PDB-9bwa: Crystal structure of the Transport and Golgi Organization protein...

ID or keywords:

Entry

Database: PDB / ID: 9bwa

Title

Crystal structure of the Transport and Golgi Organization protein 2 Homolog (TANGO2)

Components

Transport and Golgi organization protein 2 homolog

Keywords

TRANSPORT PROTEIN / TANGO2 / TANGO2-related disease / LIPID TRANSPORT

Function / homology

Function and homology information

Golgi organization / protein secretion / Golgi apparatus / mitochondrion / cytosol / cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Lovell, S. / Cooper, A. / Powers, A. / Battaile, K.P. / Mohsen, A.-W. / Ghaloul-Gonzalez, L.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of the Transport and Golgi Organization protein 2 Homolog (TANGO2)
Authors: Lovell, S. / Ghaloul-Gonzalez, L.

History

Deposition	May 21, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 30, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9bwa.cif.gz	241.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9bwa.ent.gz	193.8 KB	Display	PDB format
PDBx/mmJSON format	9bwa.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9bwa_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	9bwa_full_validation.pdf.gz	1.9 MB	Display
Data in XML	9bwa_validation.xml.gz	29.2 KB	Display
Data in CIF	9bwa_validation.cif.gz	39.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bw/9bwa ftp://data.pdbj.org/pub/pdb/validation_reports/bw/9bwa	HTTPS FTP

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Related structure data

Related structure data	9n1sC C: citing same article (ref.)
Similar structure data	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: Transport and Golgi organization protein 2 homolog

B: Transport and Golgi organization protein 2 homolog

hetero molecules

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

1

A: Transport and Golgi organization protein 2 homolog

hetero molecules

defined by author
Evidence: gel filtration
32 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Transport and Golgi organization protein 2 homolog

hetero molecules

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

Unit cell

Length a, b, c (Å)	50.011, 50.171, 241.774
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Transport and Golgi organization protein 2 homolog Mass: 31844.932 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TANGO2, C22orf25 / Plasmid: pET-27b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6ICL3
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48.35 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: Grid Salt HT screen C9: 1.0 M sodium phosphate monobasic monohydrate / potassium phosphate dibasic pH 6.9, TANGO2 at 11.4 mg/mL. plate 14002 well E10 drop 2. Puck: PSL-1404, Cryo: 80% (v/v) ...Details: Grid Salt HT screen C9: 1.0 M sodium phosphate monobasic monohydrate / potassium phosphate dibasic pH 6.9, TANGO2 at 11.4 mg/mL. plate 14002 well E10 drop 2. Puck: PSL-1404, Cryo: 80% (v/v) crystallant and 20% (v/v) glycerol

Crystal

Density Matthews: 2.38 Å³/Da / Density % sol: 48.35 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Grid Salt HT screen C9: 1.0 M sodium phosphate monobasic monohydrate / potassium phosphate dibasic pH 6.9, TANGO2 at 11.4 mg/mL. plate 14002 well E10 drop 2. Puck: PSL-1404, Cryo: 80% (v/v) ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Apr 13, 2024
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 1.7→48.97 Å / Num. obs: 68343 / % possible obs: 100 % / Redundancy: 13.2 % / CC_1/2: 0.999 / R_merge(I) obs: 0.108 / R_pim(I) all: 0.031 / R_rim(I) all: 0.112 / Χ²: 1.02 / Net I/σ(I): 13.7 / Num. measured all: 900003
Reflection shell	Resolution: 1.7→1.73 Å / % possible obs: 100 % / Redundancy: 13.7 % / R_merge(I) obs: 2.292 / Num. measured all: 49944 / Num. unique obs: 3633 / CC_1/2: 0.725 / R_pim(I) all: 0.638 / R_rim(I) all: 2.38 / Χ²: 1.07 / Net I/σ(I) obs: 1.5

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Processing

Software

Name	Version	Classification
PHENIX	(dev_5295: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.7→48.97 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.89 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1866	3393	4.98 %
R_work	0.1635	-	-
obs	0.1647	68191	99.91 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.7→48.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4302	0	20	367	4689

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4527
X-RAY DIFFRACTION	f_angle_d	1.014	6175
X-RAY DIFFRACTION	f_dihedral_angle_d	14.117	1661
X-RAY DIFFRACTION	f_chiral_restr	0.06	681
X-RAY DIFFRACTION	f_plane_restr	0.009	802

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 (%)
1.7-1.72	0.2932	156	0.2963	2716	X-RAY DIFFRACTION	100
1.72-1.75	0.2544	164	0.2474	2549	X-RAY DIFFRACTION	100
1.75-1.78	0.2649	152	0.2235	2687	X-RAY DIFFRACTION	100
1.78-1.81	0.2572	147	0.2237	2613	X-RAY DIFFRACTION	100
1.81-1.84	0.2872	133	0.2167	2657	X-RAY DIFFRACTION	100
1.84-1.87	0.282	121	0.2066	2702	X-RAY DIFFRACTION	100
1.87-1.91	0.2568	149	0.2049	2628	X-RAY DIFFRACTION	100
1.91-1.95	0.2291	149	0.2011	2646	X-RAY DIFFRACTION	100
1.95-1.99	0.2141	133	0.1793	2697	X-RAY DIFFRACTION	100
1.99-2.03	0.2076	139	0.1676	2669	X-RAY DIFFRACTION	100
2.03-2.09	0.1849	131	0.1564	2710	X-RAY DIFFRACTION	100
2.09-2.14	0.2012	132	0.1563	2640	X-RAY DIFFRACTION	100
2.14-2.2	0.1925	138	0.1495	2708	X-RAY DIFFRACTION	100
2.2-2.28	0.1714	134	0.1593	2711	X-RAY DIFFRACTION	100
2.28-2.36	0.1894	127	0.1597	2675	X-RAY DIFFRACTION	100
2.36-2.45	0.2258	131	0.1639	2680	X-RAY DIFFRACTION	100
2.45-2.56	0.209	135	0.1755	2683	X-RAY DIFFRACTION	100
2.56-2.7	0.2208	149	0.1669	2714	X-RAY DIFFRACTION	100
2.7-2.87	0.1876	115	0.1597	2755	X-RAY DIFFRACTION	100
2.87-3.09	0.1907	120	0.1792	2756	X-RAY DIFFRACTION	100
3.09-3.4	0.1599	133	0.1549	2754	X-RAY DIFFRACTION	100
3.4-3.89	0.1832	171	0.1447	2728	X-RAY DIFFRACTION	100
3.89-4.9	0.1264	158	0.1208	2782	X-RAY DIFFRACTION	100
4.9-48.97	0.1844	176	0.1811	2938	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	6.3357	0.6627	4.618	3.2526	1.1234	3.5027	0.0246	0.261	0.3562	-0.1594	-0.3323	0.1242	-0.4486	-0.3316	0.2807	0.2524	0.0872	-0.0066	0.34	0.011	0.2874	-12.9088	-4.5129	-14.2217
2	1.6877	0.2746	-0.2608	2.7278	2.2087	2.4331	-0.0162	0.2528	0.1793	-0.2676	-0.0557	0.0612	-0.4073	-0.4136	0.1297	0.2573	0.0285	-0.0097	0.2989	0.0284	0.2567	-7.1173	-4.3606	-18.7914
3	1.3961	0.2455	0.8737	0.7888	0.9183	3.6341	0.0061	-0.0245	0.0819	0.0275	0.0018	-0.0341	-0.0337	0.0928	-0.0542	0.2067	0.0341	-0.0052	0.3067	0	0.2586	-0.5592	-9.9681	-7.7183
4	6.5743	2.6863	0.903	7.1599	1.8669	7.0603	-0.0509	-0.1591	-0.1731	-0.0627	0.1246	-0.6367	-0.2508	0.4598	-0.0854	0.2096	0.0496	0.0328	0.2495	0.0157	0.1709	2.0527	-14.9711	-25.6105
5	4.4889	1.6445	0.8266	6.6549	2.8109	5.7301	0.008	-0.0972	0.3834	-0.1091	-0.0147	0.0792	-0.5203	0.0738	-0.0022	0.2325	0.0304	0.0107	0.2082	0.0235	0.1919	5.4507	1.0901	-42.5746
6	5.7149	2.4281	3.4815	4.214	1.5034	5.3187	0.2613	0.2078	-0.5164	0.3223	-0.0095	-0.632	0.5254	0.6027	-0.2655	0.2724	0.063	-0.0188	0.2716	0.0077	0.3122	15.6605	-14.665	-39.4549
7	2.9163	-1.9542	0.0993	4.9825	-0.2405	5.9726	-0.0028	0.3046	-0.2627	0.1499	-0.0541	-0.0932	0.5366	0.2392	0.024	0.222	-0.0118	0.0095	0.2657	0.0101	0.2482	14.7151	-11.0217	-45.8608
