PDB-4m8g: Crystal structure of Se-Met hN33/Tusc3

ID or keywords:

Entry

Database: PDB / ID: 4m8g

Title

Crystal structure of Se-Met hN33/Tusc3

Components

Tumor suppressor candidate 3

Keywords

OXIDOREDUCTASE / thioredoxin-like fold / thiol/disulfide oxidoreductase / thiol/disulfide exchange reactions / redox-active protein

Function / homology

Function and homology information

Asparagine N-linked glycosylation / magnesium ion transport / Miscellaneous transport and binding events / oligosaccharyltransferase complex / magnesium ion transmembrane transporter activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / transmembrane transport / cognition / Maturation of spike protein ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 Å

Authors

Mohorko, E. / Owen, R.L. / Malojcic, G. / Brozzo, M.S. / Aebi, M. / Glockshuber, R.

Citation

Journal: Structure / Year: 2014
Title: Structural basis of substrate specificity of human oligosaccharyl transferase subunit n33/tusc3 and its role in regulating protein N-glycosylation.
Authors: Mohorko, E. / Owen, R.L. / Malojcic, G. / Brozzo, M.S. / Aebi, M. / Glockshuber, R.

History

Deposition	Aug 13, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 26, 2014	Provider: repository / Type: Initial release
Revision 1.1	May 7, 2014	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4m8g.cif.gz	126.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4m8g.ent.gz	106.3 KB	Display	PDB format
PDBx/mmJSON format	4m8g.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4m8g_validation.pdf.gz	432.6 KB	Display	wwPDB validaton report
Full document	4m8g_full_validation.pdf.gz	437 KB	Display
Data in XML	4m8g_validation.xml.gz	13.6 KB	Display
Data in CIF	4m8g_validation.cif.gz	18.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m8/4m8g ftp://data.pdbj.org/pub/pdb/validation_reports/m8/4m8g	HTTPS FTP

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Related structure data

Related structure data	4m90C 4m91C 4m92C C: citing same article (ref.)
Similar structure data	3uvc-2 3ts4-d 3lo0-d 1n05-d 6enm-1 2rgb-d 6elw-d 1ztq-2 2cld-d 1dy3-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	#266 - Feb 2022 Oligosaccharyltransferase similarity (4)

Deposited unit

A: Tumor suppressor candidate 3

B: Tumor suppressor candidate 3

38.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Tumor suppressor candidate 3

defined by author&software
19.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Tumor suppressor candidate 3

defined by author&software
19.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	39.107, 64.456, 62.467
Angle α, β, γ (deg.)	90.00, 92.45, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Tumor suppressor candidate 3 / Magnesium uptake/transporter TUSC3 / Protein N33 Mass: 19470.133 Da / Num. of mol.: 2 / Fragment: soluble domain of N33/Tusc3 / Mutation: C123S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: N33, TUSC3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13454
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Tumor suppressor candidate 3 / Magnesium uptake/transporter TUSC3 / Protein N33

Mass: 19470.133 Da / Num. of mol.: 2 / Fragment: soluble domain of N33/Tusc3 / Mutation: C123S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: N33, TUSC3 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q13454

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.04 Å³/Da / Density % sol: 39.64 %
Crystal grow	Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M KSCN, 10.5% PEG 8K, 10% PEG 1K in 100 mM cacodylic acid-NaOH, pH 6.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9787 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9787 Å / Relative weight: 1
Reflection	Resolution: 2→64.45 Å / Num. obs: 20996 / % possible obs: 100 % / R_merge(I) obs: 0.072 / R_sym value: 0.072 / Net I/σ(I): 31.1
Reflection shell	Resolution: 2→2.11 Å / R_merge(I) obs: 0.322 / Mean I/σ(I) obs: 11.4 / R_sym value: 0.322 / % possible all: 100

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Processing

Software

Name: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement

Refinement

Method to determine structure:

SAD / Resolution: 2→44.836 Å / SU ML: 0.14 / σ(F): 0 / Phase error: 25.88 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2484	396	1.89 %
R_work	0.2286	-	-
obs	0.229	20996	99.57 %

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→44.836 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2269	0	0	112	2381

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2328
X-RAY DIFFRACTION	f_angle_d	1.475	3134
X-RAY DIFFRACTION	f_dihedral_angle_d	15.555	865
X-RAY DIFFRACTION	f_chiral_restr	0.11	320
X-RAY DIFFRACTION	f_plane_restr	0.009	411

