PDB-5mx5: Mouse PA28alpha-beta

ID or keywords:

Entry

Database: PDB / ID: 5mx5

Title

Mouse PA28alpha-beta

Components

Proteasome activator complex subunit 1
Proteasome activator complex subunit 2

Keywords

STRUCTURAL PROTEIN / proteasome activator / regulator / heptamer / 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: 2.9 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 20, 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 / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5mx5.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb5mx5.ent.gz	959.7 KB	Display	PDB format
PDBx/mmJSON format	5mx5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mx/5mx5 ftp://data.pdbj.org/pub/pdb/validation_reports/mx/5mx5	HTTPS FTP

-
Related structure data

Related structure data	5msjSC 5mskC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5msk-d 5msj-4 5msj-2 5msj-1 1kqn-d 2y7j-d 6dfk-1 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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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 2

C: Proteasome activator complex subunit 1

D: Proteasome activator complex subunit 2

E: Proteasome activator complex subunit 1

F: Proteasome activator complex subunit 2

G: Proteasome activator complex subunit 1

H: Proteasome activator complex subunit 1

I: Proteasome activator complex subunit 2

J: Proteasome activator complex subunit 1

K: Proteasome activator complex subunit 2

L: Proteasome activator complex subunit 1

M: Proteasome activator complex subunit 2

N: Proteasome activator complex subunit 1

hetero molecules

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

1

A: Proteasome activator complex subunit 1

B: Proteasome activator complex subunit 2

C: Proteasome activator complex subunit 1

D: Proteasome activator complex subunit 2

E: Proteasome activator complex subunit 1

F: Proteasome activator complex subunit 2

G: Proteasome activator complex subunit 1

hetero molecules

defined by author&software
196 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 2

J: Proteasome activator complex subunit 1

K: Proteasome activator complex subunit 2

L: Proteasome activator complex subunit 1

M: Proteasome activator complex subunit 2

N: Proteasome activator complex subunit 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	126.090, 137.380, 136.420
Angle α, β, γ (deg.)	90.00, 104.44, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#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.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Psme1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P97371
#2: Protein	Proteasome activator complex subunit 2 / 11S regulator complex subunit beta / REG-beta / Activator of multicatalytic protease subunit 2 / ...11S regulator complex subunit beta / REG-beta / Activator of multicatalytic protease subunit 2 / Proteasome activator 28 subunit beta / PA28beta Mass: 27094.283 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Psme2, Pa28b1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P97372
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.92 Å³/Da / Density % sol: 57.83 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2 M KH2PO4, 9 % PEG3350

-
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: Apr 6, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.9→40 Å / Num. obs: 96305 / % possible obs: 96.4 % / Redundancy: 2.3 % / R_merge(I) obs: 0.059 / Net I/σ(I): 12.1
Reflection shell	Resolution: 2.9→3 Å / R_merge(I) obs: 0.532 / Mean I/σ(I) obs: 2.3 / % possible all: 92.8

-
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: 5MSJ

5msj

Resolution: 2.9→15 Å / Cor.coef. F_o:F_c: 0.931 / Cor.coef. F_o:F_c free: 0.913 / SU B: 41.043 / SU ML: 0.351 / Cross valid method: THROUGHOUT / ESU R Free: 0.416 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27226	4784	5 %	RANDOM
R_work	0.24307	-	-	-
obs	0.24453	90889	96.29 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 82.625 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.11 Å²	0 Å²	3.76 Å²
2-	-	-4.44 Å²	-0 Å²
3-	-	-	2.31 Å²

Refinement step

Cycle: 1 / Resolution: 2.9→15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	23437	0	15	246	23698

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	23892
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	23010
X-RAY DIFFRACTION	r_angle_refined_deg	0.926	1.984	32329
X-RAY DIFFRACTION	r_angle_other_deg	0.821	3	53571
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.356	5	2901
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.422	25.099	1110
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.039	15	4418
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.868	15	132
X-RAY DIFFRACTION	r_chiral_restr	0.043	0.2	3691
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.021	25961
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4411
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	0.412	6.866	11688
X-RAY DIFFRACTION	r_mcbond_other	0.412	6.866	11687
X-RAY DIFFRACTION	r_mcangle_it	0.781	10.29	14561
X-RAY DIFFRACTION	r_mcangle_other	0.781	10.29	14562
X-RAY DIFFRACTION	r_scbond_it	0.224	6.868	12204
X-RAY DIFFRACTION	r_scbond_other	0.224	6.861	12193
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	0.464	10.294	17751
X-RAY DIFFRACTION	r_long_range_B_refined	2.004	81.219	26496
X-RAY DIFFRACTION	r_long_range_B_other	1.983	81.212	26482
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.904→2.977 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.355	333	-
R_work	0.345	6328	-
obs	-	-	94.59 %

