PDB-3t5v: Sac3:Thp1:Sem1 complex

ID or keywords:

Entry

Database: PDB / ID: 3t5v

Title

Sac3:Thp1:Sem1 complex

Components

26S proteasome complex subunit SEM1Proteasome
Nuclear mRNA export protein SAC3
Nuclear mRNA export protein THP1

Keywords

TRANSCRIPTION / PCI / mRNA nuclear export /

mRNA / nuclear

Function / homology

Function and homology information

actin filament-based process / 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 pore cytoplasmic filaments / nuclear mRNA surveillance / maintenance of DNA trinucleotide repeats / filamentous growth / mRNA 3'-end processing ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.9 Å

Authors

Stewart, M. / Ellisdon, A.M.

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structural basis for the assembly and nucleic acid binding of the TREX-2 transcription-export complex.
Authors: Ellisdon, A.M. / Dimitrova, L. / Hurt, E. / Stewart, M.

History

Deposition	Jul 28, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 22, 2012	Provider: repository / Type: Initial release
Revision 1.1	Mar 21, 2012	Group: Database references
Revision 1.2	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	3t5v.cif.gz	616.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3t5v.ent.gz	518.6 KB	Display	PDB format
PDBx/mmJSON format	3t5v.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/t5/3t5v ftp://data.pdbj.org/pub/pdb/validation_reports/t5/3t5v	HTTPS FTP

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Related structure data

Related structure data	3t5xC C: citing same article (ref.)
Similar structure data	1x7x-d 6v9l-d 4do4-d 2bfc-d 1lei-d 1v1m-d 6h57-d 2bfb-d 2bfe-d 5jub-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
Related items in Molecule of the Month	#166 - Oct 2013 Proteasome similarity (7) #172 - Apr 2014 RecA and Rad51 similarity (3)

Deposited unit

A: Nuclear mRNA export protein SAC3

B: Nuclear mRNA export protein THP1

C: 26S proteasome complex subunit SEM1

D: Nuclear mRNA export protein SAC3

E: Nuclear mRNA export protein THP1

F: 26S proteasome complex subunit SEM1

200 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Nuclear mRNA export protein SAC3

B: Nuclear mRNA export protein THP1

C: 26S proteasome complex subunit SEM1

defined by author&software
100 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Nuclear mRNA export protein SAC3

E: Nuclear mRNA export protein THP1

F: 26S proteasome complex subunit SEM1

defined by author&software
100 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	164.770, 164.770, 276.790
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	91
Space group name H-M	P4₁22

#1: Protein	Nuclear mRNA export protein SAC3 / Leucine permease transcriptional regulator Mass: 36944.461 Da / Num. of mol.: 2 / Fragment: M region, UNP 250-563 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: LEP1, SAC3, YD8358.13, YDR159W / Production host: Escherichia coli (E. coli) / References: UniProt: P46674
#2: Protein	Nuclear mRNA export protein THP1 / Bud site selection protein 29 Mass: 52734.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: BUD29, O1140, THP1, YOL072W / Production host: Escherichia coli (E. coli) / References: UniProt: Q08231
#3: Protein	26S proteasome complex subunit SEM1 / Proteasome Mass: 10397.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: DSH1, SEM1, YDR363W-A / Production host: Escherichia coli (E. coli) / References: UniProt: O94742

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.69 Å³/Da / Density % sol: 73.79 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: see publication, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2011
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.9→20 Å / Num. all: 84626 / Num. obs: 84626 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / R_merge(I) obs: 0.164 / Net I/σ(I): 7.4
Reflection shell	Resolution: 2.9→3.06 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
SHARP		phasing
REFMAC	5.6.0116	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.9→20 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.938 / SU B: 28.693 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.425 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23089	4224	5 %	RANDOM
R_work	0.20836	-	-	-
obs	0.2095	80336	99.59 %	-
all	-	84626	-	-

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: 38.991 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.09 Å²	0 Å²	0 Å²
2-	-	-0.09 Å²	0 Å²
3-	-	-	0.18 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13175	0	0	0	13175

