PDB-5msj: Mouse PA28alpha

ID or keywords:

Entry

Database: PDB / ID: 5msj

Title

Mouse PA28alpha

Components

Proteasome activator complex subunit 1

Keywords

STRUCTURAL PROTEIN / proteasome activator / regulator / heptamer / REGalpha / interferon-gamma / hydrolase

Function / homology

Function and homology information

Proteasome assembly / proteasome activator complex / antigen processing and presentation of exogenous antigen
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.5 Å

Authors

Huber, E.M. / Groll, M.

Funding support

Germany, 1items

Citation

Journal: Structure / Year: 2017
Title: The Mammalian Proteasome Activator PA28 Forms an Asymmetric alpha 4 beta 3 Complex.
Authors: Huber, E.M. / Groll, M.

History

Deposition	Jan 5, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 13, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5msj.cif.gz	2.2 MB	Display	PDBx/mmCIF format
PDB format	pdb5msj.ent.gz	1.9 MB	Display	PDB format
PDBx/mmJSON format	5msj.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/ms/5msj ftp://data.pdbj.org/pub/pdb/validation_reports/ms/5msj	HTTPS FTP

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Related structure data

Related structure data	5mskC 5mx5C 1avoS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5mx5-2 5msk-d 5mx5-1 1avo-d 2y7j-d 10161 1kqn-d 5ef1-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) 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

Related structure data

5mskC

5mx5C

1avoS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#166 - Oct 2013 Proteasome similarity (4) #60 - Dec 2004 Ubiquitin similarity (4)

Deposited unit

A: Proteasome activator complex subunit 1

B: Proteasome activator complex subunit 1

C: Proteasome activator complex subunit 1

D: Proteasome activator complex subunit 1

E: Proteasome activator complex subunit 1

F: Proteasome activator complex subunit 1

G: Proteasome activator complex subunit 1

H: Proteasome activator complex subunit 1

I: Proteasome activator complex subunit 1

J: Proteasome activator complex subunit 1

K: Proteasome activator complex subunit 1

L: Proteasome activator complex subunit 1

M: Proteasome activator complex subunit 1

N: Proteasome activator complex subunit 1

O: Proteasome activator complex subunit 1

P: Proteasome activator complex subunit 1

Q: Proteasome activator complex subunit 1

R: Proteasome activator complex subunit 1

S: Proteasome activator complex subunit 1

T: Proteasome activator complex subunit 1

U: Proteasome activator complex subunit 1

V: Proteasome activator complex subunit 1

W: Proteasome activator complex subunit 1

X: Proteasome activator complex subunit 1

Y: Proteasome activator complex subunit 1

Z: Proteasome activator complex subunit 1

a: Proteasome activator complex subunit 1

b: Proteasome activator complex subunit 1

804 kDa, 28 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Proteasome activator complex subunit 1

B: Proteasome activator complex subunit 1

C: Proteasome activator complex subunit 1

D: Proteasome activator complex subunit 1

E: Proteasome activator complex subunit 1

F: Proteasome activator complex subunit 1

G: Proteasome activator complex subunit 1

defined by author&software
201 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

H: Proteasome activator complex subunit 1

I: Proteasome activator complex subunit 1

J: Proteasome activator complex subunit 1

K: Proteasome activator complex subunit 1

L: Proteasome activator complex subunit 1

M: Proteasome activator complex subunit 1

N: Proteasome activator complex subunit 1

defined by author&software
201 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

O: Proteasome activator complex subunit 1

P: Proteasome activator complex subunit 1

Q: Proteasome activator complex subunit 1

R: Proteasome activator complex subunit 1

S: Proteasome activator complex subunit 1

T: Proteasome activator complex subunit 1

U: Proteasome activator complex subunit 1

defined by author&software
201 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

V: Proteasome activator complex subunit 1

W: Proteasome activator complex subunit 1

X: Proteasome activator complex subunit 1

Y: Proteasome activator complex subunit 1

Z: Proteasome activator complex subunit 1

a: Proteasome activator complex subunit 1

b: Proteasome activator complex subunit 1

defined by author&software
201 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	87.790, 119.800, 196.670
Angle α, β, γ (deg.)	94.21, 98.52, 87.98
Int Tables number	1
Space group name H-M	P1

#1: Protein	... Proteasome activator complex subunit 1 / 11S regulator complex subunit alpha / REG-alpha / Activator of multicatalytic protease subunit 1 / ...11S regulator complex subunit alpha / REG-alpha / Activator of multicatalytic protease subunit 1 / Proteasome activator 28 subunit alpha / PA28alpha Mass: 28717.973 Da / Num. of mol.: 28 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Psme1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P97371

#1: Protein

...
Proteasome activator complex subunit 1 / 11S regulator complex subunit alpha / REG-alpha / Activator of multicatalytic protease subunit 1 / ...