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	1.3209	-0.0782	-0.203	0.6946	0.2219	0.8168	0.0226	0.2001	0.0371	-0.2695	-0.0684	0.0137	-0.1975	-0.154	0.0458	0.221	0.0304	-0.0163	0.1252	-0.0331	0.0176	-49.155	-9.1555	131.9306
2	1.847	-0.3181	-0.2659	0.6726	0.0655	0.3248	-0.032	0.0551	-0.0069	-0.2376	0.0716	-0.0617	0.0097	-0.0265	-0.0396	0.2237	-0.0223	0.0029	0.1721	-0.0954	0.0639	-44.2704	-30.3585	137.5797
3	2.1347	0.2499	-0.1343	0.3778	-0.1022	0.6176	-0.0003	0.0549	-0.3408	-0.0648	0.0016	-0.1523	0.165	-0.0061	-0.0013	0.1048	0.0075	0.0209	0.0421	-0.0603	0.1745	-31.2263	-38.0279	154.2662
4	1.1726	0.6378	-0.406	0.8504	-0.0866	0.3901	-0.0245	-0.0526	-0.1479	0.0722	0.0353	-0.2002	0.101	0.0709	-0.0107	0.0556	0.0237	-0.0694	0.1218	0.0389	0.1816	-21.5091	-27.3743	169.1315
5	0.9275	0.1952	-0.644	1.1366	-0.171	0.5301	0.1067	-0.1184	-0.0122	0.1726	-0.0595	-0.2365	-0.1145	0.1007	-0.0472	0.1115	-0.05	-0.0512	0.1857	0.0047	0.121	-19.317	-5.2156	171.711
6	0.3854	0.1603	-0.2145	0.4846	-0.2852	1.7569	0.0041	-0.0523	0.0542	0.0207	-0.0492	-0.1287	-0.1358	-0.003	0.0451	0.2074	-0.0247	0.0119	0.0695	0.0104	0.0662	-28.3583	9.7141	160.7336
7	0.4728	0.1424	-0.0713	0.5909	0.0821	0.8597	-0.0035	0.0641	0.1068	-0.1501	-0.0384	-0.0159	-0.1915	-0.1408	0.0419	0.223	0.0114	-0.0008	0.0536	0.0188	0.0421	-41.8075	8.803	142.3236
8	1.2575	0.1067	-1.4341	0.7285	0.0373	1.9884	0.0627	0.0349	0.0729	0.0681	-0.0724	0.1566	-0.2243	-0.0164	0.0096	0.1883	-0.0324	0.0639	0.0761	-0.0551	0.1437	-89.3157	12.597	195.601
9	0.8595	0.8396	-0.9032	1.3927	-1.117	1.8003	0.1058	-0.0759	0.0514	0.2538	-0.0715	0.0377	-0.2899	0.0765	-0.0344	0.1739	-0.0562	0.0688	0.1025	-0.0818	0.0767	-78.116	0.9002	211.0708
10	2.7671	0.8348	-0.9286	0.8817	-0.3389	0.8249	0.1233	-0.2742	0.0026	0.2456	-0.0804	0.0124	-0.1195	0.1273	-0.0429	0.2106	-0.0343	0.0056	0.1198	0.0322	0.0335	-75.7743	-21.1009	213.4385
11	2.21	-0.1039	-0.6264	0.5474	0.0435	0.447	0.0397	0.0157	-0.1193	0.2131	-0.0247	0.0462	0.0508	0.0302	-0.015	0.1686	-0.0137	0.0065	0.0484	0.0598	0.1375	-85.5489	-36.6025	201.4682
12	1.6462	-0.3821	-0.6595	1.0493	0.2381	0.8524	0.0552	0.0721	-0.2592	0.0453	-0.0369	0.1789	0.0845	-0.0675	-0.0183	0.1069	-0.0595	-0.0289	0.0423	0.0042	0.1239	-99.1122	-34.3594	183.7415
13	0.879	-0.6504	-0.5394	1.2234	0.2327	0.4671	0.046	0.1055	-0.0161	-0.0839	0.014	0.135	0.0468	-0.035	-0.06	0.0581	0.0173	-0.0762	0.1617	-0.0159	0.1828	-105.3417	-16.8611	173.5192
14	0.9918	0.0389	-0.8309	0.7846	0.2945	1.7384	0.0613	0.1908	0.1904	-0.064	0.0411	0.3065	-0.2133	-0.0056	-0.1024	0.0804	0.0408	-0.0132	0.1145	0.0369	0.2235	-101.3339	4.8683	178.8909

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 242
2	X-RAY DIFFRACTION	2	B	7 - 243
3	X-RAY DIFFRACTION	3	C	6 - 243
4	X-RAY DIFFRACTION	4	D	4 - 243
5	X-RAY DIFFRACTION	5	E	4 - 242
6	X-RAY DIFFRACTION	6	F	3 - 244
7	X-RAY DIFFRACTION	7	G	3 - 242
8	X-RAY DIFFRACTION	8	H	6 - 242
9	X-RAY DIFFRACTION	9	I	9 - 243
10	X-RAY DIFFRACTION	10	J	7 - 242
11	X-RAY DIFFRACTION	11	K	5 - 242
12	X-RAY DIFFRACTION	12	L	4 - 242
13	X-RAY DIFFRACTION	13	M	5 - 244
14	X-RAY DIFFRACTION	14	N	6 - 242

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi