PDB-5b86: Crystal structure of M-Sec

ID or keywords:

Entry

Database: PDB / ID: 5b86

Title

Crystal structure of M-Sec

Components

Tumor necrosis factor alpha-induced protein 2

Keywords

IMMUNE SYSTEM / Helical protein / exocyst complex / exocytosis / membrane traffic

Function / homology

Exocyst complex component EXOC3/Sec6 / Exocyst complex component EXOC3/Sec6, C-terminal domain / Exocyst complex component Sec6 / exocyst / exocytosis / angiogenesis / cell differentiation / Tumor necrosis factor alpha-induced protein 2

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.017 Å

Authors

Yamashita, M. / Sato, Y. / Yamagata, A. / Fukai, S.

Funding support

Japan, 2items

Citation

Journal: Sci Rep / Year: 2016
Title: Distinct Roles for the N- and C-terminal Regions of M-Sec in Plasma Membrane Deformation during Tunneling Nanotube Formation.
Authors: Kimura, S. / Yamashita, M. / Yamakami-Kimura, M. / Sato, Y. / Yamagata, A. / Kobashigawa, Y. / Inagaki, F. / Amada, T. / Hase, K. / Iwanaga, T. / Ohno, H. / Fukai, S.

History

Deposition	Jun 12, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 12, 2016	Provider: repository / Type: Initial release
Revision 1.1	Feb 26, 2020	Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Oct 30, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5b86.cif.gz	480 KB	Display	PDBx/mmCIF format
PDB format	pdb5b86.ent.gz	397.7 KB	Display	PDB format
PDBx/mmJSON format	5b86.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5b86_validation.pdf.gz	421.1 KB	Display	wwPDB validaton report
Full document	5b86_full_validation.pdf.gz	460.7 KB	Display
Data in XML	5b86_validation.xml.gz	27 KB	Display
Data in CIF	5b86_validation.cif.gz	40.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b8/5b86 ftp://data.pdbj.org/pub/pdb/validation_reports/b8/5b86	HTTPS FTP

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Related structure data

Similar structure data	1tgx-2 3f85-d 5lm2-2 4y66-1 4cbz-d 3urz-d 5uk5-d 3t1w-d 1syx-d 3um0-1 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: Tumor necrosis factor alpha-induced protein 2

B: Tumor necrosis factor alpha-induced protein 2

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

1

A: Tumor necrosis factor alpha-induced protein 2

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

2

B: Tumor necrosis factor alpha-induced protein 2

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

Unit cell

Length a, b, c (Å)	91.410, 107.829, 229.580
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Tumor necrosis factor alpha-induced protein 2 / TNF alpha-induced protein 2 / Primary response gene B94 protein Mass: 68573.109 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 42-691 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfaip2 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: Q61333
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H₂O
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: 3.83 Å³/Da / Density % sol: 67.92 % / Description: CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG8000, Hepes-Na (pH 7), ethylene glycol

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97904 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97904 Å / Relative weight: 1
Reflection	Resolution: 3→50 Å / Num. obs: 43284 / % possible obs: 95.9 % / Redundancy: 3 % / Net I/σ(I): 6
Reflection shell	Resolution: 3→3.05 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.8.2_1309	refinement
HKL-2000		data reduction
HKL-2000		data scaling
autoSHARP		phasing

Refinement

Method to determine structure:

SAD / Resolution: 3.017→46.439 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.31
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS

	R_factor	Num. reflection	% reflection
R_free	0.2921	3720	5 %
R_work	0.2287	-	-
obs	0.2319	43284	86.14 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 3.017→46.439 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9266	0	0	46	9312

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	9443
X-RAY DIFFRACTION	f_angle_d	1.481	12807
X-RAY DIFFRACTION	f_dihedral_angle_d	20.611	3555
X-RAY DIFFRACTION	f_chiral_restr	0.091	1468
X-RAY DIFFRACTION	f_plane_restr	0.007	1653

