PDB-5ubp: TREX2 M-region

ID or keywords:

Entry

Database: PDB / ID: 5ubp

Title

TREX2 M-region

Components

26S proteasome complex subunit SEM1Proteasome
Leucine permease transcriptional regulator
Nuclear mRNA export protein THP1

Keywords

TRANSCRIPTION / TREX2 complex / TPR repeats

Function / homology

Function and homology information

cellular bud site selection / SAGA complex localization to transcription regulatory region / transcription export complex 2 / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear mRNA surveillance / maintenance of DNA trinucleotide repeats / filamentous growth / mRNA 3'-end processing / proteasome regulatory particle, lid subcomplex / poly(A)+ mRNA export from nucleus ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae RM11-1a (yeast)

Saccharomyces cerevisiae S288c (yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Stewart, M. / Gordon, J.

Funding support

United Kingdom, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2017
Title: Structure of the Sac3 RNA-binding M-region in the Saccharomyces cerevisiae TREX-2 complex.
Authors: Gordon, J.M.B. / Aibara, S. / Stewart, M.

History

Deposition	Dec 21, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Apr 5, 2017	Provider: repository / Type: Initial release
Revision 1.1	May 31, 2017	Group: Database references
Revision 1.2	Sep 13, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5ubp.cif.gz	598.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5ubp.ent.gz	499.7 KB	Display	PDB format
PDBx/mmJSON format	5ubp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	3t5vS S: Starting model for refinement
Similar structure data	5l3t-d 5wqi-d 5g5p-d 30368 5m94-d 4eil-1 4kp5-d 4kya-3 6a2p-d 3c8w-d 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 (7) #172 - Apr 2014 RecA and Rad51 similarity (3)

Deposited unit

A: Leucine permease transcriptional regulator

B: Nuclear mRNA export protein THP1

C: 26S proteasome complex subunit SEM1

119 kDa, 3 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)	78.368, 86.634, 168.338
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Leucine permease transcriptional regulator Mass: 56163.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae RM11-1a (yeast) Gene: SCRG_00364 / Production host: Escherichia coli (E. coli) / References: UniProt: B3LGC5
#2: Protein	Nuclear mRNA export protein THP1 / Bud site selection protein 29 Mass: 52734.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: THP1, BUD29, YOL072W, O1140 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08231
#3: Protein	26S proteasome complex subunit SEM1 / Proteasome Mass: 10397.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: SEM1, DSH1, YDR363W-A / Production host: Escherichia coli (E. coli) / References: UniProt: O94742
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 546 / 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: 2.74 Å³/Da / Density % sol: 55.16 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20 % PEG3350, 0.17 M MgFormate

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 11, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.3→19.945 Å / Num. obs: 51644 / % possible obs: 99.9 % / Redundancy: 6.1 % / Net I/σ(I): 7.5
Reflection shell	Resolution: 2.3→2.37 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.9 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3T5V

3t5v

Resolution: 2.3→19.945 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.48 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2171	2607	5.06 %
R_work	0.1783	-	-
obs	0.1803	51550	99.94 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.3→19.945 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7983	0	0	546	8529

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	8194
X-RAY DIFFRACTION	f_angle_d	0.53	11100
X-RAY DIFFRACTION	f_dihedral_angle_d	11.888	5015
X-RAY DIFFRACTION	f_chiral_restr	0.037	1227
X-RAY DIFFRACTION	f_plane_restr	0.003	1435