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 (%)
2.0001-2.2895	0.2449	142	0.2231	6784	X-RAY DIFFRACTION	99
2.2895-2.8844	0.2635	137	0.2455	6841	X-RAY DIFFRACTION	100
2.8844-44.8477	0.2416	117	0.2226	6975	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	3.7702	-1.1059	-0.8544	2.5309	0.4972	3.1754	0.1145	-0.0349	0.767	0.5675	-0.0364	0.2719	-1.3769	-0.6455	0.1221	0.3977	0.1181	-0.0096	0.1979	0.0039	0.3204	4.0659	36.866	60.1893
2	3.8055	-0.0329	-1.258	1.1198	0.1444	2.3108	-0.1693	0.1297	0.1395	0.078	0.0966	-0.0715	-0.0133	-0.065	0.0647	0.1302	0.032	-0.0265	0.083	-0.01	0.1362	10.0271	28.0997	58.7676
3	8.5694	-3.7806	-1.2723	4.3357	0.3405	2.2572	-0.0292	0.2534	0.7472	-0.0941	0.0545	-0.3488	-0.028	0.0963	-0.0939	0.1184	-0.0313	-0.0113	0.1171	-0.0136	0.1849	7.1592	31.8109	44.8436
4	4.1863	0.1935	0.2709	2.3424	0.5666	4.6354	-0.1132	-0.0826	-0.0673	0.1654	0.1031	-0.2176	0.069	0.5725	0.0083	0.1268	0.0069	-0.004	0.136	-0.0101	0.1339	11.9102	25.3986	56.4409
5	4.5616	-0.6165	-0.8724	5.1238	1.2803	6.7198	-0.2151	-0.4236	-0.3009	0.6059	0.1799	-0.0886	0.6556	-0.0505	0.0591	0.1632	0.0064	-0.0027	0.1091	0.0227	0.1228	2.096	17.8188	57.0807
6	4.4635	-2.4327	-2.2125	4.4375	0.1588	4.2381	0.0632	0.0658	0.0127	-0.2094	-0.0767	0.4023	0.0386	-0.2148	-0.0066	0.1	-0.0231	-0.0466	0.1497	-0.0362	0.1215	-0.4094	23.2625	44.4692
7	0.9306	0.549	0.808	4.1728	-0.0604	2.703	0.5963	0.4423	-0.3017	-1.1207	-0.261	1.2246	1.2257	-0.5474	-0.1797	1.1857	0.219	-0.388	0.5972	0.1124	1.0382	13.3037	6.3799	95.5413
8	1.9982	-0.4241	-0.5841	0.6267	0.0161	3.4789	-0.0619	0.0175	-0.1808	-0.0335	0.1149	-0.0832	0.524	0.1787	-0.1299	0.2612	0.0213	-0.0125	0.1399	-0.0284	0.152	6.9636	13.5716	94.2603
9	3.7819	1.5599	4.6889	1.3112	2.0536	5.1651	0.1255	0.308	0.1135	-0.0578	-0.1731	0.0789	0.0427	-0.1101	0.0533	0.181	-0.0045	-0.0229	0.1969	-0.0352	0.1725	-4.0266	15.7293	80.3278
10	3.63	-4.716	0.1436	6.4572	-0.982	3.0791	-0.0108	0.3672	-0.6988	-0.0514	0.0991	-0.0536	0.267	0.176	-0.0315	0.1961	0.03	0.0005	0.1775	-0.0616	0.2354	7.4553	11.4061	76.217
11	1.8463	0.198	-0.4012	2.1186	0.9723	4.2748	0.1814	0.0715	0.0204	0.2142	-0.1661	0.0266	0.2343	-0.2535	0.0227	0.1827	0	-0.0367	0.1895	-0.0573	0.2004	2.2911	17.867	87.0626
12	4.4863	-0.2109	2.5074	6.4873	-0.3894	2.1685	0.1938	-0.2081	0.1405	0.3219	-0.0441	-0.3244	-0.7657	0.7245	-0.0505	0.2027	-0.0081	0.0162	0.2232	-0.0649	0.1571	11.4321	25.9873	88.8095
13	4.9611	-1.9588	1.389	3.8274	0.2045	4.2671	0.0015	-0.0848	0.228	-0.2875	0.2238	-0.2986	-0.1577	0.3979	-0.228	0.0946	0.0078	0.0405	0.1784	-0.036	0.1556	14.5994	20.6923	76.7924

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 13 through 28 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 29 through 58 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 59 through 77 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 78 through 110 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 111 through 126 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 127 through 154 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 13 through 22 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 23 through 45 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 46 through 58 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 59 through 77 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 78 through 111 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 112 through 126 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 127 through 153 )

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