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 (%)
3.0168-3.055	0.4097	77	0.3924	1619	X-RAY DIFFRACTION	53
3.055-3.0952	0.38	116	0.397	2192	X-RAY DIFFRACTION	72
3.0952-3.1375	0.3633	120	0.3934	2235	X-RAY DIFFRACTION	73
3.1375-3.1824	0.4298	106	0.3832	2222	X-RAY DIFFRACTION	74
3.1824-3.2298	0.3861	134	0.3763	2221	X-RAY DIFFRACTION	74
3.2298-3.2803	0.3777	117	0.3648	2345	X-RAY DIFFRACTION	76
3.2803-3.3341	0.4234	114	0.3562	2298	X-RAY DIFFRACTION	76
3.3341-3.3915	0.371	146	0.3553	2366	X-RAY DIFFRACTION	78
3.3915-3.4532	0.4168	134	0.3304	2416	X-RAY DIFFRACTION	80
3.4532-3.5196	0.3587	121	0.3111	2507	X-RAY DIFFRACTION	83
3.5196-3.5914	0.4058	109	0.3035	2640	X-RAY DIFFRACTION	86
3.5914-3.6695	0.3324	156	0.2783	2602	X-RAY DIFFRACTION	86
3.6695-3.7548	0.3465	139	0.2566	2624	X-RAY DIFFRACTION	87
3.7548-3.8486	0.3081	122	0.2441	2780	X-RAY DIFFRACTION	89
3.8486-3.9527	0.2985	146	0.2215	2765	X-RAY DIFFRACTION	91
3.9527-4.0689	0.3008	176	0.2098	2711	X-RAY DIFFRACTION	92
4.0689-4.2001	0.2804	163	0.1836	2827	X-RAY DIFFRACTION	93
4.2001-4.3502	0.2477	128	0.1772	2861	X-RAY DIFFRACTION	93
4.3502-4.5242	0.2631	135	0.1685	2882	X-RAY DIFFRACTION	95
4.5242-4.7299	0.2088	156	0.1634	2915	X-RAY DIFFRACTION	95
4.7299-4.979	0.2588	155	0.1555	2873	X-RAY DIFFRACTION	96
4.979-5.2905	0.2582	129	0.1641	2967	X-RAY DIFFRACTION	96
5.2905-5.6984	0.2685	178	0.1976	2888	X-RAY DIFFRACTION	96
5.6984-6.2706	0.3283	142	0.2195	2935	X-RAY DIFFRACTION	96
6.2706-7.1751	0.2774	156	0.2098	2948	X-RAY DIFFRACTION	97
7.1751-9.029	0.2064	181	0.1593	2992	X-RAY DIFFRACTION	99
9.029-46.4442	0.2277	164	0.1689	2996	X-RAY DIFFRACTION	99

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	3.6264	0.0941	0.5693	3.4916	0.179	6.8036	-0.044	0.5929	-0.076	0.0966	0.1618	-0.1571	-0.1166	0.4847	-0.0953	0.3803	0.0793	0.0528	0.4017	0.0227	0.4532	-25.2358	-14.6589	-103.7749
2	0.7884	-0.9628	-1.9975	0.1276	1.6356	4.5139	0.1153	0.043	0.1398	-0.2405	-0.137	0.0304	-0.1407	-0.1198	0.0703	0.7931	-0.0102	0.1764	0.7532	-0.123	0.5816	-47.3539	0.45	-48.294
3	3.038	1.4448	0.5536	3.3577	1.3093	5.4304	-0.1447	-0.1037	-0.3673	-0.1499	-0.1039	-0.0366	0.2612	0.0466	0.2173	0.2041	0.0792	-0.0178	0.2777	-0.03	0.3565	-46.5305	14.208	3.8509
4	0.9829	0.0305	0.2951	1.928	-1.9131	4.7905	-0.0166	0.225	-0.2276	0.011	-0.0333	-0.054	0.0077	0.2361	0.0885	0.1995	-0.0015	0.0139	0.3366	-0.0456	0.4101	-7.1999	5.0411	-9.2048
5	2.0105	0.1444	1.3118	2.1406	-0.0418	4.1333	0.2134	0.1892	0.1337	0.052	-0.4136	-0.1344	0.0176	0.728	0.1725	0.6737	-0.1235	0.0565	0.6546	0.0888	0.4261	-16.2622	30.2232	-77.4731

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 67 through 178 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 179 through 478 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 479 through 650 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 67 through 407 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 408 through 650 )

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