.1693	0.1842	-34.8257	28.6709	77.1653
24	0.0118	-0.009	-0.0127	0.0094	0.0117	0.014	-0.0361	-0.0131	-0.0582	-0.0298	-0.0347	0.0315	-0.02	0.0007	-0.0064	0.1585	-0.0157	-0.0478	0.1717	0.1288	0.3778	-31.7507	19.8588	79.2817
25	0.0152	-0.0158	-0.0136	0.0184	0.0148	0.013	-0.0808	-0.0282	-0.0535	0.0567	-0.0049	-0.0135	0.0516	0.0353	-0.0002	0.1473	-0.0185	0.0012	0.148	0.1029	0.3099	-23.5004	16.4648	79.3472
26	0.0014	-0.0002	0.0009	-0.0001	-0.0007	0.0008	0.0095	-0.005	0.0051	-0.0205	0.0054	-0.0044	-0.0125	0.0023	0.0002	0.31	-0.0074	-0.0316	0.385	0.0297	0.3371	-27.894	29.5153	60.4769

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -2 through 40 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 41 through 63 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 64 through 111 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 112 through 137 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 138 through 150 )	A
6	X-RAY DIFFRACTION	6	chain 'B' and (resid -2 through 17 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 18 through 63 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 64 through 76 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 77 through 101 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 102 through 111 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 112 through 137 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 138 through 150 )	B
13	X-RAY DIFFRACTION	13	chain 'C' and (resid -2 through 40 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 41 through 63 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 64 through 94 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 95 through 110 )	C
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 111 through 126 )	C
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 127 through 137 )	C
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 138 through 149 )	C
20	X-RAY DIFFRACTION	20	chain 'D' and (resid -1 through 17 )	D
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 18 through 63 )	D
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 64 through 76 )	D
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 77 through 94 )	D
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 95 through 116 )	D
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 117 through 137 )	D
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 138 through 149 )	D

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