PDB-5irs: crystal structure of the proteasomal Rpn13 PRU-domain

ID or keywords:

Entry

Database: PDB / ID: 5irs

Title

crystal structure of the proteasomal Rpn13 PRU-domain

Components

Proteasomal ubiquitin receptor ADRM1

Keywords

PROTEIN BINDING /

Ubiquitin

Function / homology

Function and homology information

proteasome regulatory particle, lid subcomplex / molecular function inhibitor activity /

proteasome binding / endopeptidase activator activity /

proteasome assembly /

proteasome complex / transcription elongation by RNA polymerase II / UCH proteinases / proteasome-mediated ubiquitin-dependent protein catabolic process /

protease binding ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.796 Å

Authors

Chen, X. / Shi, K. / Walters, K. / Aihara, H.

Citation

Journal: Structure / Year: 2016
Title: Structures of Rpn1 T1:Rad23 and hRpn13:hPLIC2 Reveal Distinct Binding Mechanisms between Substrate Receptors and Shuttle Factors of the Proteasome.
Authors: Chen, X. / Randles, L. / Shi, K. / Tarasov, S.G. / Aihara, H. / Walters, K.J.

History

Deposition	Mar 14, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 20, 2016	Provider: repository / Type: Initial release
Revision 1.1	Aug 3, 2016	Group: Data collection
Revision 1.2	Aug 17, 2016	Group: Database references
Revision 1.3	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5irs.cif.gz	86.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5irs.ent.gz	66.4 KB	Display	PDB format
PDBx/mmJSON format	5irs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	2nbuC 2nbvC 2nbwC 2r2yS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2r2y-d 1fsp-d 6a65-d 3gjn-3 1xyi-d 3ub2-d 4dx9-3 3hh1-3 1i7a-1 6swf-1 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	#60 - Dec 2004 Ubiquitin similarity (1) #166 - Oct 2013 Proteasome similarity (5) #92 - Aug 2007 Anabolic Steroids similarity (1) #127 - Jul 2010 Crystallins similarity (1) #174 - Jun 2014 GFP-like Proteins similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

Deposited unit

A: Proteasomal ubiquitin receptor ADRM1

hetero molecules

16.9 kDa, 1 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)	42.555, 56.476, 64.089
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Proteasomal ubiquitin receptor ADRM1 / 110 kDa cell membrane glycoprotein / Gp110 / Adhesion-regulating molecule 1 / ARM-1 / Proteasome ...110 kDa cell membrane glycoprotein / Gp110 / Adhesion-regulating molecule 1 / ARM-1 / Proteasome regulatory particle non-ATPase 13 / hRpn13 / Rpn13 homolog Mass: 16610.850 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADRM1, GP110 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16186
#2: Chemical	ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₂S₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.32 Å³/Da / Density % sol: 46.94 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG4000, Sodium acetate

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.796→50 Å / Num. obs: 14838 / % possible obs: 99.06 % / Redundancy: 6 % / R_merge(I) obs: 0.066 / Net I/σ(I): 15.72
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 4.9 % / R_merge(I) obs: 0.96 / Mean I/σ(I) obs: 1.82 / % possible all: 96.35

-
Processing

Software

Name	Version	Classification
PHENIX	dev_1218	refinement
HKL-2000	HKL-2000	data reduction
HKL-2000	HKL-2000	data scaling
PHENIX		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 2R2Y

2r2y

Resolution: 1.796→35.451 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.63

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2092	1433	9.97 %	Random selection
R_work	0.167	-	-	-
obs	0.1713	14367	95.91 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.796→35.451 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	911	0	16	67	994

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.019	972
X-RAY DIFFRACTION	f_angle_d	1.501	1307
X-RAY DIFFRACTION	f_dihedral_angle_d	13.881	375
X-RAY DIFFRACTION	f_chiral_restr	0.1	137
X-RAY DIFFRACTION	f_plane_restr	0.006	170

