PDB-3zdm: Crystal structure of the Sgt2 N domain and the Get5 UBL domain complex

ID or keywords:

Entry

Database: PDB / ID: 3zdm

Title

Crystal structure of the Sgt2 N domain and the Get5 UBL domain complex

Components

SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT- CONTAINING PROTEIN 2
UBIQUITIN-LIKE PROTEIN MDY2

Keywords

CHAPERONE/SIGNALING PROTEIN / CHAPERONE-SIGNALING PROTEIN COMPLEX

Function / homology

Function and homology information

cell morphogenesis involved in conjugation with cellular fusion / TRC complex / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / protein insertion into ER membrane /

post-translational protein targeting to endoplasmic reticulum membrane / cytoplasmic stress granule / response to heat / molecular adaptor activity /

membrane / identical protein binding ...
Similarity search - Function

Biological species

SACCHAROMYCES CEREVISIAE (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.803 Å

Authors

Tung, J.-Y. / Li, Y.-C. / Hsiao, C.-D.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of the Sgt2 Dimerization Domain Complexed with the Get5 Ubl Domain Involved in the Targeting of Tail-Anchored Membrane Proteins to the Endoplasmic Reticulum.
Authors: Tung, J.-Y. / Li, Y.-C. / Lin, T.-W. / Hsiao, C.-D.

History

Deposition	Nov 29, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 2, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2013	Group: Database references
Revision 1.2	May 8, 2024	Group: Data collection / Database references / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3zdm.cif.gz	183.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3zdm.ent.gz	150.4 KB	Display	PDB format
PDBx/mmJSON format	3zdm.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/zd/3zdm ftp://data.pdbj.org/pub/pdb/validation_reports/zd/3zdm	HTTPS FTP

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Related structure data

Similar structure data	4xtw-d 3zu6-d 3r1j-d 4cvy-2 4z1f-d 4q3b-6 4xtv-d 5y3n-d 4q3a-6 4q3b-5 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	#141 - Sep 2011 O-GlcNAc Transferase similarity (6) #230 - Feb 2019 Initiation Factor eIF4E similarity (4) #166 - Oct 2013 Proteasome similarity (3)

Deposited unit

A: SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT- CONTAINING PROTEIN 2

B: SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT- CONTAINING PROTEIN 2

C: UBIQUITIN-LIKE PROTEIN MDY2

D: SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT- CONTAINING PROTEIN 2

E: SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT- CONTAINING PROTEIN 2

F: UBIQUITIN-LIKE PROTEIN MDY2

49 kDa, 6 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)	137.109, 34.127, 92.092
Angle α, β, γ (deg.)	90.00, 105.84, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-2021- HOH
2	1	D-2022- HOH

#1: Protein	SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT- CONTAINING PROTEIN 2 / SGT/UBP / VIRAL PROTEIN U-BINDING PROTEIN Mass: 7719.621 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-72 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q12118
#2: Protein	UBIQUITIN-LIKE PROTEIN MDY2 / GOLGI TO ER TRAFFIC PROTEIN 5 / MATING-DEFICIENT PROTEIN 2 / TRANSLATION MACHINERY-ASSOCIATED PROTEIN 24 Mass: 9053.587 Da / Num. of mol.: 2 / Fragment: UBIQUITIN-LIKE DOMAIN, RESIDUES 71-151 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q12285
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48 % / Description: NONE
Crystal grow	pH: 7 / Details: 0.1 M MIB BUFFER, PH 7.0 25% PEG 1500

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Data collection

Diffraction	Mean temperature: 287 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1.05584
Detector	Type: BRUKER SMART 6500 / Detector: CCD / Date: Oct 15, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.05584 Å / Relative weight: 1
Reflection	Resolution: 1.8→30 Å / Num. obs: 37569 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 7 % / B_iso Wilson estimate: 25.31 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 27.2
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 5.8 % / R_merge(I) obs: 0.43 / Mean I/σ(I) obs: 4.2 / % possible all: 97.2

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MAD
Starting model: NONE

Resolution: 1.803→28.467 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 45.5 / Stereochemistry target values: ML
Details: CHAIN A,D,RESIDUES 1, 71, 72 ARE DISORDERED. CHAIN B,E, RESIDUES 1, 52-72 ARE DISORDERED. CHAIN C,F, RESIDUES 71, 151 ARE DISORDERED.