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 (%)
2.3-2.3418	0.2996	128	0.2539	2533	X-RAY DIFFRACTION	100
2.3418-2.3868	0.3067	127	0.251	2537	X-RAY DIFFRACTION	100
2.3868-2.4354	0.2991	107	0.2363	2568	X-RAY DIFFRACTION	100
2.4354-2.4883	0.2666	148	0.2254	2530	X-RAY DIFFRACTION	100
2.4883-2.546	0.2675	140	0.2166	2537	X-RAY DIFFRACTION	100
2.546-2.6096	0.2691	119	0.2049	2553	X-RAY DIFFRACTION	100
2.6096-2.68	0.2438	134	0.2009	2543	X-RAY DIFFRACTION	100
2.68-2.7586	0.2628	125	0.2074	2571	X-RAY DIFFRACTION	100
2.7586-2.8474	0.2214	158	0.1998	2544	X-RAY DIFFRACTION	100
2.8474-2.9489	0.2672	141	0.2024	2552	X-RAY DIFFRACTION	100
2.9489-3.0666	0.2388	133	0.2007	2574	X-RAY DIFFRACTION	100
3.0666-3.2056	0.2422	141	0.1936	2554	X-RAY DIFFRACTION	100
3.2056-3.3738	0.2378	137	0.1859	2572	X-RAY DIFFRACTION	100
3.3738-3.5841	0.2281	121	0.1779	2606	X-RAY DIFFRACTION	100
3.5841-3.8589	0.1909	121	0.1615	2595	X-RAY DIFFRACTION	100
3.8589-4.2439	0.1867	151	0.1486	2594	X-RAY DIFFRACTION	100
4.2439-4.8503	0.1599	132	0.1288	2632	X-RAY DIFFRACTION	100
4.8503-6.082	0.1845	168	0.16	2616	X-RAY DIFFRACTION	100
6.082-19.9462	0.1901	176	0.1582	2732	X-RAY DIFFRACTION	100