Mass: 28717.973 Da / Num. of mol.: 28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: Psme1 / Production host:

Escherichia coli BL21 (bacteria) / References: UniProt: P97371

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.54 Å³/Da / Density % sol: 51.5 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Hepes, 25 % PEG 1000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 8, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.5→30 Å / Num. obs: 92743 / % possible obs: 93.1 % / Redundancy: 1.8 % / R_merge(I) obs: 0.087 / Net I/σ(I): 9.1
Reflection shell	Resolution: 3.5→3.6 Å / R_merge(I) obs: 0.434 / Mean I/σ(I) obs: 1.9 / % possible all: 93.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1AVO

1avo

Resolution: 3.5→29.65 Å / Cor.coef. F_o:F_c: 0.921 / Cor.coef. F_o:F_c free: 0.903 / SU B: 103.857 / SU ML: 0.658 / Cross valid method: THROUGHOUT / ESU R Free: 0.746 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28279	4638	5 %	RANDOM
R_work	0.24953	-	-	-
obs	0.25122	88105	93.1 %	-

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: 97.792 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.73 Å²	-0.56 Å²	-0.21 Å²
2-	-	4.02 Å²	0.71 Å²
3-	-	-	-4.58 Å²

Refinement step

Cycle: 1 / Resolution: 3.5→29.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	46128	0	0	0	46128

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	46967
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	44998
X-RAY DIFFRACTION	r_angle_refined_deg	0.996	1.982	63461
X-RAY DIFFRACTION	r_angle_other_deg	0.848	3	104918
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.581	5	5667
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.608	25.47	2278
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.559	15	8845
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.969	15	239
X-RAY DIFFRACTION	r_chiral_restr	0.047	0.2	7190
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	51096
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	8555
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	0.611	7.292	22836
X-RAY DIFFRACTION	r_mcbond_other	0.611	7.292	22835
X-RAY DIFFRACTION	r_mcangle_it	1.147	10.929	28447
X-RAY DIFFRACTION	r_mcangle_other	1.147	10.929	28448
X-RAY DIFFRACTION	r_scbond_it	0.328	7.24	24131
X-RAY DIFFRACTION	r_scbond_other	0.328	7.24	24132
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	0.682	10.872	35015
X-RAY DIFFRACTION	r_long_range_B_refined	2.634	85.87	52228
X-RAY DIFFRACTION	r_long_range_B_other	2.634	85.869	52228
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 3.5→3.59 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.372	339	-
R_work	0.35	6433	-
obs	-	-	93.59 %

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	0.4136	0.1534	0.5703	0.7569	0.0348	2.7171	-0.0236	0.1271	0.0437	0.0637	-0.0441	-0.0495	-0.1473	0.2863	0.0678	0.352	0.0226	-0.0448	0.2428	0.0329	0.1094	1.4864	24.5436	2.3975
2	0.5886	0.2007	-0.359	0.0936	0.0256	1.2934	0.0079	0.0362	0.0705	0.0019	0.0085	0.042	0.2571	-0.1136	-0.0164	0.4321	0.0316	-0.0684	0.268	0.0501	0.0702	-18.9135	17.6118	-0.8942
3	1.7377	-0.9244	-2.0011	2.0142	1.8402	2.7543	0.0056	0.0874	-0.0088	0.1357	-0.0155	-0.1354	-0.0082	-0.0834	0.0099	0.3661	-0.0041	-0.0822	0.2384	-0.0039	0.0737	-25.7004	-3.3416	-3.6599
4	2.1582	-0.4735	-1.4279	0.6846	-0.0557	1.1805	-0.0554	-0.016	-0.0141	0.0147	0.057	0.0463	0.0527	-0.0371	-0.0016	0.41	-0.0455	0.0486	0.3267	-0.1483	0.0764	-13.5068	-22.2775	-2.7336
5	0.728	-0.1213	0.7474	0.2409	-0.066	1.2326	-0.0498	0.0281	-0.2458	0.0413	-0.0995	-0.0442	0.052	0.1247	0.1494	0.4137	0.0297	0.1229	0.302	0.066	0.4907	7.1124	-24.8874	1.0687
6	0.1411	-0.037	0.3831	1.9849	-2.0024	3.0657	-0.0014	0.0351	-0.083	0.0615	-0.0033	-0.2031	-0.0769	-0.1342	0.0047	0.3279	0.0501	-0.0015	0.3051	0.0019	0.1172	22.9679	-8.3362	4.0539
7	1.3111	-0.2621	0.948	1.5288	-1.1093	3.6662	-0.0958	-0.0255	-0.1311	0.0706	-0.0188	-0.1731	-0.005	0.0675	0.1145	0.2772	-0.0101	0.0172	0.1739	-0.0151	0.0989	19.9244	13.0204	5.5923
8	1.7126	0.16	0.7396	0.6392	0.4972	4.0954	-0.0938	-0.0531	0.3002	0.1065	-0.0549	-0.2795	-0.0687	-0.0585	0.1487	0.3241	0.0226	-0.0915	0.1738	0.1013	0.2618	27.6217	-40.8823	100.6432
9	1.1882	1.0339	-0.1769	2.2578	1.0086	1.4539	-0.0905	-0.0867	0.2724	0.0403	0.0785	0.221	0.0073	-0.0431	0.012	0.2933	0.0564	-0.0704	0.3081	0.1092	0.1719	7.9202	-49.7284	96.863
10	2.3607	-1.034	-1.7574	1.1667	1.171	3.3625	-0.1494	0.055	0.1369	-0.0738	0.0683	0.0546	-0.2641	-0.2187	0.0811	0.3019	-0.0611	-0.0107	0.2079	0.0548	0.0723	3.9185	-71.2901	92.5222
11	0.2523	0.2394	-0.1529	0.6609	-0.329	0.1889	-0.1361	0.0197	-0.2295	-0.1513	0.0211	-0.1142	0.0539	-0.0649	0.1149	0.2798	-0.019	0.1697	0.4353	-0.0775	0.2452	17.9219	-88.6804	93.009
12	1.3439	1.0436	-0.5961	1.3079	-1.1398	1.1891	0.0428	-0.0134	-0.1273	0.0602	-0.0429	-0.0868	-0.056	0.0538	0.0001	0.2836	-0.0274	0.1914	0.2786	-0.1319	0.1982	39.6768	-88.5917	97.7549
13	0.098	0.2849	-0.0733	3.0952	-1.9234	1.4042	-0.0409	0.0799	-0.1103	0.1354	0.0552	-0.2228	-0.0798	-0.0127	-0.0142	0.209	-0.0387	0.0688	0.4321	0.0108	0.1623	52.5338	-71.325	102.7976
14	1.1238	-0.2344	1.1401	0.4548	-0.9796	4.0578	-0.1415	-0.0244	-0.024	0.0245	0.0795	-0.1847	-0.0221	-0.127	0.062	0.2609	-0.0346	-0.0128	0.2102	0.0437	0.1699	47.1546	-50.6947	104.3131
15	0.9383	-0.4076	-0.546	0.5599	0.9859	2.1284	-0.0744	-0.0218	-0.1632	-0.0377	-0.0381	0.1184	-0.1185	0.1907	0.1125	0.3398	0.0081	0.0747	0.2809	-0.0394	0.1154	-6.7224	-88.7266	157.2195
16	1.0859	0.4997	0.2402	1.2238	0.6199	3.4273	-0.0963	0.1356	-0.0233	-0.0508	0.0146	0.1861	0.1739	0.0373	0.0817	0.2385	0.0438	0.0905	0.2078	-0.022	0.1597	-11.5318	-67.8782	157.7968
17	0.732	-0.1579	0.7776	0.6796	-0.6348	1.1673	-0.0255	-0.0536	0.2225	0.005	-0.0674	0.1428	-0.0665	0.004	0.0928	0.4159	0.0098	0.0799	0.2687	-0.0669	0.1462	1.6253	-50.1897	162.7647
18	0.8458	-0.1388	0.2929	0.7963	-1.1734	1.7787	-0.051	-0.1461	0.2479	0.068	-0.0619	-0.0504	-0.0811	-0.0314	0.1129	0.5101	-0.0102	-0.0505	0.2476	-0.0969	0.0902	23.5761	-50.8897	168.3071
19	0.2309	-0.0532	0.0442	0.2499	-0.19	0.1502	-0.1078	-0.1465	-0.0102	0.0874	-0.0066	-0.1485	-0.1128	0.0176	0.1145	0.4249	-0.0225	-0.0325	0.3396	0.0911	0.1117	37.1548	-68.0468	169.34
20	1.8022	0.5399	-1.7383	0.4002	-0.267	2.1477	-0.0814	0.0167	-0.2431	0.109	-0.0317	-0.1896	-0.0257	-0.0698	0.1132	0.3881	0.0221	-0.0448	0.3156	0.1413	0.1406	32.8198	-88.7755	165.8882
21	1.0885	0.2871	-0.6424	0.1363	0.0226	1.1423	0.0928	0.025	-0.3015	0.015	-0.1209	-0.126	-0.0848	-0.2164	0.028	0.387	0.0528	0.0846	0.3035	0.0902	0.1494	11.3537	-98.0484	162.6582
22	0.3478	-0.1159	0.3989	1.1103	0.5276	1.161	0.0811	-0.0198	-0.0764	-0.0626	-0.0924	-0.0357	-0.1032	-0.1008	0.0113	0.2832	0.0135	0.007	0.2275	0.025	0.139	-34.268	-18.342	62.4064
23	1.172	-0.1858	0.4042	0.1221	0.3974	3.0735	0.0535	0.0574	-0.1132	0.0514	-0.0314	0.0578	0.0704	-0.0612	-0.0221	0.3833	-0.0093	0.0305	0.2097	-0.0203	0.0934	-36.4309	3.0957	62.9478
24	0.6919	0.1152	0.8531	0.3874	-0.3527	1.7733	0.0244	-0.0589	0.1995	-0.0239	-0.1012	0.1492	-0.0082	0.1764	0.0767	0.361	-0.0256	0.0122	0.3188	-0.0911	0.101	-20.7918	19.1092	66.8786
25	1.4913	-0.3087	-0.1325	1.6507	-1.2537	1.0766	0.1323	0.0047	0.1375	-0.033	-0.1086	0.0125	0.0317	0.0007	-0.0237	0.4239	-0.0624	-0.0298	0.2816	-0.0583	0.0325	0.5564	16.355	69.9788
26	0.4113	0.5412	-0.758	1.7546	-1.2054	1.4595	-0.0482	-0.0134	-0.0308	-0.0547	-0.014	-0.0892	0.01	-0.0227	0.0621	0.3866	-0.0286	-0.084	0.3257	0.1059	0.0545	12.1059	-2.137	70.7106
27	1.4065	-0.3756	-1.6092	0.6769	-0.282	3.0495	-0.1123	0.0368	-0.0892	0.0948	-0.2344	-0.2828	0.0238	0.0057	0.3467	0.2673	-0.0271	-0.0391	0.2794	0.1969	0.218	4.8689	-23.0531	68.8866
28	0.9067	-0.2496	-1.6063	0.8743	0.5945	3.1833	-0.0781	0.0752	-0.3352	0.0201	-0.3378	-0.0391	-0.0449	-0.2353	0.4159	0.2573	0.0042	0.0305	0.2113	0.0705	0.2538	-15.208	-30.5132	64.6196