	R_factor	Num. reflection	% reflection
R_free	0.2261	1788	5 %
R_work	0.1867	-	-
obs	0.1887	35615	92.49 %

Solvent computation

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

Displacement parameters

B_iso mean: 31.81 Å²

Refinement step

Cycle: LAST / Resolution: 1.803→28.467 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3036	0	0	456	3492

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	3074
X-RAY DIFFRACTION	f_angle_d	1.343	4132
X-RAY DIFFRACTION	f_dihedral_angle_d	14.641	1136
X-RAY DIFFRACTION	f_chiral_restr	0.087	492
X-RAY DIFFRACTION	f_plane_restr	0.006	524

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 (%)
1.8027-1.8514	0.4158	114	0.3336	2601	X-RAY DIFFRACTION	93
1.8514-1.9059	0.3101	151	0.2909	2681	X-RAY DIFFRACTION	96
1.9059-1.9674	0.3178	141	0.268	2685	X-RAY DIFFRACTION	97
1.9674-2.0377	0.2987	153	0.2283	2711	X-RAY DIFFRACTION	97
2.0377-2.1192	0.2548	141	0.2085	2702	X-RAY DIFFRACTION	97
2.1192-2.2156	0.268	146	0.1874	2692	X-RAY DIFFRACTION	97
2.2156-2.3324	0.2142	133	0.1667	2712	X-RAY DIFFRACTION	96
2.3324-2.4785	0.2367	136	0.1694	2677	X-RAY DIFFRACTION	95
2.4785-2.6697	0.2193	153	0.178	2663	X-RAY DIFFRACTION	95
2.6697-2.9381	0.213	136	0.18	2597	X-RAY DIFFRACTION	92
2.9381-3.3627	0.2045	124	0.1715	2487	X-RAY DIFFRACTION	88
3.3627-4.2344	0.1819	128	0.1551	2238	X-RAY DIFFRACTION	79
4.2344-28.471	0.2112	132	0.1835	2381	X-RAY DIFFRACTION	81

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	2.1344	-0.2421	0.2732	1.0865	0.1264	1.4091	0.2943	0.3356	1.06	-0.0585	-0.1195	0.0367	0.1429	0.1785	0.0475	0.0907	-0.0523	-0.0711	0.3161	-0.0509	-0.0481	-14.9124	-2.6645	25.6574
2	1.2069	0.1116	-0.319	0.4256	0.3506	0.8429	-0.1373	0.0532	-0.1856	0.031	-0.1077	0.0826	0.4086	-0.0427	-0.0768	0.1471	-0.0245	-0.0223	0.2308	-0.0472	0.0927	-19.0431	-9.1639	29.4137
3	3.7021	1.9419	-0.5791	7.5014	0.8266	1.0873	0.0279	-0.2754	0.7501	0.0486	0.2265	0.084	-0.1811	-0.3849	0.0931	0.2065	0.072	-0.0175	0.3464	0.0229	0.2546	-5.4456	1.9753	14.9311
4	3.739	-0.4708	2.5013	0.7223	-0.1973	3.181	-0.2769	-0.0246	0.8265	0.028	0.0311	0.0962	-0.4432	0.2266	0.1071	0.1979	-0.0296	-0.0068	0.192	-0.0034	0.334	-19.6949	6.4194	31.0161
5	4.127	-0.089	2.4334	1.5283	0.0287	3.8518	-0.0673	-0.3203	0.296	0.3198	0.1003	0.3565	-0.2617	-0.3162	0.0013	0.1287	-0.087	-0.0013	0.1303	-0.1526	0.2099	-27.5019	-0.4828	33.4389
6	3.7109	-1.0362	3.3532	2.4956	-1.2033	3.5488	0.0137	-0.263	0.5949	0.1839	-0.2157	0.3176	-0.8059	-0.5398	0.072	0.3917	0.068	-0.0192	0.4373	-0.1846	0.2402	-22.67	5.1542	42.4796
7	5.2182	4.3704	4.0164	5.8649	3.4653	4.5318	0.0513	0.033	-0.4725	-0.0059	0.0875	0.0755	0.4741	-0.0678	-0.0515	0.2251	-0.0896	0.0405	0.2682	-0.026	0.2148	-37.5376	-20.6193	36.5332
8	0.0777	0.1146	-0.3944	0.218	-0.2131	4.4227	-0.1241	-0.1123	0.0741	0.1084	0.0054	-0.1111	-0.0686	0.1288	-0.0022	0.7268	-0.0896	0.103	0.9468	-0.0943	0.434	-28.0215	-8.0333	45.3367
9	1.9146	0.544	1.8526	1.2613	0.315	2.5745	-0.007	-0.204	-0.3147	-0.1837	-0.1261	0.1931	0.4156	0.017	-0.1048	0.3251	-0.1244	0.0349	0.3302	0.0783	0.4413	-41.3127	-19.117	38.0529
10	1.4928	0.339	-0.7152	1.5129	-1.5357	3.7956	0.1413	-0.3719	-0.0194	0.2612	-0.1486	0.6913	-0.2016	-0.3529	-0.0121	-0.0843	0.0926	0.3997	0.2519	-0.1991	0.1208	-44.4243	-11.1136	39.2739
11	1.1156	-0.2631	-0.1261	1.69	-1.559	3.0971	-0.0455	-0.2052	-0.0797	0.3048	0.1423	0.3044	-0.0482	-0.2954	-0.051	0.6931	-0.306	0.4561	0.7272	-0.1722	0.0787	-41.3687	-9.9968	48.501
12	0.4382	-0.3985	-0.2787	0.4471	0.5401	0.9853	0.0052	-0.3035	0.341	0.2669	-0.0486	0.1687	-0.4503	-0.0143	0.0039	0.2536	0.1144	0.2221	0.0315	-0.4152	0.0756	-39.3564	-4.1737	39.2453
13	5.4889	0.8035	0.5983	2.0389	-0.7111	2.514	0.1415	0.4056	0.1527	-0.1595	-0.0298	0.4498	-0.3768	0.0659	0.0002	0.1586	-0.0233	-0.0334	0.2479	-0.0674	0.2096	-37.8417	-8.3856	28.913
14	5.7815	-4.9504	2.8588	6.1645	-2.9342	2.0759	-0.0613	0.2009	-0.0499	-0.0071	-0.411	-0.4305	0.3636	0.0739	0.0541	0.2167	-0.0104	-0.035	0.1125	-0.0403	0.4006	-38.1432	-20.1524	27.923
15	2.5891	0.1891	-0.0043	3.8115	1.3931	2.7998	0.1071	-0.3763	0.1898	0.3293	0.204	0.1799	-0.5867	-0.0573	0.0345	0.3056	0.0356	0.0839	0.2048	-0.0912	0.1486	-33.3522	-8.3509	39.1844
16	1.1989	0.2619	0.3972	1.0923	-0.0127	2.095	0.1773	-0.3022	0.6047	-0.0293	-0.2204	0.0828	0.3132	-0.2943	0.0778	0.0631	0.0309	0.0214	0.236	-0.0869	0.1793	2.343	-2.6659	18.6394
17	1.1397	-0.2004	-0.2846	0.4154	-0.2104	0.8321	-0.0391	-0.1731	-0.1714	-0.1151	-0.0411	-0.1096	0.2855	0.1011	-0.0339	0.1718	0.0087	0.0103	0.1395	-0.003	0.1009	6.4713	-9.1649	14.8859
18	3.6308	-1.842	-0.7984	7.6955	-0.6887	1.1096	0.0563	0.2365	0.7578	-0.0352	0.2543	-0.0923	-0.2099	0.3983	0.0711	0.2166	-0.0823	-0.0035	0.3128	-0.0382	0.2712	-7.1208	1.9759	29.3673
19	1.7803	-0.1258	1.4958	0.5221	0.0458	1.8667	-0.3807	-0.0217	0.7224	-0.1585	-0.0586	-0.1914	-0.5103	-0.0951	0.0346	0.2392	0.0183	-0.0366	0.0686	-0.0286	0.3198	7.1232	6.3954	13.2735
20	3.853	0.1332	2.5211	1.4191	0.0467	3.7721	-0.1624	0.2888	0.2683	-0.3273	0.0668	-0.3202	-0.1229	0.4567	-0.0125	0.1379	-0.0411	0.0142	0.0159	-0.0103	0.26	14.9318	-0.4807	10.8592
21	2.9276	1.6945	2.8908	1.9924	1.1987	3.0777	-0.0235	0.2942	0.5734	-0.1717	-0.2506	-0.263	-0.7659	0.5035	0.0439	0.3769	-0.091	-0.0041	0.3536	0.1211	0.4309	10.1156	5.1414	1.8068
22	6.0555	-4.1948	4.2938	6.039	-3.3575	5.3704	0.0876	-0.0255	-0.449	0.0406	0.005	-0.1047	0.4755	0.1441	-0.046	0.2922	0.0741	0.0363	0.196	-0.0075	0.27	24.9632	-20.6194	7.7628
23	1.5741	0.218	0.453	1.2519	0.2921	1.7608	0.1511	0.6634	-0.2108	-0.3194	-0.0842	-0.4805	0.0517	0.1066	-0.0164	0.256	0.0748	0.0699	0.2971	0.0231	0.299	27.6197	-14.2481	4.6147
24	0.8035	0.024	-0.0812	1.9019	1.5295	2.7064	0.0031	0.2776	-0.0327	-0.3605	0.1417	-0.3717	-0.0041	0.2691	-0.0083	0.4781	0.321	0.7038	0.7298	0.1513	-0.1403	28.7623	-9.9819	-4.1225
25	0.4695	0.4545	-0.263	0.6019	-0.6804	1.144	0.0551	0.3016	0.2905	-0.2954	-0.0282	-0.1608	-0.4685	0.0264	-0.021	0.3432	0.0402	0.1309	0.2171	0.2014	0.3012	26.7882	-4.1816	5.048
26	6.6462	-1.2773	0.3998	1.8619	0.6665	2.9176	0.2342	-0.3659	0.0963	0.0478	-0.0737	-0.4111	-0.3049	0.023	-0.0103	0.1635	0.0021	-0.002	0.1146	0.0401	0.2256	25.2792	-8.388	15.3804
27	4.9568	4.4372	2.3671	5.4762	2.6916	1.5835	-0.0372	-0.1841	-0.0371	0.0087	-0.3922	0.349	0.3496	-0.0161	0.057	0.2091	0.0125	-0.0476	0.2442	0.0363	0.4232	25.5763	-20.1835	16.3808
28	1.4751	-0.5488	0.1149	2.3666	-0.4854	2.2064	0.0865	0.307	0.2639	-0.2988	0.0571	-0.0968	-0.6469	-0.0432	0.1049	0.2799	-0.0799	0.2502	-0.0927	0.4358	-0.1771	20.8141	-8.2758	5.0875