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 (%)
1.7956-1.8598	0.2699	131	0.2395	1191	X-RAY DIFFRACTION	89
1.8598-1.9342	0.2528	137	0.2304	1237	X-RAY DIFFRACTION	94
1.9342-2.0222	0.2433	136	0.1881	1275	X-RAY DIFFRACTION	95
2.0222-2.1288	0.2015	136	0.1751	1257	X-RAY DIFFRACTION	95
2.1288-2.2622	0.2272	143	0.1735	1273	X-RAY DIFFRACTION	97
2.2622-2.4368	0.2541	146	0.1826	1294	X-RAY DIFFRACTION	97
2.4368-2.682	0.207	147	0.1705	1301	X-RAY DIFFRACTION	96
2.682-3.0699	0.221	147	0.1775	1318	X-RAY DIFFRACTION	98
3.0699-3.867	0.1905	151	0.1503	1360	X-RAY DIFFRACTION	99
3.867-35.4584	0.1983	159	0.1577	1428	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	1.1001	-0.0779	-0.9509	0.7948	1.3219	2.874	-0.6498	0.6454	0.3509	-0.6213	0.5799	0.7731	-1.3008	-1.7865	-0.0972	0.4285	0.0536	-0.0948	0.4461	0.0869	0.2854	14.7463	52.0946	1.0626
2	2.4277	2.1358	-0.4565	7.6794	0.0843	0.1311	-0.0439	1.0642	-0.1867	-1.3731	-0.144	0.2955	-0.6958	-1.2266	-0.3808	0.2745	0.0473	-0.0507	0.3785	-0.0501	0.1484	13.6056	41.6566	3.1515
3	0.5576	-0.0171	0.5761	3.2278	-0.4955	0.664	0.0426	-0.9123	-0.1788	0.9776	0.0413	1.1822	0.19	-0.1575	0.0034	0.3722	0.017	-0.0253	0.3956	0.0291	0.3623	13.5631	38.1462	16.6615
4	0.6033	0.4195	0.4751	0.432	0.135	1.3556	-0.1071	-0.4766	-0.1979	0.1867	0.0541	-0.0228	0.4947	0.7746	0.2084	1.1428	0.5175	0.2272	0.6532	-0.1732	-0.004	14.8728	36.1156	27.0272
5	2.552	0.1125	2.8275	0.8347	0.7334	7.3167	0.2032	-1.2846	-0.5871	0.8202	0.251	0.0849	1.0274	-1.5432	0.0103	0.3828	0.024	0.0233	0.3536	0.0403	0.3062	12.2988	33.6962	19.2824
6	1.0821	-1.0732	0.2957	1.0082	-0.3247	0.6864	0.0105	0.1031	-0.141	0.0152	0.0718	0.088	-0.1986	-0.6594	0.0118	0.2022	-0.0209	-0.0132	0.2343	-0.0104	0.2448	10.8423	43.6271	8.0941
7	1.5243	0.727	-0.6063	1.2282	0.9495	1.9952	-0.6821	0.673	1.1646	-0.1782	-0.2232	1.6048	-1.4454	-0.6976	-0.115	0.5895	-0.0261	-0.1417	0.2678	0.0039	0.4618	17.0828	60.2584	7.4434
8	0.3759	0.5045	0.2639	0.7559	0.7728	1.4606	-0.1541	-0.0655	0.2173	-0.5046	-0.0787	0.5532	-0.827	-0.1833	0.0002	0.2208	-0.0119	-0.0172	0.2042	-0.0136	0.2537	13.144	48.4243	10.7049
9	0.3597	-0.1366	1.203	5.8291	1.1964	5.0414	0.5907	-0.5316	0.0452	0.4593	-0.3561	1.2042	0.4246	-1.5808	0.5306	0.1016	0.0155	0.0404	0.4212	-0.077	0.4117	4.3132	44.6734	10.796
10	0.2966	0.1056	0.0565	0.5728	0.2883	0.2121	0.2941	-0.7541	0.2961	0.1771	-0.2991	0.1986	-0.2008	-0.0733	0.0031	0.244	-0.0262	-0.0226	0.2109	-0.0478	0.2654	19.6089	53.6399	14.1195
11	0.8897	0.8565	-0.2691	1.5862	0.9832	2.0568	-0.1105	-0.3367	0.3934	0.6387	0.7727	-1.2944	-0.115	1.2759	0.1836	0.3015	-0.0697	-0.0184	0.3941	-0.022	0.4879	27.5276	46.7135	12.5128
12	1.8513	-1.3992	1.1541	3.1075	-0.1381	1.0104	0.1207	0.0002	-2.0507	-1.5078	-0.4491	-1.4242	1.4554	1.145	-0.0274	0.463	0.0993	0.1284	0.3654	0.08	0.5828	27.1603	31.4911	11.5607
13	0.1013	0.0245	-0.0657	0.188	-0.1658	0.1477	0.6309	0.1032	-0.4685	-1.6928	0.019	-1.1812	-0.0733	-0.0543	0.0072	0.8118	0.1487	-0.1273	0.4498	-0.0739	0.5523	22.1605	27.9529	11.0411
14	0.4497	-0.083	-0.2379	0.3929	-0.2639	0.5433	-0.1044	0.1367	-0.333	-0.6132	-0.2048	-0.0386	0.2414	0.4883	-0.0027	0.248	0.0188	-0.0378	0.2005	-0.0426	0.2929	21.3957	35.4837	9.4801
15	1.7003	-0.3007	0.4465	0.3253	0.4205	1.0898	0.406	-0.5333	-0.6423	0.9394	-0.1808	-1.236	-0.2226	1.0557	-0.0425	0.2735	-0.151	-0.0898	0.3432	-0.0114	0.4485	27.0357	46.5735	17.4046
16	0.1857	-0.6692	-0.809	2.8777	3.262	3.7407	-0.4039	-0.7001	0.0172	2.2855	0.084	-0.3777	-0.0389	-0.4995	-0.3634	0.5622	-0.0223	-0.1966	0.3536	0.031	0.3352	23.7915	43.7322	20.975
17	2.0712	-0.5305	-0.8112	1.6291	-0.6848	0.8193	-0.0424	0.9904	-0.692	-0.1733	0.3483	0.214	0.1633	0.5123	0.02	0.2428	-0.0145	-0.0477	0.3077	-0.0943	0.3256	15.5513	35.6693	6.9825
18	1.4732	-0.2596	-1.272	6.6968	0.803	1.1835	-0.1844	0.4726	-0.6768	-1.8972	-0.0958	-0.0958	0.5941	-0.3411	-0.0462	0.4694	-0.0016	0.1077	0.3588	-0.0538	0.3694	22.5557	37.2328	-0.1901
19	0.7216	0.3254	-0.3684	0.5196	0.2632	0.5526	-0.1322	0.2391	0.0747	-0.8478	0.1647	-0.8285	-0.4021	0.2375	0.0019	0.3271	-0.0684	0.0296	0.3419	0.0104	0.2705	25.2619	46.6383	2.8318
20	3.9713	-0.039	-3.4825	1.6016	-3.768	1.998	-0.2377	0.6223	0.6961	-0.5205	0.4055	-1.536	-0.5585	2.5492	0.2539	0.3447	-0.1652	0.1128	0.4374	-0.0442	0.45	27.7627	52.3832	6.7676

