PDB-3hie: Structure of the membrane-binding domain of the Sec3 subunit of t...

ID or keywords:

Entry

Database: PDB / ID: 3hie

Title

Structure of the membrane-binding domain of the Sec3 subunit of the Exocyst complex

Components

Exocyst complex component SEC3

Keywords

EXOCYTOSIS / PH domain / dimer / domain swapping / phosphate-binding / Coiled coil / Phosphoprotein / Protein transport / Transport / LIPID BINDING PROTEIN

Function / homology

Function and homology information

exocyst assembly / exocyst localization / endoplasmic reticulum inheritance / exocyst / prospore membrane / incipient cellular bud site / cellular bud tip / Golgi to plasma membrane transport / cellular bud neck / mating projection tip ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2 Å

Authors

Baek, K. / Dominguez, R.

Citation

Journal: J.Biol.Chem. / Year: 2010
Title: Structure-function study of the N-terminal domain of exocyst subunit Sec3.
Authors: Baek, K. / Knodler, A. / Lee, S.H. / Zhang, X. / Orlando, K. / Zhang, J. / Foskett, T.J. / Guo, W. / Dominguez, R.

History

Deposition	May 19, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 23, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3hie.cif.gz	276.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3hie.ent.gz	232.8 KB	Display	PDB format
PDBx/mmJSON format	3hie.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/hi/3hie ftp://data.pdbj.org/pub/pdb/validation_reports/hi/3hie	HTTPS FTP

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Related structure data

Similar structure data	4je8-d 1zy0-d 4je7-d 6u9m-d 5l9k-d 3bxl-2 1zy1-d 6nxw-2 6jmg-1 4yxg-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

Deposited unit

A: Exocyst complex component SEC3

B: Exocyst complex component SEC3

C: Exocyst complex component SEC3

D: Exocyst complex component SEC3

hetero molecules

80.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Exocyst complex component SEC3

B: Exocyst complex component SEC3

hetero molecules

defined by author&software
40.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Exocyst complex component SEC3

D: Exocyst complex component SEC3

defined by author&software
40.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	40.697, 68.486, 68.036
Angle α, β, γ (deg.)	89.90, 82.17, 71.79
Int Tables number	1
Space group name H-M	P1

#1: Protein	Exocyst complex component SEC3 / Protein PSL1 Mass: 20083.654 Da / Num. of mol.: 4 / Fragment: UNP residues 71-241, Membrane-binding domain Source method: isolated from a genetically manipulated source Details: glutathione-S-transferase (GST) fusion Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SEC3, PSL1, YER008C / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33332
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.22 Å³/Da / Density % sol: 44.58 %
Crystal grow	Temperature: 293 K / pH: 7.5 Details: 0.1M Bicine, pH9.5, 14% PEG 5000 MME, 1mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
3	100	1
4	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength
SYNCHROTRON	APS	17-BM	1	1
SYNCHROTRON	APS	17-BM	2	0.9796
SYNCHROTRON	APS	17-BM	3	0.9798
SYNCHROTRON	APS	17-BM	4	0.974

Detector

Type	ID	Detector	Date
MAR CCD 165 mm	1	CCD	Oct 20, 2008
MAR CCD 165 mm	2	CCD	Oct 20, 2008
MAR CCD 165 mm	3	CCD	Oct 20, 2008
MAR CCD 165 mm	4	CCD	Oct 20, 2008

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	MAD	M	x-ray	1
3	MAD	M	x-ray	1
4	MAD	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1	1
2	0.9796	1
3	0.9798	1
4	0.974	1

Reflection

Resolution: 2→50 Å / Num. all: 46605 / Num. obs: 43622 / % possible obs: 93.6 % / Observed criterion σ(I): 0 / Redundancy: 10.1 % / B_iso Wilson estimate: 41.7 Å² / R_merge(I) obs: 0.069 / R_sym value: 0.053 / Net I/σ(I): 24.6

Reflection shell

Resolution: 2→2.07 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.52 / Mean I/σ(I) obs: 1.5 / R_sym value: 0.52 / % possible all: 62.7