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 2 THROUGH 21 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 22 THROUGH 57 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 58 THROUGH 70 )
4	X-RAY DIFFRACTION	4	CHAIN B AND (RESID 2 THROUGH 26 )
5	X-RAY DIFFRACTION	5	CHAIN B AND (RESID 27 THROUGH 44 )
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESID 45 THROUGH 51 )
7	X-RAY DIFFRACTION	7	CHAIN C AND (RESID 72 THROUGH 80 )
8	X-RAY DIFFRACTION	8	CHAIN C AND (RESID 81 THROUGH 85 )
9	X-RAY DIFFRACTION	9	CHAIN C AND (RESID 86 THROUGH 97 )
10	X-RAY DIFFRACTION	10	CHAIN C AND (RESID 98 THROUGH 107 )
11	X-RAY DIFFRACTION	11	CHAIN C AND (RESID 108 THROUGH 113 )
12	X-RAY DIFFRACTION	12	CHAIN C AND (RESID 114 THROUGH 120 )
13	X-RAY DIFFRACTION	13	CHAIN C AND (RESID 121 THROUGH 131 )
14	X-RAY DIFFRACTION	14	CHAIN C AND (RESID 132 THROUGH 142 )
15	X-RAY DIFFRACTION	15	CHAIN C AND (RESID 143 THROUGH 150 )
16	X-RAY DIFFRACTION	16	CHAIN D AND (RESID 2 THROUGH 21 )
17	X-RAY DIFFRACTION	17	CHAIN D AND (RESID 22 THROUGH 57 )
18	X-RAY DIFFRACTION	18	CHAIN D AND (RESID 58 THROUGH 70 )
19	X-RAY DIFFRACTION	19	CHAIN E AND (RESID 2 THROUGH 26 )
20	X-RAY DIFFRACTION	20	CHAIN E AND (RESID 27 THROUGH 44 )
21	X-RAY DIFFRACTION	21	CHAIN E AND (RESID 45 THROUGH 51 )
22	X-RAY DIFFRACTION	22	CHAIN F AND (RESID 72 THROUGH 80 )
23	X-RAY DIFFRACTION	23	CHAIN F AND (RESID 81 THROUGH 107 )
24	X-RAY DIFFRACTION	24	CHAIN F AND (RESID 108 THROUGH 113 )
25	X-RAY DIFFRACTION	25	CHAIN F AND (RESID 114 THROUGH 120 )
26	X-RAY DIFFRACTION	26	CHAIN F AND (RESID 121 THROUGH 131 )
27	X-RAY DIFFRACTION	27	CHAIN F AND (RESID 132 THROUGH 142 )
28	X-RAY DIFFRACTION	28	CHAIN F AND (RESID 143 THROUGH 150 )

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-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

-
Basic information

-
Structure visualization

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Downloads & links

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Download

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Validation report

-
Related structure data

-
Links

-
Assembly

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Components

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Experimental details

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Experiment

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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

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Yorodumi