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 243
2	X-RAY DIFFRACTION	2	B	5 - 243
3	X-RAY DIFFRACTION	3	C	5 - 243
4	X-RAY DIFFRACTION	4	D	7 - 243
5	X-RAY DIFFRACTION	5	E	3 - 244
6	X-RAY DIFFRACTION	6	F	8 - 241
7	X-RAY DIFFRACTION	7	G	6 - 244
8	X-RAY DIFFRACTION	8	H	4 - 243
9	X-RAY DIFFRACTION	9	I	6 - 244
10	X-RAY DIFFRACTION	10	J	4 - 242
11	X-RAY DIFFRACTION	11	K	4 - 242
12	X-RAY DIFFRACTION	12	L	5 - 243
13	X-RAY DIFFRACTION	13	M	7 - 241
14	X-RAY DIFFRACTION	14	N	3 - 243
15	X-RAY DIFFRACTION	15	O	8 - 243
16	X-RAY DIFFRACTION	16	P	4 - 244
17	X-RAY DIFFRACTION	17	Q	6 - 243
18	X-RAY DIFFRACTION	18	R	8 - 241
19	X-RAY DIFFRACTION	19	S	8 - 242
20	X-RAY DIFFRACTION	20	T	4 - 243
21	X-RAY DIFFRACTION	21	U	7 - 242
22	X-RAY DIFFRACTION	22	V	8 - 243
23	X-RAY DIFFRACTION	23	W	5 - 243
24	X-RAY DIFFRACTION	24	X	8 - 243
25	X-RAY DIFFRACTION	25	Y	6 - 243
26	X-RAY DIFFRACTION	26	Z	4 - 243
27	X-RAY DIFFRACTION	27	a	4 - 243
28	X-RAY DIFFRACTION	28	b	4 - 242

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News

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