8	4.821	-1.1906	0.4718	3.0042	-0.6652	4.8327	0.1182	0.3012	-0.8262	-0.1381	-0.0115	-0.3585	0.7537	0.504	-0.1163	0.2881	0.0352	0.0568	0.2783	-0.0051	0.3672	16.0839	-9.9523	-55.7069
9	3.9754	2.4871	1.7051	8.4436	5.6679	8.9001	0.0445	0.1985	-0.0363	-0.545	0.0933	-0.9875	-0.1233	0.6983	-0.212	0.2042	0.052	0.0364	0.3261	0.0387	0.4208	21.8523	-1.546	-57.3931
10	2.6285	-0.3298	-0.1049	1.9013	-0.176	2.2654	0.0056	-0.0147	0.0882	0.0765	-0.0327	-0.2401	-0.1176	0.2278	0.0347	0.2181	-0.0096	-0.0103	0.1805	0.0153	0.2423	10.987	2.4437	-53.0765
11	4.4881	2.7024	3.2831	7.3635	5.1647	4.1879	-0.1665	-0.3515	0.5549	0.2704	-0.1122	0.4488	0.0673	-0.7525	0.3488	0.2186	0.0516	0.0299	0.2688	-0.0273	0.3038	-6.3299	2.9379	-45.9944
12	1.1118	0.2459	1.2831	1.1027	0.5968	3.8575	0.0342	-0.079	0.0286	0.1051	-0.0361	0.0834	0.0994	-0.1392	0.011	0.2093	-0.004	0.0267	0.1803	-0.0114	0.236	-2.0736	-7.4391	-45.6346
13	6.8247	6.1458	2.9438	9.3474	2.183	4.808	0.1953	-0.0454	-0.2935	0.3153	-0.1216	-0.2799	0.4175	-0.0476	-0.1249	0.2559	0.0534	0.0302	0.2464	-0.0029	0.1874	4.3493	-13.152	-35.215
14	6.9834	1.6673	3.4551	3.8513	0.9346	6.9543	0.1179	-0.1889	-0.1456	-0.0207	-0.0767	0.2882	0.1639	-0.4744	-0.0236	0.2098	0.0472	0.0284	0.2957	0.0111	0.2307	-10.846	-15.8866	-18.8188
15	6.0429	1.8122	1.5145	5.1151	3.1419	7.1235	-0.1409	0.1205	-0.4844	0.14	0.2403	-0.3954	0.4491	0.6756	-0.1351	0.2388	0.0616	0.0532	0.2796	-0.0064	0.2569	4.6651	-24.9115	-22.3041
16	2.5553	-0.0691	-1.2641	2.3563	-0.1595	3.7342	-0.1306	-0.0816	-0.2998	0.0922	0.0011	-0.2968	0.3334	0.4677	0.0833	0.267	0.063	-0.0018	0.2831	0.0189	0.3045	-1.5329	-28.3474	-10.1708
17	2.3091	-0.5299	-0.8914	3.4932	0.138	2.3664	0.0005	0.03	-0.2113	-0.0302	-0.0815	0.0371	0.164	-0.0579	0.0887	0.1749	-0.0033	0.0186	0.2859	-0.01	0.2215	-12.3817	-22.5708	-8.6975

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 165 through 181 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 182 through 206 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 207 through 248 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 249 through 276 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 2 through 29 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 30 through 48 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 49 through 75 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 76 through 101 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 102 through 115 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 116 through 164 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 165 through 180 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 181 through 260 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 261 through 275 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 2 through 29 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 30 through 48 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 49 through 115 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 116 through 164 )

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