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
SnB		phasing
PHENIX	(phenix.refine)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 2→38.74 Å / SU ML: 0.35 / Isotropic thermal model: Anisotropic / σ(F): 1.96 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.248	2203	5.05 %
R_work	0.202	-	-
obs	0.204	43585	93.5 %
all	-	43624	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 55.13 Å² / k_sol: 0.31 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.4722 Å²	0.6602 Å²	-0.9418 Å²
2-	-	1.3535 Å²	-0.6486 Å²
3-	-	-	1.1187 Å²

Refinement step

Cycle: LAST / Resolution: 2→38.74 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5357	0	10	249	5616

Refine LS restraints

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	f_bond_d	0.025
X-RAY DIFFRACTION	f_angle_d
X-RAY DIFFRACTION	f_dihedral_angle_d	21.689
X-RAY DIFFRACTION	f_chiral_restr
X-RAY DIFFRACTION	f_plane_restr

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 (%)
2-2.0436	0.3737	81	0.3298	1432	X-RAY DIFFRACTION	52
2.0436-2.0911	0.3548	119	0.3038	2180	X-RAY DIFFRACTION	79
2.0911-2.1434	0.3102	144	0.2895	2521	X-RAY DIFFRACTION	90
2.1434-2.2013	0.3255	140	0.2789	2555	X-RAY DIFFRACTION	94
2.2013-2.2661	0.2865	142	0.267	2706	X-RAY DIFFRACTION	97
2.2661-2.3392	0.3076	156	0.267	2647	X-RAY DIFFRACTION	98
2.3392-2.4228	0.3176	136	0.2634	2727	X-RAY DIFFRACTION	98
2.4228-2.5198	0.3218	149	0.263	2702	X-RAY DIFFRACTION	98
2.5198-2.6345	0.3151	149	0.2563	2713	X-RAY DIFFRACTION	98
2.6345-2.7733	0.297	142	0.2439	2711	X-RAY DIFFRACTION	98
2.7733-2.947	0.2863	131	0.2315	2763	X-RAY DIFFRACTION	98
2.947-3.1745	0.2785	145	0.224	2718	X-RAY DIFFRACTION	99
3.1745-3.4938	0.2533	146	0.1897	2727	X-RAY DIFFRACTION	99
3.4938-3.9989	0.2149	138	0.1699	2779	X-RAY DIFFRACTION	99
3.9989-5.0364	0.1676	148	0.1389	2726	X-RAY DIFFRACTION	99
5.0364-38.7488	0.2024	137	0.1657	2775	X-RAY DIFFRACTION	100

Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

ID	Method	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	refined	-0.3618	0.7075	-0.8693	1.1256	-0.6852	4.5878	-0.0718	-0.1767	0.6238	-0.0938	-0.2956	-0.4787	0.0293	-0.1867	0.1908	0.1111	-0.0391	0.004	0.1748	0.0316	0.2548	-2.3036	-12.0192	14.4202
2		2.0578	-0.0613	-0.2058	1.8749	-0.0959	1.5253	-0.0034	-0.1233	0.485	0.1212	-0.0051	-0.1182	-0.1803	0.0232	-0.1409	0.029	-0.0313	-0.0079	0.0246	-0.0368	0.1189
3		-0.7298	0.0756	0.5784	4.1327	-0.6513	1.3545	0.079	-0.004	0.6411	0.0077	-0.111	-0.8117	0.004	0.2552	0.1724	0.0734	-0.0266	-0.0364	0.0989	0.0386	0.2207
4		1.7052	-1.7239	0.8811	6.2497	0.9888	1.088	0.1632	-0.5083	0.3374	-0.0616	-0.2399	-0.7542	-0.1338	0.2805	-0.0598	0.0706	-0.0029	-0.0108	0.0859	0.0224	0.1923
5		1.8924	0.1765	-0.1166	2.2584	0.0658	1.2479	0.041	-0.1267	0.0953	0.0204	0.0065	-0.1099	0.0718	-0.0953	-0.0233	0.0506	0.0003	0.0143	0.0337	-0.0032	0.0554
6		0.2402	0.2203	0.0337	2.2272	0.3198	0.3133	-0.0352	-0.1216	-0.1541	0.2441	-0.0092	-0.4191	-0.2273	-0.2121	0.1833	0.297	-0.0279	0.0053	0.0986	0.0373	0.1269
7		2.4894	-0.5183	0.4148	1.8021	-1.0611	0.975	0.7647	-0.4394	-0.5972	-0.0254	-0.4265	-0.0487	0.2631	0.1063	-0.1657	0.5467	-0.1032	-0.0069	0.1981	0.01	0.1471
8		2.045	-0.8641	0.1968	1.1429	0.5377	1.4236	-0.1158	0.4818	-0.1852	-0.2339	-0.2733	0.0385	0.5145	0.0581	0.1777	0.3191	-0.0939	0.0128	0.1401	-0.026	0.1193
9		4.6017	2.3709	1.1958	-0.2367	0.4881	0.629	-0.2482	-0.1749	-0.3317	-0.0599	-0.006	-0.3514	0.509	-0.0595	0.1927	0.2888	-0.0199	0.0743	0.029	-0.0508	0.2514
10		0.9496	-0.2331	0.1425	0.3904	0.799	0.7238	0.0919	0.0856	-0.8308	-0.1391	-0.0291	-0.9646	0.632	0.0602	0.1825	0.421	-0.0856	0.0151	0.1126	-0.0367	0.281
11		1.1548	0.2651	0.6338	2.9999	0.7337	1.6461	0.0807	0.0005	0.0815	-0.2611	-0.1608	-0.0971	0.1388	-0.1759	0.0848	0.1879	-0.0126	0.0319	0.0747	-0.0231	0.0466
12		-0.7212	1.5735	0.2046	2.316	2.0442	0.2213	0.2103	0.1513	-0.1436	-0.0869	-0.1177	-0.1008	-0.1858	-0.2147	-0.0518	0.1457	0.0063	0.0448	0.138	-0.0026	0.1681
13		0.7215	-0.7456	3.8455	1.0863	-0.0369	5.2085	0.0845	-0.2013	0.1124	-0.2937	0.0004	0.3398	-0.8699	0.3622	0.0782	0.6371	0.0205	0.1932	0.7177	-0.0315	0.6989
14		-0.0213	0.3197	-0.2988	0.7399	-1.4708	1.1545	0.2036	0.132	0.1488	-0.0135	-0.0838	0.1571	-0.2726	0.0361	0.0501	0.2754	0.0234	-0.0259	0.2287	0.0256	0.2906
15		3.1941	1.4103	0.7746	1.1082	-0.1354	0.6436	0.1387	-0.012	0.6368	-0.0897	-0.1388	0.0883	-0.3393	-0.1698	-0.0572	0.3561	-0.0097	-0.0915	0.2063	0.1336	0.2649
16		1.0818	0.8112	0.522	1.7048	-0.3469	0.9751	-0.0013	0.3191	0.5972	-1.2746	0.3434	0.4877	0.0159	-0.1178	-0.0687	0.3055	0.0195	-0.1123	0.2726	0.1249	0.2959
17		1.2464	0.0246	-0.1707	2.7421	-1.0595	0.8556	-0.0085	0.0946	0.1461	0.0396	-0.1062	-0.0859	-0.0895	0.1148	0.0925	0.2509	-0.0473	-0.0296	0.2132	0.0063	0.0691
18		1.1161	0.5643	1.5073	0.361	-1.3367	-1.0881	0.6166	-0.1749	-0.9694	-0.0393	0.5414	0.0509	2.1178	0.5068	-0.2209	0.9973	-0.2544	-0.1195	0.7694	-0.1206	0.6475
19		0.8348	1.0281	-1.5412	0.7909	-0.2789	1.5237	-0.2342	0.1373	-0.2023	-0.0603	0.3027	0.297	0.2725	-0.3066	0.0043	0.1848	-0.0791	-0.0271	0.2292	0.0688	0.2055
20		0.1419	0.328	0.5049	1.2235	-1.1658	3.179	0.0035	-0.0383	0.0042	0.136	0.149	0.1958	-0.137	-0.2802	-0.1341	0.1364	0.0207	0.0689	0.1747	0.0203	0.1112

Refinement TLS group

Selection details: CHAIN D AND RESI 161:241

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