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	5.9216	-0.0284	1.2969	3.7958	-0.9028	5.4733	0.1369	0.3926	0.8641	-0.7511	-0.0292	-0.782	-0.9405	0.1958	-0.1545	0.7121	-0.0303	0.1956	0.2803	-0.0578	0.5847	14.4226	16.3186	-2.5038
2	1.9978	0.7742	0.7195	4.0836	1.0696	1.8161	0.0455	-0.1169	0.2778	0.3126	0.0224	-0.6964	-0.2142	0.1201	-0.0581	0.3303	-0.0028	-0.0388	0.2366	0.011	0.3562	47.7045	-2.1742	-23.5357
3	2.5492	0.7897	-1.0325	3.9923	4.7751	7.3366	0.0284	-0.9614	-1.3663	0.1911	0.5156	-1.017	0.0042	0.8056	-0.6142	0.912	0.1255	-0.0398	0.7686	-0.2277	0.6447	43.5429	-28.0818	-28.9187
4	0.9595	0.4981	-0.4789	2.7088	0.9013	1.0307	-0.0188	0.0527	-0.0415	0.1496	-0.1414	0.2734	0.0486	-0.2005	0.1699	0.2032	0.002	0.0209	0.2813	-0.032	0.2068	21.8371	-22.9906	-26.3969
5	3.6698	0.8741	-0.3321	7.007	0.0908	4.5459	-0.166	0.0034	-0.4975	0.2524	-0.0998	-0.0482	0.7014	-0.0181	0.1738	0.3583	-0.0016	0.0802	0.2657	-0.0738	0.3258	29.3447	-46.7848	-29.6416
6	1.2941	2.1779	-0.3251	7.6947	-1.4568	2.6079	-0.2256	0.3125	-0.0347	-0.9305	0.1593	-0.3972	0.196	-0.0033	0.0583	0.3034	-0.0053	0.065	0.3248	-0.0156	0.1604	34.3306	-23.3697	-40.8346
7	1.6191	-0.1433	0.7107	4.6451	-0.7216	3.105	0.0995	-0.1571	0.2317	-0.0082	0.0104	-0.2561	-0.3669	0.0666	-0.0933	0.4212	0.0077	0.0882	0.2898	-0.1157	0.4625	11.7054	12.863	15.0467
8	1.177	-0.2161	0.6688	4.3546	-3.6629	8.7333	-0.0323	0.0351	0.0209	-0.1856	-0.022	-0.3611	-0.1509	0.1121	0.0925	0.2803	-0.016	0.0954	0.2041	-0.0783	0.446	13.9059	-1.8829	4.9013
9	0.4708	0.654	0.451	0.9813	0.5424	3.9739	-0.0466	-0.0008	-0.0924	-0.0279	-0.079	-0.0252	0.2227	-0.1411	0.1218	0.3101	0.0078	0.1131	0.3	-0.0842	0.4104	7.4369	-19.6062	1.5517
10	1.6555	-0.3876	-0.2218	2.1459	0.8807	1.3291	-0.1528	0.2875	-0.1929	-0.0381	-0.331	0.678	0.067	-0.7389	0.374	0.2487	-0.0494	0.0192	0.6317	-0.2414	0.5953	-1.966	-29.1753	-23.9761
11	1.9743	1.0765	-0.5539	3.9597	1.7869	1.6427	-0.129	0.3591	-0.4936	0.2023	-0.2482	0.6452	0.5712	-0.3824	0.178	0.3235	-0.1053	0.1011	0.5154	-0.2193	0.5959	7.5145	-41.9259	-27.8083
12	2.8767	-3.1907	-3.4546	3.5694	3.6741	4.9998	0.5004	1.8421	-1.6151	-1.3801	-0.0933	-0.1196	0.9314	-2.0418	-0.3725	1.1212	-0.1267	-0.0144	0.9421	-0.3329	0.6726	6.9275	-30.5856	1.7461
13	3.869	-3.4149	-2.5055	8.79	3.6215	6.2264	0.3215	0.4602	1.6006	-0.2076	-0.0757	0.2716	0.0432	0.2114	-0.1865	0.9054	0.0485	-0.259	1.0865	0.0796	1.2703	-3.3545	-4.3254	-12.3041
14	7.5335	3.3817	-2.7669	3.4701	0.7597	3.0704	0.4681	0.2633	0.7031	-0.4068	-0.1212	1.4383	-0.0947	0.4485	-0.2736	0.4357	-0.0068	0.0506	0.4218	-0.0624	0.5163	0.4144	-10.3334	-7.2917
15	4.348	-0.301	-5.3794	0.1219	-0.0278	8.4406	-0.1143	-0.6751	-0.0159	1.0808	-0.6561	2.1643	0.4963	-1.0515	0.7117	0.4956	0.0637	0.1201	1.0859	-0.0571	0.8626	-7.8723	-17.8566	0.6641
16	0.2269	0.5157	-0.6113	1.7059	-1.8312	2.0224	-0.8013	0.8339	-1.7721	-0.5696	0.516	0.2685	1.0571	-1.646	0.3855	0.6229	-0.3121	0.4805	1.4458	-0.4636	1.4907	-10.2368	-38.3119	-20.2062
17	7.2618	-1.6499	0.6001	2.9894	-2.5161	2.2262	-0.1015	0.6764	-0.0793	-0.7809	-0.3602	0.8516	0.1948	-0.3947	0.1446	0.4254	-0.1228	-0.178	1.1334	-0.5066	1.0661	-6.0422	-43.9671	-41.6657

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 82:125)
2	X-RAY DIFFRACTION	2	(chain A and resid 126:324)
3	X-RAY DIFFRACTION	3	(chain A and resid 325:331)
4	X-RAY DIFFRACTION	4	(chain A and resid 332:465)
5	X-RAY DIFFRACTION	5	(chain A and resid 466:524)
6	X-RAY DIFFRACTION	6	(chain A and resid 525:547)
7	X-RAY DIFFRACTION	7	(chain B and resid 1:86)
8	X-RAY DIFFRACTION	8	(chain B and resid 87:160)
9	X-RAY DIFFRACTION	9	(chain B and resid 161:252)
10	X-RAY DIFFRACTION	10	(chain B and resid 253:382)
11	X-RAY DIFFRACTION	11	(chain B and resid 383:448)
12	X-RAY DIFFRACTION	12	(chain B and resid 449:455)
13	X-RAY DIFFRACTION	13	(chain C and resid 27:31)
14	X-RAY DIFFRACTION	14	(chain C and resid 32:36)
15	X-RAY DIFFRACTION	15	(chain C and resid 37:59)
16	X-RAY DIFFRACTION	16	(chain C and resid 60:71)
17	X-RAY DIFFRACTION	17	(chain C and resid 72:89)

-
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