PDB-3knd: TPX2:importin-alpha complex

ID or keywords:

Entry

Database: PDB / ID: 3knd

Title

TPX2:importin-alpha complex

Components

Importin subunit alpha-2
Targeting protein for Xklp2

Keywords

PROTEIN TRANSPORT / mitosis / importin / Transport

Function / homology

Function and homology information

Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / regulation of mitotic spindle organization / spindle pole ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Xenopus laevis (African clawed frog)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.151 Å

Authors

Stewart, M.

Citation

Journal: J.Biol.Chem. / Year: 2010
Title: Novel binding of the mitotic regulator TPX2 (target protein for Xenopus kinesin-like protein 2) to importin-alpha.
Authors: Giesecke, A. / Stewart, M.

History

Deposition	Nov 12, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 23, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Dec 26, 2012	Group: Database references
Revision 1.3	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.4	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3knd.cif.gz	190.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3knd_validation.pdf.gz	450.2 KB	Display	wwPDB validaton report
Full document	3knd_full_validation.pdf.gz	454.5 KB	Display
Data in XML	3knd_validation.xml.gz	19.7 KB	Display
Data in CIF	3knd_validation.cif.gz	28.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kn/3knd ftp://data.pdbj.org/pub/pdb/validation_reports/kn/3knd	HTTPS FTP

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Related structure data

Related structure data	1eyjS S: Starting model for refinement
Similar structure data	3zio-d 4mz5-d 3ve6-d 4oih-d 6bw0-d 5x8n-d 4mz6-d 5ctt-d 5svz-d 3wpt-1 4u5n-d 4u54-d 6wx7-d 7l04-d 4htv-d 4u58-d 7jjm-d 6bw1-d 1iq1-d 4ba3-d 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	#85 - Jan 2007 Importins similarity (12) #205 - Jan 2017 Nuclear Pore Complex similarity (2) #99 - Mar 2008 Cadherin similarity (4) #88 - Apr 2007 Clathrin similarity (2)

Deposited unit

A: Importin subunit alpha-2

B: Targeting protein for Xklp2

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	78.527, 89.317, 99.273
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Importin subunit alpha-2 / Karyopherin subunit alpha-2 / SRP1-alpha / RAG cohort protein 1 / Pendulin / Pore targeting complex ...Karyopherin subunit alpha-2 / SRP1-alpha / RAG cohort protein 1 / Pendulin / Pore targeting complex 58 kDa subunit / PTAC58 / Importin alpha P1 Mass: 49886.633 Da / Num. of mol.: 1 / Fragment: residues 70-529 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: importin alpha 2, Kpna2, Rch1 / Plasmid: pMW172 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P52293
#2: Protein	Targeting protein for Xklp2 Mass: 9316.822 Da / Num. of mol.: 1 / Fragment: residues 270-350 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: TPX2 / Plasmid: pGEX-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9I8N0, UniProt: Q6NUF4*PLUS
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.94 Å³/Da / Density % sol: 58.17 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.1-1.2 M ammonium sulphate, 100 mM Tris-Hcl, 10 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9814 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2009 / Details: mirrors
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9814 Å / Relative weight: 1
Reflection	Resolution: 2.151→27.85 Å / Num. all: 36138 / Num. obs: 36111 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / B_iso Wilson estimate: 39.3 Å² / R_merge(I) obs: 0.109 / Net I/σ(I): 11.9
Reflection shell	Resolution: 2.2→2.32 Å / Redundancy: 6.9 % / R_merge(I) obs: 0.959 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHENIX	(phenix.refine: 1.5_2)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1EYJ

1eyj

Resolution: 2.151→19.712 Å / SU ML: 0.27 / Isotropic thermal model: isotropic / σ(F): 0.94 / Phase error: 21.94 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2143	4923	6.77 %
R_work	0.1824	-	-
obs	0.1846	-	99.38 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 50.532 Å² / k_sol: 0.357 e/Å³

Displacement parameters

B_iso max: 169.88 Å² / B_iso mean: 51.189 Å² / B_iso min: 18.49 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.077 Å²	-0 Å²	0 Å²
2-	-	-7.913 Å²	0 Å²
3-	-	-	10.99 Å²

Refinement step

Cycle: LAST / Resolution: 2.151→19.712 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3380	0	25	236	3641

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3459
X-RAY DIFFRACTION	f_angle_d	0.993	4709
X-RAY DIFFRACTION	f_dihedral_angle_d	16.337	1257
X-RAY DIFFRACTION	f_chiral_restr	0.055	563
X-RAY DIFFRACTION	f_plane_restr	0.005	598