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	13475
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	9186
X-RAY DIFFRACTION	r_angle_refined_deg	0.908	1.956	18265
X-RAY DIFFRACTION	r_angle_other_deg	3.191	3	22395
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.928	5	1589
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.157	24.419	688
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.632	15	2414
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.72	15	84
X-RAY DIFFRACTION	r_chiral_restr	0.053	0.2	2035
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	14757
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	2743
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.9→2.974 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.366	258	-
R_work	0.332	5363	-
obs	-	-	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	1.7	-0.2821	0.619	1.8969	1.1901	2.551	0.089	0.0223	0.1038	0.0393	0.1883	0.3237	0.208	-0.1052	-0.2773	0.2737	-0.0178	-0.0921	0.1728	0.0351	0.4185	-5.8656	-18.7565	-33.8552
2	0.255	-0.0068	0.368	0.6919	-0.0119	1.1467	0.0079	-0.1121	0.1269	-0.0621	0.0254	0.1444	0.3322	0.1034	-0.0333	0.3482	0.0507	-0.0528	0.2652	-0.0616	0.3615	10.6906	-30.4986	-24.3798
3	2.4599	0.2173	-0.3989	1.1437	0.0516	1.3208	0.0404	-0.4302	0.2754	0.0233	0.0772	0.0346	0.1324	0.1273	-0.1176	0.2139	0.05	-0.0165	0.4493	-0.1767	0.2845	20.067	-17.2021	-2.9021
4	1.2934	1.4283	-0.5572	3.1299	-0.7426	0.8015	-0.0194	-0.0698	0.2303	-0.307	0.1861	-0.1181	-0.1694	0.2504	-0.1667	0.2479	-0.0251	0.0178	0.3133	-0.0732	0.4352	9.4603	-14.1736	-27.4837
5	0.9297	0.0398	-0.5748	1.4991	-0.2369	3.4397	-0.2086	-0.0085	-0.1236	0.0008	0.0505	0.2637	0.1889	-0.6326	0.1581	0.4903	-0.1491	0.0717	0.248	-0.0356	0.2286	-13.2115	-69.2596	-32.6852
6	2.0668	1.2842	-0.3858	0.9287	0.2077	1.8328	-0.1243	-0.1757	-0.0538	0.104	-0.0695	-0.0439	0.6664	0.0372	0.1938	0.7263	0.1438	0.0235	0.1068	0.004	0.2058	12.7837	-60.0564	-18.0285
7	1.209	0.2885	-0.1251	0.7987	0.0756	0.2199	-0.0726	-0.2877	0.0074	-0.0852	0.0337	-0.1269	0.246	0.2331	0.0389	0.396	0.2272	-0.0203	0.4261	-0.0348	0.2563	32.4917	-36.4039	-15.1355
8	4.9819	11.8738	-6.7715	29.7783	-16.5777	9.3346	0.5368	-0.1214	-0.3743	0.573	-1.0284	-0.8102	-0.5315	0.3918	0.4916	0.8616	0.1648	-0.0621	0.5477	-0.0027	0.4109	8.5882	-58.7051	-4.5997
9	5.2335	0.7948	5.1934	3.0821	2.507	6.1725	0.0516	-0.0105	-0.1785	0.2384	-0.4051	0.9198	0.3481	-0.1695	0.3535	0.9601	0.1907	0.1576	0.1944	-0.0513	0.3366	10.4149	-58.3395	-31.3969
10	0.9622	1.3448	3.4211	2.0351	5.0428	12.6306	0.2684	-0.4413	0.0633	-0.0092	-0.6203	0.0849	0.2909	-1.5199	0.3519	1.0492	0.0135	0.0161	0.5778	0.3268	0.5822	28.225	-62.9919	-9.6435
11	0.0099	-0.0542	-0.0606	0.3751	0.4292	0.4991	-0.0009	0.008	0.0366	-0.0574	-0.0075	-0.0259	-0.0276	0.0312	0.0085	0.3271	0.1143	-0.0248	0.6549	0.1077	0.5739	41.5963	-49.8573	-12.8225
12	2.9475	5.6733	-2.5949	24.3195	0.826	4.8962	-0.0068	-0.376	-0.0433	0.7471	0.3423	-0.5216	0.2884	0.9536	-0.3355	0.1322	0.2051	0.0097	0.6056	-0.1127	0.4469	49.5966	-32.7476	-16.6401
13	1.0455	-0.1732	-1.0465	3.0651	-1.742	2.2788	-0.1424	0.0358	0.0578	0.0016	0.0802	-0.1745	0.0507	-0.1114	0.0623	0.6202	0.0022	0.013	0.0699	-0.0241	0.2182	-0.8264	-103.8509	-75.2073
14	3.7497	0.1573	-0.4437	0.5111	0.8362	1.9427	-0.2738	0.1951	0.2421	-0.0041	0.1547	-0.1186	-0.0825	0.2995	0.1191	0.6025	-0.0039	-0.0426	0.0688	0.0416	0.3633	-0.7188	-103.3405	-59.0316
15	0.6676	0.067	0.1644	1.2945	-0.3837	0.3525	-0.223	-0.0116	-0.2255	0.069	0.0145	-0.1608	-0.1702	-0.0127	0.2085	0.478	0.0629	0.0887	0.1261	0.037	0.3856	-1.0772	-124.9607	-50.9712
16	2.1049	-0.306	1.6118	0.9323	-0.3948	2.347	-0.1341	0.1063	-0.1028	-0.1759	-0.0373	-0.1662	0.0218	-0.0918	0.1714	0.5109	0.0095	0.096	0.1029	-0.0058	0.2596	-2.6943	-120.3662	-64.8028
17	1.4699	0.6441	0.2422	1.5432	-0.1023	1.4201	0.1024	0.0245	-0.0561	-0.075	-0.1315	-0.1309	-0.0287	0.2648	0.0291	0.4811	-0.0852	-0.0314	0.1667	0.0354	0.2469	14.2736	-67.9927	-47.4399
18	1.6176	0.3797	-0.0223	2.8435	-0.1722	0.3545	-0.018	-0.1187	0.0974	0.0598	-0.1108	-0.3927	0.1469	0.2294	0.1288	0.6294	0.0556	-0.1943	0.1654	0.0606	0.3078	13.6135	-92.3587	-33.4476
19	0.5032	0.7014	-0.1036	1.1168	-0.1357	0.7504	-0.0165	-0.1607	-0.1085	0.1751	-0.1219	-0.0478	-0.1527	-0.055	0.1384	0.5717	0.1424	0.0067	0.1878	0.0576	0.2335	-8.1736	-117.1453	-31.5247
20	15.0625	0.6907	-0.6097	0.0449	-0.0194	0.1486	-0.3667	-0.4413	-0.3763	-0.0764	0.0485	0.0038	-0.1953	-0.0483	0.3183	1.0164	0.1119	-0.3662	0.5526	-0.0818	0.7713	18.7081	-103.081	-29.1496
21	6.5532	11.5182	3.6988	24.4278	15.1905	20.7607	0.0513	-0.0872	0.5183	-0.5509	-0.3717	0.6675	-0.9788	-0.5732	0.3204	0.6543	0.0297	0.0311	0.0159	-0.0055	0.5549	2.27	-86.391	-31.0738
22	3.7654	-1.0975	-0.2986	0.3326	0.0836	0.0358	0.1102	-0.265	0.74	-0.0442	-0.0014	-0.2284	-0.0641	0.0423	-0.1088	1.1446	-0.1027	-0.1425	0.4717	0.0895	0.587	5.8519	-102.0765	-15.3419
23	0.0264	-0.1764	0.0464	1.6663	-0.4884	0.1613	0.0456	0.0146	0.002	0.1344	-0.1917	-0.1977	-0.0535	0.0354	0.1461	0.5123	-0.028	-0.0175	0.4846	-0.0337	0.4539	-8.2492	-116.3786	-17.3177
24	5.7733	2.21	-1.4545	14.8305	9.072	7.0162	-0.0895	-0.2173	-0.1489	1.0975	-0.0766	0.2376	0.6898	0.0866	0.166	0.558	0.0757	0.1028	0.3059	0.0432	0.1452	-22.008	-131.0268	-26.5412