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 21:24)
2	X-RAY DIFFRACTION	2	(chain A and resid 25:28)
3	X-RAY DIFFRACTION	3	(chain A and resid 29:32)
4	X-RAY DIFFRACTION	4	(chain A and resid 33:36)
5	X-RAY DIFFRACTION	5	(chain A and resid 37:42)
6	X-RAY DIFFRACTION	6	(chain A and resid 43:49)
7	X-RAY DIFFRACTION	7	(chain A and resid 50:57)
8	X-RAY DIFFRACTION	8	(chain A and resid 58:62)
9	X-RAY DIFFRACTION	9	(chain A and resid 63:70)
10	X-RAY DIFFRACTION	10	(chain A and resid 71:77)
11	X-RAY DIFFRACTION	11	(chain A and resid 78:83)
12	X-RAY DIFFRACTION	12	(chain A and resid 84:87)
13	X-RAY DIFFRACTION	13	(chain A and resid 88:91)
14	X-RAY DIFFRACTION	14	(chain A and resid 92:95)
15	X-RAY DIFFRACTION	15	(chain A and resid 96:100)
16	X-RAY DIFFRACTION	16	(chain A and resid 101:105)
17	X-RAY DIFFRACTION	17	(chain A and resid 106:113)
18	X-RAY DIFFRACTION	18	(chain A and resid 114:120)
19	X-RAY DIFFRACTION	19	(chain A and resid 121:127)
20	X-RAY DIFFRACTION	20	(chain A and resid 128:131)

-
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