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 (%)
2.151-2.1757	0.3286	140	0.3067	2206	X-RAY DIFFRACTION	97
2.1757-2.2012	0.316	140	0.2921	2293	X-RAY DIFFRACTION	99
2.2012-2.228	0.4004	174	0.3194	2127	X-RAY DIFFRACTION	95
2.228-2.2562	0.4459	142	0.4153	2286	X-RAY DIFFRACTION	99
2.2562-2.2858	0.3406	144	0.329	2127	X-RAY DIFFRACTION	94
2.2858-2.3171	0.2509	121	0.2312	2353	X-RAY DIFFRACTION	100
2.3171-2.3502	0.2781	163	0.2074	2264	X-RAY DIFFRACTION	100
2.3502-2.3852	0.2223	132	0.2096	2316	X-RAY DIFFRACTION	100
2.3852-2.4224	0.206	182	0.2004	2223	X-RAY DIFFRACTION	100
2.4224-2.462	0.2437	191	0.194	2259	X-RAY DIFFRACTION	100
2.462-2.5044	0.2556	195	0.1831	2205	X-RAY DIFFRACTION	100
2.5044-2.5498	0.2387	184	0.189	2289	X-RAY DIFFRACTION	100
2.5498-2.5988	0.2247	168	0.1826	2256	X-RAY DIFFRACTION	100
2.5988-2.6517	0.234	183	0.1828	2253	X-RAY DIFFRACTION	100
2.6517-2.7092	0.2207	176	0.1742	2276	X-RAY DIFFRACTION	100
2.7092-2.7721	0.2118	179	0.1716	2237	X-RAY DIFFRACTION	100
2.7721-2.8412	0.2182	142	0.1702	2281	X-RAY DIFFRACTION	100
2.8412-2.9178	0.2082	166	0.1664	2305	X-RAY DIFFRACTION	100
2.9178-3.0034	0.2382	140	0.1789	2286	X-RAY DIFFRACTION	100
3.0034-3.0999	0.1997	171	0.1762	2257	X-RAY DIFFRACTION	100
3.0999-3.2103	0.2337	156	0.1806	2277	X-RAY DIFFRACTION	100
3.2103-3.3382	0.2201	171	0.1861	2257	X-RAY DIFFRACTION	100
3.3382-3.4894	0.1876	188	0.1769	2246	X-RAY DIFFRACTION	100
3.4894-3.6722	0.2177	160	0.165	2288	X-RAY DIFFRACTION	100
3.6722-3.9006	0.1894	161	0.1488	2268	X-RAY DIFFRACTION	100
3.9006-4.1991	0.1563	182	0.136	2266	X-RAY DIFFRACTION	100
4.1991-4.6168	0.1553	179	0.1275	2242	X-RAY DIFFRACTION	100
4.6168-5.2736	0.1586	180	0.1447	2260	X-RAY DIFFRACTION	100
5.2736-6.6025	0.2081	154	0.1821	2289	X-RAY DIFFRACTION	100
6.6025-19.7125	0.1677	159	0.1417	2260	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	0.6714	0.4624	-0.3815	1.103	0.291	0.7652	0.1749	-0.0439	0.3677	-0.2576	-0.0898	0.1973	-0.1971	-0.03	-0.1084	0.3129	0.0727	0.094	0.2352	-0.007	0.2318	37.0429	82.645	56.4442
2		1.1116	0.0097	-0.8741	2.808	-0.0012	-0.589	0.2452	-0.006	0.0132	0.0444	-0.0563	0.0268	-0.1313	-0.0739	-0.1264	0.1892	-0.0031	0.0278	0.1611	-0.0066	0.0568
3		0.9083	0.6987	-0.0402	0.6887	-0.2778	0.5163	0.1461	0.0451	-0.1013	0.0846	0.0063	0.0901	-0.0146	0.0507	-0.0823	0.2009	-0.0108	0.0349	0.1909	0.0192	0.2461
4		1.1315	1.0696	0.5751	2.0034	1.0068	1.3793	0.3081	0.1192	-0.4627	0.0624	-0.0973	-0.2499	0.0311	0.0083	-0.2022	0.1671	-0.0008	-0.0604	0.1693	-0.0236	0.3109
5		1.4126	0.4069	1.5528	1.091	0.8898	1.7027	0.0767	0.4002	-0.2515	0.0292	0.2036	-0.4859	0.0226	0.2962	-0.2644	0.1716	0.0071	0.0302	0.2838	-0.1079	0.3355
6		2.9193	1.0362	-0.754	2.8053	-0.1103	0.2542	0.0247	1.2205	-0.3313	-1.1019	0.378	-0.1094	0.1778	0.1403	-0.2559	0.6117	-0.0753	0.2023	0.9539	-0.2913	0.3433
7		2.0073	8.562	1.2037	6.9364	-1.3402	4.412	0.3563	0.5584	0.0804	0.3163	0.2103	1.0565	-0.7266	0.5178	-0.3827	0.3536	-0.0893	0.0491	0.3936	-0.3291	1.0726
8		2.0481	-0.0681	0.6528	2.8628	1.4824	1.2103	0.0645	-0.2502	-0.3723	-0.2319	0.0249	0.45	-0.1063	-0.4743	0.0057	0.2626	-0.0371	-0.0447	0.3538	0.0007	0.3521

Refinement TLS group

Selection details: chain B and resid 322:331)

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