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	253 - 329
2	X-RAY DIFFRACTION	2	A	330 - 458
3	X-RAY DIFFRACTION	3	A	459 - 520
4	X-RAY DIFFRACTION	4	A	521 - 551
5	X-RAY DIFFRACTION	5	B	2 - 167
6	X-RAY DIFFRACTION	6	B	168 - 303
7	X-RAY DIFFRACTION	7	B	304 - 449
8	X-RAY DIFFRACTION	8	B	450 - 455
9	X-RAY DIFFRACTION	9	C	23 - 42
10	X-RAY DIFFRACTION	10	C	53 - 63
11	X-RAY DIFFRACTION	11	C	64 - 71
12	X-RAY DIFFRACTION	12	C	72 - 89
13	X-RAY DIFFRACTION	13	D	253 - 326
14	X-RAY DIFFRACTION	14	D	327 - 385
15	X-RAY DIFFRACTION	15	D	386 - 513
16	X-RAY DIFFRACTION	16	D	514 - 550
17	X-RAY DIFFRACTION	17	E	2 - 149
18	X-RAY DIFFRACTION	18	E	150 - 262
19	X-RAY DIFFRACTION	19	E	263 - 448
20	X-RAY DIFFRACTION	20	E	449 - 455
21	X-RAY DIFFRACTION	21	F	30 - 40
22	X-RAY DIFFRACTION	22	F	53 - 60
23	X-RAY DIFFRACTION	23	F	61 - 71
24	X-RAY DIFFRACTION	24	F	72 - 89

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